WO2012009551A1 - Promoter, promoter control elements, and combinations, and uses thereof - Google Patents

Abstract

The present document is directed to promoter sequences and promoter control elements, polynucleotide constructs comprising the promoters and control elements, and methods of identifying the promoters, control elements, or fragments thereof. The document further relates to the use of such promoters or promoter control elements to modulate transcript levels in plants, and plants containing such promoters or promoter control elements.

Description

PROMOTER, PROMOTER CONTROL ELEMENTS, AND

COMBINATIONS, AND USES THEREOF

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This Application claims priority under 35 U.S. C. 119(e) to U.S.

Provisional Application No. 61/364,903 filed July 16, 2010, which is incorporated herein by reference in its entirety.

TECHNICAL FIELD

[0002] The present invention relates to promoters and promoter control elements that are useful for modulating transcription of a desired polynucleotide. Such promoters and promoter control elements can be included in polynucleotide constructs, expression cassettes, vectors, or inserted into the chromosome or as an exogenous element, to modulate in vivo and in vitro transcription of a polynucleotide. Host cells, including plant cells, and organisms, such as regenerated plants therefrom, with desired traits or characteristics using polynucleotides comprising the promoters and promoter control elements described herein are also a part of the invention.

INCORPORATION-BY-REFERENCE OF SEQUENCE LISTING

[0003] The material in the accompanying sequence listing is hereby

incorporated by reference into this application. The accompanying file, named 11696- 0274WOl_sequence_listing_7_2_10.txt was created on July 2, 2010, and is 85.6 KB. The file can be accessed using Microsoft Word on a computer that uses Windows OS.

BACKGROUND

[0004] This document relates to promoter sequences and promoter control element sequences which are useful for the transcription of polynucleotides in a host cell or transformed host organism.

[0005] The introduction of genes into plants has resulted in the development of plants having new and useful phenotypes such as pathogen resistance, higher levels of healthier types of oils, novel production of healthful components such as beta-carotene synthesis in rice. An introduced gene is generally a chimeric gene composed of the coding region that confers the desired trait and regulatory sequences. One regulatory sequence is the promoter, which is located 5' to the coding region. This sequence is involved in regulating the pattern of expression of a coding region 3' thereof. The promoter sequence binds R A polymerase complex as well as one or more transcription factors that are involved in producing the RNA transcript of the coding region.

[0006] The promoter region of a gene used in plant transformation is most often derived from a different source than is the coding region. It may be from a different gene of the same species of plant, from a different species of plant, from a plant virus, an algae species, a fungal species, or it may be a composite of different natural and/or synthetic sequences. Properties of the promoter sequence generally determine the pattern of expression for the coding region that is operably linked to the promoter. Promoters with different characteristics of expression have been described. The promoter may confer broad expression as in the case of the widely-used cauliflower mosaic virus (CaMV) 35 S promoter. The promoter may confer tissue-specific expression as in the case of the seed- specific phaseolin promoter. The promoter may confer a pattern for developmental changes in expression. The promoter may be induced by an applied chemical compound, or by an environmental condition applied to the plant.

[0007] The promoter that is used to regulate a particular coding region is determined by the desired expression pattern for that coding region, which itself is determined by the desired resulting phenotype in the plant. For example, herbicide resistance is desired throughout the plant so the 35 S promoter is appropriate for expression of an herbicide-resistance gene. A seed-specific promoter is appropriate for changing the oil content of soybean seed. An endosperm-specific promoter is appropriate for changing the starch composition of corn seed. A root-specific promoter can be important for improving water or nutrient up-take in a plant. Control of expression of an introduced gene by the promoter is important because it is sometimes detrimental to have expression of an introduced gene in non-target tissues. For example, a gene which induces cell death can be expressed in male and/or female gamete cells in connection with bioconfmement. [0008] One of the primary goals of biotechnology is to obtain organisms, such as plants, mammals, yeast, and prokaryotes having particular desired characteristics or traits. Examples of these characteristics or traits abound and may include, for example, in plants, virus resistance, insect resistance, herbicide resistance, enhanced stability or additional nutritional value. Recent advances in genetic engineering have enabled researchers in the field to incorporate polynucleotide sequences into host cells to obtain the desired qualities in the organism of choice. This technology permits one or more polynucleotides from a source different than the organism of choice to be transcribed by the organism of choice. If desired, the transcription and/or translation of these new polynucleotides can be modulated in the organism to exhibit a desired characteristic or trait. Alternatively, new patterns of transcription and/or translation of polynucleotides endogenous to the organism can be produced.

SUMMARY

[0009] The present document is directed to isolated polynucleotide sequences that comprise promoters and promoter control elements from plants, especially Sorghum bicolor, Panicum virgatum, Oryza sativa, and Arabidopsis thaliana, and other promoters and promoter control elements functional in plants. It is an object of the present document to provide isolated polynucleotides that are promoter or promoter control sequences. These promoter sequences comprise, for example,

(1) a polynucleotide having a nucleotide sequence according to SEQ. ID. NOs. 1-44;

(2) a polynucleotide having a nucleotide sequence having at least 80% sequence identity to a sequence according to SEQ. ID. NOs. 1 - 44; and

(3) a polynucleotide having a nucleotide sequence which hybridizes to a sequence according to SEQ. ID. NOs. 1 - 44 under a condition establishing a T_m-5°C.

[0010] Promoter or promoter control element sequences of the present document are capable of modulating preferential transcription. In one embodiment, this document features an isolated nucleic acid that includes a regulatory region having 90 percent or greater sequence identity (e.g., 95 percent or greater, or 98 percent or greater) to the nucleotide sequence set forth in any one of SEQ ID NOs. 1 - 44 or a fragment thereof, wherein the regulatory region directs transcription of an operably linked heterologous polynucleotide. The regulatory region can consist of any one of the nucleotide sequences set forth in SEQ ID NOs. 1 - 44 or a fragment thereof. The nucleic acid can include one or more motifs selected from the group consisting of an ABRE motif, ABREATCONSENSUS motif, ABREL ATERD 1 motif, ACE motif,

ACGTABREMOTIFAOSOSEM motif, ACIIPVPAL2 motif, 3-AFl\binding\site light responsive element motif, ATCT motif, ATHB2ATCONSENSUS motif,

ATHB6COREAT motif, CAAT-box motif, CACGTGMOTIF motif,

CACGCAATGMGH3 motif, CARGCW8GAT motif, CARGNCAT motif,

CTRMC AM V35 S motif, Cytokinin-inducible\element motif, E2FCONSENSUS motif, ELI-box3 motif, enhancer motif, GAGAGMGSA1 motif, GARE20SREP1 motif, GAREAT motif, GATABOX motif, GCC\Box motif, GT1MOTIFPSRBCS motif, HSE motif, IBOX motif, LEAFYATAG motif, MBS motif, MYBPLANT motif, MYB1AT motif, OSE2ROOTNODULE motif, P1BS motif, P-box gibberellin-responsive element motif, Phosphate-starvation induced binding site motif, PRECONSCRHSP70A motif, RGATAOS motif, ROOTMOTIFTAPOX1 motif, RYREPEATVFLEB4 motif,

SORLREP2AT motif, SP8BFIBSP8AIB motif, TATABOX motif, TATABOX2 motif, TATABOX4 motif, TATABOX5 motif, TATC-box motif, TCA1 Motif motif, TCA- Element motif, TC richVepeats motif, UP1ATMSD motif, UP2ATMSD motif, and UPRMOTIFIIAT motif.

[0011] This document also features a vector construct that includes a first nucleic acid that includes a regulatory region having 90 percent or greater sequence identity (e.g., 95 percent or greater, or 98 percent or greater) to any one of SEQ ID NOs. 1 - 44 or a fragment thereof, wherein the regulatory region directs transcription of an operably linked heterologous polynucleotide; and a second nucleic acid to be transcribed, wherein the first and second nucleic acids are heterologous to each other and are operably linked. In some embodiments, the first nucleic acid consists of the nucleic acid set forth in any one of SEQ ID NOs: 1-44. In some embodiments, the second nucleic acid includes a nucleic acid sequence that encodes a polypeptide. The second nucleic acid can be operably linked to the first nucleic acid in sense orientation. In some embodiments, the second nucleic acid can be transcribed into an RNA molecule that expresses the polypeptide encoded by the second nucleic acid. The second nucleic acid can be operably linked to the first nucleic acid in antisense orientation. The second nucleic acid can be transcribed into an antisense R A molecule. The second nucleic acid can be transcribed into an interfering RNA against an endogenous gene.

[0012] In another aspect, this document features a transgenic plant or plant cell transformed with an isolated nucleic acid described herein that is operably linked to a heterologous polynucleotide, or a vector construct described herein. This document also features seeds of such a plant. In some embodiments, the heterologous nucleic acid encodes a polypeptide of agronomic interest.

[0013] This document also features a method of directing transcription by combining, in an environment suitable for transcription: a first nucleic acid that includes a regulatory region having 90 percent or greater sequence identity (e.g., 95 percent or greater, or 98 percent or greater) to any one of SEQ ID NOs. 1 - 44 or a fragment thereof; and a second nucleic acid to be transcribed; wherein the first and second nucleic acids are heterologous to each other and operably linked. The first nucleic acid molecule can consist of a sequence according to any one of SEQ ID NOs: 1 - 44. The operably linked first and second nucleic acids can be inserted into a plant cell and the plant cell regenerated into a plant.

[0014] In yet another aspect, this document features a method of expressing an exogenous coding region in a plant. The method includes transforming a plant cell with a vector described herein; regenerating a stably transformed plant from the transformed plant cell; and selecting plants containing a transformed plant cell, wherein expression of the vector results in production of a polypeptide encoded by the second nucleic acid.

[0015] This document also features a method of altering the expression of a gene in a plant. The method includes transforming a plant cell with a nucleic acid described herein that is operably linked to a heterologous polynucleotide, and

regenerating stably transformed plants from the transformed plant cell. Plants prepared according to such a method also are featured, as well as seeds obtained from such plants.

[0016] In another aspect, this document features a method of producing a transgenic plant. The method introducing into a plant cell (i) an isolated polynucleotide described herein that is operably linked to a heterologous polynucleotide, or (ii) a vector described herein, and growing a plant from the plant cell. The heterologous

polynucleotide can include a nucleic acid sequence encoding a polypeptide. The heterologous polynucleotide can be operably linked to the regulatory region in the antisense orientation. The heterologous polynucleotide can be transcribed into an interfering RNA.

[0017] In another embodiment, the present promoter control elements are capable of serving as or fulfilling the function, for example, as a core promoter, a TATA box, a polymerase binding site, an initiator site, a transcription binding site, an enhancer, an inverted repeat, a locus control region, and/or a scaffold/matrix attachment region.

[0018] It is yet another object of the present document to provide a

polynucleotide that includes at least a first and a second promoter control element. The first promoter control element is a promoter control element sequence as discussed above, and the second promoter control element is heterologous to the first control element; wherein, the first and second control elements are operably linked. Such promoters may modulate transcript levels preferentially in a particular tissue or under particular conditions.

[0019] In another embodiment, the present isolated polynucleotide comprises a promoter or a promoter control element as described above, wherein the promoter or promoter control element is operably linked to a polynucleotide to be transcribed.

[0020] In another embodiment of the present document, the promoter and promoter control elements of the instant document are operably linked to a heterologous polynucleotide that is a regulatory sequence.

[0021] It is another object of the present document to provide a host cell comprising an isolated polynucleotide or vector as described above or fragment thereof. Host cells include, for instance, bacterial, yeast, insect, mammalian, fungus, algae, and plant. The host cell can comprise a promoter or promoter control element exogenous to the genome. Such a promoter can modulate transcription in cis- and in trans-. In yet another embodiment, the host cell is a plant cell capable of regenerating into a plant.

[0022] It is another object of the present document to provide a method of modulating transcription in a sample that contains either a cell-free system of transcription or host cell. This method comprises providing a polynucleotide or vector according to the present document as described above, and contacting the sample of the polynucleotide or vector with conditions that permit transcription.

[0023] In another embodiment of the present method, the polynucleotide or vector preferentially modulates, depending upon the function of the particular promoter, constitutive transcription, stress induced transcription, light induced transcription, dark induced transcription, leaf transcription, root transcription, stem or shoot transcription, silique or fruit transcription, callus transcription, rhizome transcription, stem node transcription, gamete tissue transcription, flower transcription, immature bud or floret and inflorescence specific transcription, senescing induced transcription, germination transcription and/or drought transcription.

[0024] Other and further objects of the present document will be made clear or become apparent from the following description.

BRIEF DESCRIPTION OF THE TABLES AND FIGURES

[0025] The Tables consist of the Expression Report(s) for each promoter described herein and provide the nucleotide sequence for each promoter and details for expression driven by each of the nucleic acid promoter sequences as observed in transgenic plants. The results are presented as summaries of the spatial expression, which provides information as to gross and/or specific expression in various plant organs and tissues. The observed expression pattern is also presented, which gives details of expression during different generations or different developmental stages within a generation. Additional information is provided regarding the source organism of the promoter, and the vector and marker genes used for the construct. The following symbols are used consistently throughout the Tables:

- TO: First generation trans formant

- Tl : Second generation transformant [0026] Each row of the table begins with heading of the data to be found in the section. The following provides a description of the data to be found in each section:

18 Tl Mature Plant Expression: Identifies plant tissues that were observed for possible expression

19 Promoter Utility Provides a description of the utility of the

sequence.

FIGURE 1 - CRS380_Promoter EGFP

[0027] Figure 1 is a schematic representation of a vector that is useful to insert promoters described herein into a plant. The definitions of the abbreviations used in the vector map are as follows: Ori - the origin of replication used by an E. coli host; RB - sequence for the right border of the T-DNA from pMOG800; Sfil - restriction enzyme cleavage site used for cloning; EGFP - an enhanced version of the green fluorescent protein gene; OCS - the terminator sequence from the octopine synthase gene; p28716 (a.k.a 28716 short) - promoter used to drive expression of the PAT (BAR) gene; PAT (BAR) - a marker gene conferring herbicide resistance; LB - sequence for the left border of the T-DNA from pMOG800; Spec - a marker gene conferring spectinomycin resistance; TrfA - transcription repression factor gene; RK2-OriV - origin of replication for Agrobacterium.

DETAILED DESCRIPTION

[0028] The following definitions and methods are provided to better define the present invention and to guide those of ordinary skill in the art in the practice of the present invention. Unless otherwise noted, terms are to be understood according to conventional usage by those of ordinary skill in the relevant art.

[0029] The document disclosed herein provides promoters capable of driving the expression of an operably linked transgene. The design, construction, and use of these promoters is one object of this document. The promoter sequences, SEQ ID NOs: 1 - 44, are capable of transcribing operably linked nucleic acid molecules in particular plant tissues/organs or during particular plant growth stages, and therefore can selectively regulate expression of transgenes in these tissues/organs or at these times of plant development. 1. Definitions

[0030] The terms "nucleic acid" and "polynucleotide" are used interchangeably herein, and refer to both RNA and DNA, including cDNA, genomic DNA, synthetic DNA, and DNA or RNA containing nucleic acid analogs. Polynucleotides can have any three-dimensional structure. A nucleic acid can be double-stranded or single-stranded, i.e., a sense strand or an antisense strand. Non-limiting examples of polynucleotides include genes, gene fragments, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, siRNA, micro-RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers, as well as nucleic acid analogs.

[0031] An isolated nucleic acid can be, for example, a naturally-occurring DNA molecule, provided one of the nucleic acid sequences normally found immediately flanking that DNA molecule in a naturally-occurring genome is removed or absent. Thus, an isolated nucleic acid includes, without limitation, a DNA molecule that exists as a separate molecule, independent of other sequences, e.g., a chemically synthesized nucleic acid, or a cDNA or genomic DNA fragment produced by the polymerase chain reaction (PCR) or restriction endonuclease treatment. An isolated nucleic acid also refers to a DNA molecule that is incorporated into a vector, an autonomously replicating plasmid, or a virus, or transformed into the genome of a prokaryote or eukaryote. In addition, an isolated nucleic acid can include an engineered nucleic acid such as a DNA molecule that is part of a hybrid or fusion nucleic acid. A nucleic acid existing among hundreds to millions of other nucleic acids within, for example, cDNA libraries or genomic libraries, or gel slices containing a genomic DNA restriction digest, is not to be considered an isolated nucleic acid.

[0032] Chimeric: The term "chimeric" is used to describe polynucleotides or genes, or constructs wherein at least two of the elements of the polynucleotide or gene or construct, such as the promoter and the polynucleotide to be transcribed and/or other regulatory sequences and/or filler sequences and/or complements thereof, are heterologous to each other.

[0033] Broadly Expressing Promoter: Promoters referred to herein as

"broadly expressing promoters" actively promote transcription under most, but not necessarily all, environmental conditions and states of development or cell differentiation. Examples of broadly expressing promoters include the cauliflower mosaic virus (CaMV) 35S transcript initiation region and the 1 ' or 2' promoter derived from T-DNA of

Agrobacterium tumefaciens, and other transcription initiation regions from various plant genes, such as the maize ubiquitin-1 promoter, known to those of skill.

[0034] Domain: Domains are fingerprints or signatures that can be used to characterize protein families and/or parts of proteins. Such fingerprints or signatures can comprise conserved (1) primary sequence, (2) secondary structure, and/or (3) three- dimensional conformation. A similar analysis can be applied to polynucleotides.

Generally, each domain has been associated with either a conserved primary sequence or a sequence motif. Generally these conserved primary sequence motifs have been correlated with specific in vitro and/or in vivo activities. A domain can be any length, including the entirety of the polynucleotide to be transcribed. Examples of domains include, without limitation, AP2, helicase, homeobox, zinc finger, etc.

[0035] Endogenous: The term "endogenous," within the context of the current document refers to any polynucleotide, polypeptide or protein sequence which is a natural part of a cell or organism(s) regenerated from said cell. In the context of promoter, the term "endogenous coding region" or "endogenous cDNA" refers to the coding region that is naturally operably linked to the promoter.

[0036] Enhancer/Suppressor: An "enhancer" is a DNA regulatory element that can increase the steady state level of a transcript, usually by increasing the rate of transcription initiation. Enhancers usually exert their effect regardless of the distance, upstream or downstream location, or orientation of the enhancer relative to the start site of transcription. In contrast, a "suppressor" is a corresponding DNA regulatory element that decreases the steady state level of a transcript, again usually by affecting the rate of transcription initiation. The essential activity of enhancer and suppressor elements is to bind a protein factor(s). Such binding can be assayed, for example, by methods described below. The binding is typically in a manner that influences the steady state level of a transcript in a cell or in an in vitro transcription extract.

[0037] Exogenous: As referred to within, "exogenous" is any polynucleotide, polypeptide or protein sequence, whether chimeric or not, that is introduced into the genome of a host cell or organism regenerated from said host cell by any means other than by a sexual cross. Examples of means by which this can be accomplished are described below, and include Agrobacterium-mediatGd transformation (of dicots - e.g. Salomon et al. (1984) EMBO J. 3 : 141 ; Herrera-Estrella et al. (1983) EMBO J. 2:987; of monocots, representative papers are those by Escudero et al. (1996) Plant J. 10:355), Ishida et al. (1996) Nature Biotech 14:745, May et al. (1995) Bio/Technology 13 :486), biolistic methods (Armaleo et al. (1990) Current Genetics 17:97), electroporation, in planta techniques, and the like. Such a plant containing the exogenous nucleic acid is referred to here as a To for the primary transgenic plant and Ti for the first generation. The term "exogenous" as used herein is also intended to encompass inserting a naturally found element into a non-naturally found location.

[0038] Heterologous sequences: "Heterologous sequences" are those that are not operatively linked or are not contiguous to each other in nature. For example, a promoter from corn is considered heterologous to an Arabidopsis coding region sequence. Also, a promoter from a gene encoding a growth factor from corn is considered heterologous to a sequence encoding the corn receptor for the growth factor. Regulatory element sequences, such as UTRs or 3 ^' end termination sequences that do not originate in nature from the same gene as the coding sequence, are considered heterologous to said coding sequence.

Elements operatively linked in nature and contiguous to each other are not heterologous to each other. On the other hand, these same elements remain operatively linked but become heterologous if other filler sequence is placed between them. Thus, the promoter and coding sequences of a corn gene expressing an amino acid transporter are not heterologous to each other, but the promoter and coding sequence of a corn gene operatively linked in a novel manner are heterologous.

[0039] Homologous: In the current document, a "homologous" polynucleotide refers to a polynucleotide that shares sequence similarity with the polynucleotide of interest. This similarity may be in only a fragment of the sequence and often represents a functional domain such as, examples including, without limitation, a DNA binding domain or a domain with tyrosine kinase activity. The functional activities of homologous

polynucleotides are not necessarily the same. [0040] Inducible Promoter: An "inducible promoter" in the context of the current document refers to a promoter, the activity of which is influenced by certain conditions, such as light, temperature, chemical concentration, protein concentration, conditions in an organism, cell, or organelle, etc. A typical example of an inducible promoter, which can be utilized with the polynucleotides of the present document, is PARSK1, the promoter from an Arabidopsis gene encoding a serine-threonine kinase enzyme, and which promoter is induced by dehydration, abscissic acid and sodium chloride (Wang and Goodman (1995) Plant J. 8:37). Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions, elevated temperature, the presence or absence of a nutrient or other chemical compound or the presence of light.

[0041] Misexpression: The term "misexpression" refers to an increase or a decrease in the transcription of a coding region into a complementary R A sequence as compared to the wild-type. This term also encompasses expression and/or translation of a gene or coding region or inhibition of such transcription and/or translation for a different time period as compared to the wild-type and/or from a non-natural location within the plant genome, including a gene or coding region from a different plant species or from a non- plant organism.

[0042] Modulate Transcription Level: As used herein, the phrase "modulate transcription" describes the biological activity of a promoter sequence or promoter control element. Such modulation includes, without limitation, up- and down-regulation of initiation of transcription, rate of transcription, and/or transcription levels.

[0043] Operable Linkage: An "operable linkage" is a linkage in which a promoter sequence or promoter control element is connected to a polynucleotide sequence (or sequences) in such a way as to place transcription of the polynucleotide sequence under the influence or control of the promoter or promoter control element. Two DNA sequences (such as a polynucleotide to be transcribed and a promoter sequence linked to the 5' end of the polynucleotide to be transcribed) are said to be operably linked if induction of promoter function results in the transcription of mRNA encoding the polynucleotide and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter sequence to direct the expression of the protein, antisense R A, R Ai or ribozyme, or (3) interfere with the ability of the DNA template to be transcribed. Thus, a promoter sequence would be operably linked to a polynucleotide sequence if the promoter was capable of effecting transcription of that polynucleotide sequence.

[0044] Percentage of sequence identity: As used herein, the term "percent sequence identity" refers to the degree of identity between any given query sequence and a subject sequence. A subject sequence typically has a length that is from about 80 percent to 250 percent of the length of the query sequence, e.g., 82, 85, 87, 89, 90, 93, 95, 97, 99, 100, 105, 110, 115, or 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, or 250 percent of the length of the query sequence. A query nucleic acid or amino acid sequence is aligned to one or more subject nucleic acid or amino acid sequences using the computer program ClustalW (version 1.83, default parameters), which allows alignments of nucleic acid or protein sequences to be carried out across their entire length (global alignment). Chenna et al. (2003) Nucleic Acids Res. 31(13):3497-500.

[0045] ClustalW calculates the best match between a query and one or more subject sequences, and aligns them so that identities, similarities and differences can be determined. Gaps of one or more residues can be inserted into a query sequence, a subject sequence, or both, to maximize sequence alignments. For fast pairwise alignment of nucleic acid sequences, the following default parameters are used: word size: 2;

window size: 4; scoring method: percentage; number of top diagonals: 4; and gap penalty: 5. For an alignment of multiple nucleic acid sequences, the following parameters are used: gap opening penalty: 10.0; gap extension penalty: 5.0; and weight transitions: yes. For fast pairwise alignment of protein sequences, the following parameters are used: word size: 1; window size: 5; scoring method: percentage; number of top diagonals: 5; gap penalty: 3. For multiple alignment of protein sequences, the following parameters are used: weight matrix: blosum; gap opening penalty: 10.0; gap extension penalty: 0.05; hydrophilic gaps: on; hydrophilic residues: Gly, Pro, Ser, Asn, Asp, Gin, Glu, Arg, and Lys; residue-specific gap penalties: on. The output is a sequence alignment that reflects the relationship between sequences. ClustalW can be run, for example, at the Baylor College of Medicine Search Launcher website and at the

European Bioinformatics Institute website on the World Wide Web.

[0046] To determine a percent identity for polypeptide or nucleic acid sequences between a query and a subject sequence, the sequences are aligned using Clustal W and the number of identical matches in the alignment is divided by the query length, and the result is multiplied by 100. The output is the percent identity of the subject sequence with respect to the query sequence. It is noted that the percent identity value can be rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 are rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 are rounded up to 78.2.

[0047] Plant Promoter: A "plant promoter" is a promoter capable of initiating transcription in plant cells and can modulate transcription of a polynucleotide. Such promoters need not be of plant origin. For example, promoters derived from plant viruses, such as the CaMV35S promoter or from Agrobacterium tumefaciens such as the T-DNA promoters, can be plant promoters. A typical example of a plant promoter of plant origin is the maize ubiquitin-1 (ubi-1) promoter known to those of skill in the art.

[0048] Plant Tissue: The term "plant tissue" includes differentiated and undifferentiated tissues or plants, including but not limited to roots, stems, shoots, rhizomes, cotyledons, epicotyl, hypocotyl, leaves, pollen, seeds, gall tissue and various forms of cells in culture such as single cells, protoplast, embryos, and callus tissue. The plant tissue may be in plants or in organ, tissue or cell culture.

[0049] Preferential Transcription: "Preferential transcription" is defined as transcription that occurs in a particular pattern of cell types or developmental times or in response to specific stimuli or combination thereof. Non-limitive examples of preferential transcription include: high transcript levels of a desired sequence in root tissues; detectable transcript levels of a desired sequence in certain cell types during embryogenesis; and low transcript levels of a desired sequence under drought conditions. Such preferential transcription can be determined by measuring initiation, rate, and/or levels of transcription.

[0050] Promoter: A "promoter" is a DNA sequence that directs the transcription of a polynucleotide. Typically a promoter is located in the 5' region of a polynucleotide to be transcribed, proximal to the transcriptional start site of such polynucleotide. More typically, promoters are defined as the region upstream of the first exon; more typically, as a region upstream of the first of multiple transcription start sites; more typically, as the region downstream of the preceding gene and upstream of the first of multiple transcription start sites; more typically, the region downstream of the polyA signal and upstream of the first of multiple transcription start sites; even more typically, about 3,000 nucleotides upstream of the ATG of the first exon; even more typically, 2,000 nucleotides upstream of the first of multiple transcription start sites. The promoters of the document comprise at least a core promoter as defined above. Frequently promoters are capable of directing transcription of genes located on each of the complementary DNA strands that are 3' to the promoter. Stated differently, many promoters exhibit bidirectionality and can direct transcription of a downstream gene when present in either orientation (i.e. 5' to 3' or 3' to 5' relative to the coding region of the gene). Additionally, the promoter may also include at least one control element such as an upstream element. Such elements include UARs and optionally, other DNA sequences that affect transcription of a polynucleotide such as a synthetic upstream element.

[0051] Promoter Control Element: The term "promoter control element" as used herein describes elements that influence the activity of the promoter. Promoter control elements include transcriptional regulatory sequence determinants such as, but not limited to, enhancers, scaffold/matrix attachment regions, TATA boxes, transcription start locus control regions, UARs, URRs, other transcription factor binding sites and inverted repeats.

[0052] Public sequence: The term "public sequence," as used in the context of the instant application, refers to any sequence that has been deposited in a publicly accessible database prior to the filing date of the present application. This term encompasses both amino acid and nucleotide sequences. Such sequences are publicly accessible, for example, on the BLAST databases on the NCBI FTP web site (accessible via the internet). The database at the NCBI FTP site utilizes "gi" numbers assigned by NCBI as a unique identifier for each sequence in the databases, thereby providing a non- redundant database for sequence from various databases, including GenBank, EMBL, DBBJ (DNA Database of Japan) and PDB (Brookhaven Protein Data Bank).

[0053] Regulatory Regions: The term "regulatory region" refers to nucleotide sequences that, when operably linked to a sequence, influence transcription initiation or translation initiation or transcription termination of said sequence and the rate of said processes, and/or stability and/or mobility of a transcription or translation product. As used herein, the term "operably linked" refers to positioning of a regulatory region and said sequence to enable said influence. Regulatory regions include, without limitation, promoter sequences, enhancer sequences, response elements, protein recognition sites, inducible elements, protein binding sequences, 5' and 3' untranslated regions (UTRs), transcriptional start sites, termination sequences, polyadenylation sequences, and introns. Regulatory regions can be classified in two categories, promoters and other regulatory regions.

[0054] Regulatory Sequence: The term "regulatory sequence," as used in the current document, refers to any nucleotide sequence that influences transcription or translation initiation and rate, or stability and/or mobility of a transcript or polypeptide product. Regulatory sequences include, but are not limited to, promoters, promoter control elements, protein binding sequences, 5' and 3' UTRs, transcriptional start sites, termination sequences, polyadenylation sequences, introns, certain sequences within amino acid coding sequences such as secretory signals, protease cleavage sites, etc.

[0055] Specific Promoters: In the context of the current document, "specific promoters" refers to a subset of promoters that have a high preference for modulating transcript levels in a specific tissue, or organ or cell and/or at a specific time during development of an organism. By "high preference" is meant at least 3-fold, preferably 5- fold, more preferably at least 10-fold still more preferably at least 20-fold, 50-fold or 100-fold increase in transcript levels under the specific condition over the transcription under any other reference condition considered. Typical examples of temporal and/or tissue or organ specific promoters of plant origin that can be used with the polynucleotides of the present document, are: PTA29, a promoter which is capable of driving gene transcription specifically in tapetum and only during anther development (Koltonow et al. (1990) Plant Cell 2: 1201; RCc2 and RCc3, promoters that direct root-specific gene transcription in rice (Xu et al. (1995) Plant Mol. Biol. 2Ί 2Ί>Ί; TobRB27, a root-specific promoter from tobacco (Yamamoto et al. (1991) Plant Cell 3:371). Examples of tissue-specific promoters under developmental control include promoters that initiate transcription only in certain tissues or organs, such as root, ovule, fruit, seeds, or flowers. Other specific promoters include those from genes encoding seed storage proteins or the lipid body membrane protein, oleosin. A few root-specific promoters are noted above. See also "Preferential transcription."

[0056] Stringency: "Stringency," as used herein is a function of nucleic acid molecule probe length, nucleic acid molecule probe composition (G + C content), salt concentration, organic solvent concentration and temperature of hybridization and/or wash conditions. Stringency is typically measured by the parameter T_m, which is the temperature at which 50% of the complementary nucleic acid molecules in the hybridization assay are hybridized, in terms of a temperature differential from T_m. High stringency conditions are those providing a condition of T_m - 5°C to T_m - 10°C. Medium or moderate stringency conditions are those providing T_m - 20°C to T_m - 29°C. Low stringency conditions are those providing a condition of T_m - 40°C to T_m - 48°C. The relationship between hybridization conditions and T_m (in °C) is expressed in the mathematical equation:

T_m = 81.5 -16.6(logio[Na⁺]) + 0.41(%G+C) - (600/N) (I)

[0057] where N is the number of nucleotides of the nucleic acid molecule probe.

This equation works well for probes 14 to 70 nucleotides in length that are identical to the target sequence. The equation below, for T_m of DNA-DNA hybrids, is useful for probes having lengths in the range of 50 to greater than 500 nucleotides, and for conditions that include an organic solvent (formamide):

T_m = 81.5+16.6 log {[Na⁺]/(l+0.7[Na⁺])}+ 0.41(%G+C)-500/L 0.63(%formamide) (II)

[0058] where L represents the number of nucleotides in the probe in the hybrid

(21). The T_m of Equation II is affected by the nature of the hybrid: for DNA-R A hybrids, T_m is 10-15 °C higher than calculated; for RNA-RNA hybrids, T_m is 20-25 °C higher. Because the T_m decreases about 1°C for each 1% decrease in homology when a long probe is used (Frischauf et al. (1983) J. Mol Biol, 170: 827-842), stringency conditions can be adjusted to favor detection of identical genes or related family members.

[0059] Equation II is derived assuming the reaction is at equilibrium.

Therefore, hybridizations according to the present document are most preferably performed under conditions of probe excess and allowing sufficient time to achieve equilibrium. The time required to reach equilibrium can be shortened by using a hybridization buffer that includes a hybridization accelerator such as dextran sulfate or another high volume polymer.

[0060] Stringency can be controlled during the hybridization reaction, or after hybridization has occurred, by altering the salt and temperature conditions of the wash solutions. The formulas shown above are equally valid when used to compute the stringency of a wash solution. Preferred wash solution stringencies lie within the ranges stated above; high stringency is 5-8°C below T_m, medium or moderate stringency is 26- 29°C below T_m and low stringency is 45-48°C below T_m.

[0061] To: The term "T₀" refers to the whole plant, explant or callus tissue, inoculated with the transformation medium.

[0062] Τχ : The term Ti refers to either the progeny of the T₀ plant, in the case of whole-plant transformation, or the regenerated seedling in the case of explant or callous tissue transformation.

[0063] T₂: The term T₂ refers to the progeny of the Ti plant. T₂ progeny are the result of self-fertilization or cross-pollination of a Ti plant.

[0064] T3 : The term T3 refers to second generation progeny of the plant that is the direct result of a transformation experiment. T3 progeny are the result of self- fertilization or cross-pollination of a T₂ plant.

[0065] TATA to start: "TATA to start" shall mean the distance, in number of nucleotides, between the primary TATA motif and the start of transcription.

[0066] Transgenic plant: A "transgenic plant" is a plant having one or more plant cells that contain at least one exogenous polynucleotide introduced by recombinant nucleic acid methods.

[0067] Translational start site: In the context of the present document, a

"translational start site" is usually an ATG or AUG in a transcript, often the first ATG or AUG. A single protein encoding transcript, however, may have multiple translational start sites.

[0068] Transcription start site: "Transcription start site" is used in the current document to describe the point at which transcription is initiated. This point is typically located about 25 nucleotides downstream from a TFIID binding site, such as a TATA box. Transcription can initiate at one or more sites within the gene, and a single polynucleotide to be transcribed may have multiple transcriptional start sites, some of which may be specific for transcription in a particular cell-type or tissue or organ. is stated relative to the transcription start site and indicates the first nucleotide in a transcript.

[0069] Upstream Activating Region (UAR): An "Upstream Activating

Region" or "UAR" is a position or orientation dependent nucleic acid element that primarily directs tissue, organ, cell type, or environmental regulation of transcript level, usually by affecting the rate of transcription initiation. Corresponding DNA elements that have a transcription inhibitory effect are called herein "Upstream Repressor

Regions" or "URR"s. The essential activity of these elements is to bind a protein factor. Such binding can be assayed by methods described below. The binding is typically in a manner that influences the steady state level of a transcript in a cell or in vitro transcription extract.

[0070] Untranslated region (UTR): Untranslated region (UTR): A "UTR" is any contiguous series of nucleotide bases that is transcribed, but is not translated. A 5' UTR lies between the start site of the transcript and the translation initiation codon (ATG codon) and includes the +1 nucleotide of the messenger RNA or cDNA. Alternately, 5' UTR can be synthetically produced or manipulated DNA elements. A "plant 5' UTR" can be a native or non-native 5 ' UTR that is functional in plant cells. A 5 ' UTR can be used as a 5' regulatory element for modulating expression of an operably linked transcribable polynucleotide molecule. For example, 5' UTRs derived from heat shock protein genes have been demonstrated to enhance gene expression in plants (see for example, U.S. Pat. No. 5,659,122 and U.S. Pat. No. 5,362,865, all of which are incorporated herein by reference). Examples of 5' UTRs include those shown in SEQ ID NOs: l-7, 9-12, 16-18. A 3' UTR lies between the translation termination codon and the end of the transcript. UTRs can have particular functions such as increasing mRNA message stability or translation attenuation. Examples of 3' UTRs include, but are not limited to polyadenylation signals and transcription termination sequences.

2. Use Of the Promoters

[0071] The promoters and promoter control elements of this document are capable of modulating transcription. Such promoters and promoter control elements can be used in combination with native or heterologous promoter fragments, control elements or other regulatory sequences to modulate transcription and/or translation.

[0072] Specifically, promoters and control elements of the document can be used to modulate transcription of a desired polynucleotide, which includes without limitation:

a) antisense;

b) ribozymes;

c) coding sequences; or

d) fragments thereof.

[0073] The promoter also can modulate transcription in a host genome in cis- or in trans-.

[0074] In an organism, such as a plant, the promoters and promoter control elements of the instant document are useful to produce preferential transcription which results in a desired pattern of transcript levels in a particular cells, tissues, or organs, or under particular conditions.

3. Identifying and Isolating Promoter Sequences

[0075] The promoters and promoter control elements of the present document are presented in the Promoter Reports of the Tables and were identified from Sorghum bicolor, Panicum virgatum, Oryza sativa, and Arabidopsis thaliana. Isolation from genomic libraries of polynucleotides comprising the sequences of the promoters and promoter control elements of the present document is possible using known techniques. For example, polymerase chain reaction (PCR) can amplify the desired polynucleotides utilizing primers designed from SEQ ID NOs: 1 - 44. Polynucleotide libraries comprising genomic sequences can be constructed according to Sambrook et al.,

Molecular Cloning: A Laboratory Manual 2^nd Ed. (1989) Cold Spring Harbor Press, Cold Spring Harbor, NY), for example. [0076] Other procedures for isolating polynucleotides comprising the promoter sequences of the document include, without limitation, tail-PCR, and 5' rapid

amplification of cDNA ends (RACE). See, for tail-PCR, for example, Liu et al. (1995) Plant ^r 8(3): 457-463; Liu et al. (1995) Genomics 25: 674-681; Liu et al. (1993) Nucl. Acids Res. 21(14): 3333-3334; and Zoe et al. (1999) BioTechniques 27(2): 240-248; for RACE, see, for example, PCR Protocols: A Guide to Methods and Applications, (1990) Academic Press, Inc.

[0077] In addition, the promoters and promoter control elements described in the Promoter Reports in the Tables (SEQ. ID. Nos. 1 - 44) can be chemically synthesized according to techniques in common use. See, for example, Beaucage et al. (1981) Tet. Lett. 22: 1859 and U.S. Pat. No. 4,668,777. Such chemical oligonucleotide synthesis can be carried out using commercially available devices, such as, Biosearch 4600 or 8600 DNA synthesizer, by Applied Biosystems, a division of Perkin-Elmer Corp., Foster City, California, USA; and Expedite by Perceptive Biosystems, Framingham, Massachusetts, USA.

[0078] Included in the present document are promoters exhibiting nucleotide sequence identity to SEQ. ID. Nos. 1 - 44. In particular, promoters of this document can exhibit at least 80% sequence identity (e.g., at least 85%>, at least 90%>, at least 95%>, 96%>, 97%), 98%o or 99%> sequence identity) compared to the nucleotide sequence set forth in any one of SEQ. ID. Nos. 1 - 44. Sequence identity can be calculated by the algorithms and computers programs described above. Furthermore, promoters described herein also can be a fragment of any one of SEQ ID NO: 1 - 44 as long as the fragment retains the ability to direct transcription of a polynucleotide. Suitable fragments can be, for example at least 80% (e.g., at least 85, 90, 95, 96, 97, 98, or 99%) of the length of the nucleotide sequence set forth in any one of SEQ ID NOs: 1 - 44. For example, a regulatory region can be a fragment of anyone of SEQ ID NOs: 1-44 that is 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, or 2400 nucleotides in length that retains the ability to direct expression of an operably linked nucleic acid.

[0079] A regulatory region can contain conserved regulatory motifs. Such a regulatory region can be have a nucleotide sequence set forth in anyone of SEQ ID NOs: 1-44, or a regulatory region having a nucleotide sequence that deviates from that set forth in SEQ ID NOs: 1-44, while retaining the ability to direct expression of an operably linked nucleic acid. For example, a regulatory region can contain a CAAT box or a TATA box. A CAAT box is a conserved nucleotide sequence involved in initiation of transcription. A CAAT box functions as a recognition and binding site for regulatory proteins called transcription factors. A TATA box is another conserved nucleotide sequence involved in transcription initiation. A TATA box seems to be important in determining accurately the position at which transcription is initiated.

[0080] Other conserved regulatory motifs can be identified using methods known in the art. For example, a regulatory region can be analyzed using the PLACE (PLAnt Cis-acting regulatory DNA Elements) Web Signal Scan program on the world wide web at dna.affrc.go.jp/PLACE/signalscan.html. See, Higo et al., Nucleic Acids Research, 27(l):297-300 (1999); and Prestridge, CABIOS, 7:203-206 (1991). Examples of conserved regulatory motifs can be found in the PLACE database on the world wide web at dna.affrc.go.jp/PLACE/. See, Higo et al, supra.

[0081] A regulatory region having a nucleotide sequence set forth in anyone of

SEQ ID NOs: 1-44, or a regulatory region having a nucleotide sequence that deviates from that set forth in SEQ ID NOs: 1-44, while retaining the ability to direct expression of an operably linked nucleic acid, can contain one or more conserved regulatory motifs, which can be found in the PLACE database. For example, a regulatory region can have an ABA-responsive element such as an ABREATCONSENSUS motif having the consensus sequence (C/T)ACGTGGC. See, Choi et al., J Biol Chem. 275: 1723-1730 (2000). A regulatory region can contain an ABRE motif having the consensus sequence ACGTG or an ABRELATRDl motif having the consensus sequence CGMCACGTGB (SEQ ID NO: 45). See, Simpson et al, Plant J. 33: 259-270 (2003); Nakashima et al, Plant Mol Biol. 60:51-68 (2006). A regulatory region can contain an ABREATRD22 motif having the consensus sequence RYACGTGGYR (SEQ ID NO:46). See, Iwasaki et al., Mol Gen Genet 247:391-398 (1995); Bray, Trends Plant Sci. 2:48-54 (1997); Busk and Pages, Plant Mol Biol 37:425-435 (1998). A regulatory region can contain an ABRERATCAL motif having the consensus sequence MACGYGB. See, Kaplan et al., Plant Cell. 18:2733-2748 (2006). A regulatory region can contain an ABREZMRAB28 motif having the consensus sequence CCACGTGG. See, Suzuki et al., Plant

Physiol.139 437-447 (2005); Busk and Pages, Plant Mol Biol 37:425-435 (1998);

Alonso-Blanco et al, Plant Physiology 139: 1304-1312 (2005); Guan et al, Plant J 22: 87-95 (2000); Benedict et al, Plant Cell Environ. 29: 1259-1272 (2006); Jaglo-Ottosen et al, Science 1998 3: 104-106 (1998); and Gilmour et al, Plant J 16: 433-442 (1998). A regulatory region can contain an ACGTABREMOTIFA20SEM motif having the consensus sequence ACGTGKC. See, Hattori et al, Plant Cell Physiol 43: 136-140 (2002); and Narusaka et al. , Plant J. 34: 137-148 (2003). A regulatory region can have an ACE motif having the consensus sequence GACACGTAGA. See, Hartmann et al, Plant Mol Biol 36: 741-754 (1998). A regulatory region can contain an ACIIPVPAL2 motif having the consensus sequence CCACCAACCCCC (SEQ ID NO: 47). See, Patzlaff et al, Plant Mol Biol. 53:597-608 (2003); Hatton et al, Plant J 7:859-876 (1995); and Gomez-Maldonado et al, Plant J. 39:513-526 (2004). A regulatory region can contain an 3-AFl\binding\site light responsive element having the consensus sequence AAATAGATAAATAAAAACATT. See, Gilmartin et al, Plant Cell, 2:369- 378 (1990). A regulatory region can contain an AMYBOX1 motif having the consensus sequence TAACARA. See, Huang et al, Plant Mol Biol 14:655-668 (1990). A regulatory region can contain an ARE1 motif having the consensus sequence

PvGTGACNNNGC (SEQ ID NO: 48). See, Rushmore et al, J Biol Chem 266:11632- 11639 (1991). A regulatory region can contain an ATCT motif having the consensus sequence AATCT(A/G)ATCB (SEQ ID NO: 49). A regulatory region can contain an ATHB1ATCONSENSUS motif having the consensus sequence CAATWATTG. See, Sessa et al., EMBO J 12:3507-3517 (1993). A regulatory region can contain an

ATHB6COREAT motif having the consensus sequence CAATTATTA. See,

Himmelbach et al, EMBO J. 21 :3029-3038 (2002). A regulatory region can contain an AUXRETGA2GMGH3 motif having the consensus sequence TGACGTAA. See, Liu et al, Plant Cell 6:645-657 (1994); Liu et al, Plant Physiol 115:397-407 (1997); and Guilfoyle et al, Plant Physiol 118: 341-347 (1998). A regulatory region can contain a BOXllPCCHS motif having the consensus sequence ACGTGGC. See, Block et al., Proc Natl Acad Sci USA 87:5387-5391 (1990); Terzaghi and Cashmore, Annu Rev Plant Physiol Plant Mol Biol 46:445-474 (1995); and Nakashima et al, Plant Mol Biol. 60: 51- 68 (2006). A regulatory region can contain a CAATBOX1 motif having the consensus sequence CCAAT. See, Shirsat et al, Mol Gen Genet 215:326-331 (1989). A regulatory region can contain a CACGCAATGMGH3 motif having the consensus sequence CACGCAAT. See, Ulmasov et al, Plant Cell 7: 1611-1623 (1995). A regulatory region can contain a CACGTGMOTIF motif having the consensus sequence CACGTG. See, Hudson and Quail, Plant Physiol 133: 1605-1616 (2003). A regulatory region can contain a CARGCW8GAT motif having the consensus sequence CWWWWWWWWG (SEQ ID NO: 50). See, Tang and Perry, J Biol C/zem.278:28154-28159 (2003); Folter and Angenent, Trends Plant Sci. 11 :224-231 (2006). A regulatory region can contain a CARGNCAT motif having the consensus sequence CCWWWWWWWWGG (SEQ ID NO: 51). See Wang et al, Plant Cell, 16: 1206-1219 (2004). A regulatory region can contain a CACGTGMOTIF motif having the consensus sequence CACGTG. See, Hudson and Quail, Plant Physiol. 133: 1605-1616 (2003). A regulatory region can contain a CCA1ATLHCB1 motif having the consensus sequence AAMAATCT. See, Wang et al, Plant Cell 9:491-507 (1997). A regulatory region can contain a

CEREGLUBOX2PSLEGA motif having the consensus sequence TGAAAACT. See, Shirsat et al, supra. A regulatory region can contain a CTRMCAMV35S motif having the consensus sequence TCTCTCTCT. A regulatory region can contain an E2FAT motif having the consensus sequence TYTCCCGCC. See, Ramirez-Parra et al, Plant J. 33: 801-811 (2003). A regulatory region can contain an E2FCONSENSUS motif having the consensus sequence WTTSSCSS. See, Vandepoele et al, Plant Physiol.139: 316-328 (2005). A regulatory region can contain an ELI -box 3 motif having the consensus sequence AAACCAATT in any orientation. See, Lois et al. , EMBO J 8 : 1641 - 1648 (1989); Ohl et al, The Plant Cell 2: 837-848 (1990); Pastuglia et al, The Plant Cell 9: 49-60 (1997)). A regulatory region can contain an ERELEE4 motif having the consensus sequence AWTTCAAA. See, Itzhaki et al, Proc Natl Acad Sci USA 91 :8925-8929 (1994); Montgomery et al, Proc Natl Acad Sci USA 90:5939-5943 (1993); Tapia et al, Plant Physiol. 138:2075-2086 (2005); and Rawat et al, Plant Mol Biol. 57: 629-643 (2005). A regulatory region can contain a GADOWNAT motif having the consensus sequence ACGTGTC. See, Ogawa et al, Plant Cell 15: 1591-1604 (2003); and

Nakashima et al, Plant Mol Biol. 60: 51-68 (2006). A regulatory region can contain a GADOWNAT motif having the consensus sequence ACGTGTC. See Sangwan and O'Brian, Plant Physiol. 129: 1788-1794 (2002). A regulatory region can contain a GAGAGMGSA1 motif having the consensus sequence GAGAGAGAGAGAGAGAGA (SEQ ID NO: 52). See, Sutoh and Yamauchi, Plant J. 34: 636-645 (2003). A regulatory region can contain a GARE20SREP1 motif having the consensus sequence TAACGTA. Sutoh and Yamauchi, Plant J. 34: 636-645 (2003). A regulatory region can contain a GAREAT motif having the consensus sequence TAACAAR. See, Ogawa et al, Plant Cell 15: 1591-1604 (2003). A regulatory region can contain a GATABox motif having the consensus sequence GATAGGA. See, Mongkolsiriwatana et al, KasetsartJ. (Nat. Sci.) 43 : 164 - 177 (2009). A regulatory region can contain a GCCYBox motif having the consensus sequence TAAGAGCCGCC. See, Yamamoto et al, Plant J 20:571-579 (1999). A regulatory region can contain a GT1MOTIFPSRBCS motif having the consensus sequence KWGTGRWAAWRW. See, Villain et al, J Biol Chem 271 :32593- 32598 (1996). A regulatory region can contain a HSE motif having the consensus sequence AGAANNTTCT. See, Nover et al, Cell Stress Chaperones. 6(3): 177-89 (2001). A regulatory region can contain an IBOX motif having the consensus sequence GATAAG. See, Giuliano et al, Proc Natl Acad Sci USA 85:7089-7093 (1988). A regulatory region can contain an IBOXCORENT motif having the consensus sequence GATAAGR. See, Martinez-Hernandez et al, Plant Physiol 128: 1223-1233 (2002). A regulatory region can contain an INRNTPSADB motif having the consensus sequence YTCANTYY. See, Nakamura et a/., /antJ29: 1-10 (2002). A regulatory region can contain a LEAFY ATAG motif having the consensus sequence CCAATGT. A regulatory region can contain a LRENPCABE motif having the consensus sequence ACGTGGCA. See, Castresana et al, EMBO J 1:1929-1936 (1988). A regulatory region can contain a MARTBOX motif having the consensus sequence TTWTWTTWTT (SEQ ID NO: 53). See, Gasser et al, Int Rev Cyto 119:57-96 (1989). A regulatory region can contain a MBS motif having the consensus sequence TAACTG. See, Mongkolsiriwatana et al, Kasetsart J. (Nat. Sci.) 43: 164 - 177 (2009). A regulatory region can contain a

MYBGAHV motif having the consensus sequence TAACAAA. See, Gubler et al, Plant Cell 7: 1879-1891 (1995); Morita et al, FEBS Lett 423:81-85 (1998); Gubler et al, Plant J. 17: 1-9(1999). A regulatory region can contain a MYBIAT motif having the consensus sequence AAACCA. A regulatory region can contain a MYBPLANT motif having the consensus sequence MACCWAMC. See, Sablowski et al, EMBO J 13: 128-137 (1994); Tamagnone et al, Plant Cell 10: 135-154 (1998). A regulatory region can contain a NR BNEXTA motif having the consensus sequence TAGTGGAT. See, Elliott and Shirsat, Plant Mol Biol 37:675-687 (1998). A regulatory region can contain an

OSE2ROOTNODULE motif having the consensus sequence CTCTT. See, Vieweg et αΙ., ΜΡΜΙ , 17(l):62-69 (2004). A regulatory region can contain a P1BS motif having the consensus sequence GNATATNC. See, Rubio et al, Genes Dev. 15: 2122- 2133.(2001); Shunmann et al., J Exp Bot. 55: 855-865. (2004); and Shunmann et al, Plant Physiol. 136: 4205-4214 (2004). A regulatory region can contain a P-box gibberellin-responsive element having the consensus sequence TAACAAA. See, Gubler and Jacobsen, Plant Cell, Vol. 4, 1435-1441 (1992). A regulatory region can contain a phosphate starvation induced binding motif. See, Rubio et al, Genes Dev 15:2122-2133 (2001). A regulatory region can contain a PRECONSCRHSP70A motif having the consensus sequence SCGAYNRNNNNNNNNNNNNNNNHD (SEQ ID NO: 54). See, von Gromoff et al, Nucleic Acids Res. 34:4767-4779 (2006). A regulatory region can contain an RGATAOS (R-GATA (GATA motif binding factor) binding site) motif having the consensus sequence CAGAAGATAA. See, Yin et al, Plant J., 12: 1179-1188 (1997). A regulatory region can contain a ROOTMOTIFTAPOX1 motif having the consensus sequence ATATT. See, Elmayan and Tepfer, Transgenic Res 4:388-396 (1995). A regulatory region can contain a RYREPEATGMGY2 motif having the consensus sequence CATGCAT. See, Lelievre et al, Plant Physiol 98:387-391 (1992). A regulatory region can contain a RYREPEATVFLEB4 motif having the consensus sequence CATGCATG. See, Curaba et al, Plant Physiol. 136: 3660-3669 (2004); and Nag et al, Plant Mol Biol. 59: 821-838 (2005). A regulatory region can contain a SBOXATRBCS motif having the consensus sequence CACCTCCA. See, Acevedo- Hernandez et al, Plant J. 43:506-519 (2005). A regulatory region can contain a

SORLREP2AT motif having the consensus sequence GGGCC. See, Ma and Bohnert, Genome Biol. 8(4): R49 (2007). A regulatory region can contain a SP8BFIBSP8BIB motif having the consensus sequence TACT ATT. See, Ishiguro and Nakamura, Plant Mol Biol 18:97-108 (1992); Ishiguro and Nakamura, Mol Gen Genet 244: 563-571 (1994). A regulatory region can contain a TATAbox motif such as a TATABOX1, TATABOX2, TATABOX4, or TATABOX5 motif having the consensus sequence CTATAAATAC (SEQ ID NO: 55), TATAAAT, TATATAA, and TTATTT,

respectively. See, Grace et al, J Biol Chem. 279:8102-8110 (2004); and Shirsat et al, supra. A regulatory region can contain a TATABOXOSPAL motif having the consensus sequence TATTTAA. See, Zhu et al, Plant Cell 14: 795-803 (2002). A regulatory region can contain a TATC-box motif having the consensus sequence TATCCCA. A regulatory region can contain a TCA1 motif having the sequence TATCCCA. A regulatory region can contain a TC_rich\repeats motif having the consensus sequence ATTCTCTAAC (SEQ ID NO: 56). A regulatory region can contain a TCA-element motif having the consensus sequence CCATCTTTTT (SEQ ID NO:57). See,

Mongkolsiriwatana et al, Kasetsart J. (Nat. Sci.) 43: 164-177 (2009). A regulatory region can contain a TATCCAYMOTIFOSRAMY3D motif having the consensus sequence TATCCAY. See, Toyofuku et al, FEBS Lett, 428:275-280 (1998); and Rubio- Somoza et al, Plant J. 47: 269-281 (2006). A regulatory region can contain a

TE2F2NTPCNA motif having the consensus sequence ATTCCCGC. See, Kosugi and Ohashi, Plant J 29: 45-59 (2002). A regulatory region can contain a

TRANSINITMONOCOTS motif having the consensus sequence RMNAUGGC. See, Joshi et al, Plant Mol Biol 35:993-1001 (1997). A regulatory region can contain a UP1ATMSD motif having the consensus sequence GGCCCA(A/T)(A/T)(A/T). See, Ma and Bohnert, Genome Biol. 8(4): R49 (2007). A regulatory region can contain a

UP2ATMSD motif having the consensus sequence AAACCCTA. See, Tatematsu et al, Plant Physiol. 138: 757-766 (2005). A regulatory region can contain an

UPRMOTIFIIAT motif having the consensus sequence CCNNNNNNNNNNNNCCACG (SEQ ID NO:58). See, Martinez and Chrispeels, Plant Cell. 15:561-576 (2003); and Oh et al, Biochem Biophys Res Commun. 301 :225-230 (2003).

[0082] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: l or a fragment thereof, wherein the nucleic acid contains a TATABOX4, GAREAT, and CARGCW8GAT motif. The TATABOX4 motif can be the motif at nucleotides 1408 to 1414 of SEQ ID NO: 1 or a TATABOX4 motif heterologous to those in SEQ ID NO: 1. The GAREAT motif can be the motif at nucleotides 338 to 344 of SEQ ID NO: 1 or a GAREAT motif heterologous to that in SEQ ID NO: l . The CARGCW8GAT motif can be the motif at nucleotides 298 to 307 of SEQ ID NO:l or a CARGCW8GAT motif heterologous to that in SEQ ID NO: 1. In some cases, such a regulatory region can also include a 5' UTR.

[0083] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:2 or a fragment thereof, wherein the nucleic acid contains a CARGNCAT and a CARGCW8GAT motif. The CARGNCAT motif can be the motif at nucleotides 844 to 855 of SEQ ID NO:2 or a CARGNCAT motif heterologous to that in SEQ ID NO:2. The CARGCW8GAT motif can be the motif at nucleotides 291 to 300, nucleotides 706 to 717, or nucleotides 845 to 854 of SEQ ID NO:2 or a CARGCW8GAT motif heterologous to those in SEQ ID NO:2. In some cases, such a regulatory region can also include a 5' UTR.

[0084] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 3 or a fragment thereof, wherein the nucleic acid contains an UPRMOTIFIIAT, a CACGCAATGMGH3, and a SP8BFIBSP8AIB motif. The UPRMOTIFIIAT motif can be the motif at nucleotides 769 to 787 of SEQ ID NO:3 or an UPRMOTIFIIAT motif heterologous to that in SEQ ID NO:3. The CACGCAATGMGH3 motif can be the motif at nucleotides 715 to 722 of SEQ ID NO:3 or a CACGCAATGMGH3 motif heterologous to that in SEQ ID NO:3. The SP8BFIBSP8AIB motif can be the motif at nucleotides 488 to 495 of SEQ ID NO:3 or a SP8BFIBSP8AIB motif heterologous to that in SEQ ID NO:3. In some cases, such a regulatory region can contain an intron (e.g., at nucleotides 1184 to 1199 of SEQ ID NO:3. In some cases, such a regulatory region can also include a 5' UTR.

[0085] In some embodiments, a regulatory region has a nucleotide sequence with 90%) or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:4 or a fragment thereof, wherein the nucleic acid contains a TATABOX2 motif and OSE1ROOTNODULE motif. The TATABOX2 motif can be the motif at nucleotides 910 to 916 of SEQ ID NO:4 or a TATABOX2 motif heterologous to that in SEQ ID NO:4. The OSEIROOTNODULE motif can be the motif at nucleotides 58 to 63, 359 to 363, 522 to 526, or 801 to 806 of SEQ ID NO:4 or a OSEIROOTNODULE motif heterologous to those in SEQ ID NO:4. In some cases, such a regulatory region can also include a 5' UTR.

[0086] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 5 or a fragment thereof, wherein the nucleic acid contains an

ATHBIATCONSENSUS, GAREAT, P1BS, GARE20SREP 1 , ABRE, and TATC-box motif The ATHBIATCONSENSUS motif can be the motif at nucleotides 1569 to 1577 of SEQ ID NO:5 or a ATHBIATCONSENSUS motif heterologous to that in SEQ ID NO:5. The GAREAT motif can be the motif at nucleotides 862 to 868 of SEQ ID NO:5 or a GAREAT motif heterologous to that in SEQ ID NO:5. The P IBS motif can be the motif at nucleotides 119 to 126 of SEQ ID NO:5 or a P1BS motif heterologous to that in SEQ ID NO:5. The GARE20SREP1 motif can be the motif at nucleotides 891 to 897 of SEQ ID NO:5 or a GARE20SREP1 motif heterologous to that in SEQ ID NO:5. The ABRE motif can be the motif at nucleotides 1521 to 1527 of SEQ ID NO:5 or an ABRE motif heterologous to that in SEQ ID NO:5. The TATC-box motif can be the motif at nucleotides 621 to 627 of SEQ ID NO: 5 or a TATC-box motif heterologous to that in SEQ ID NO:5. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 1690 to 1760 of SEQ ID NO: 5 or can be a heterologous UTR.

[0087] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:6 or a fragment thereof (e.g., SEQ ID NO:7, which contains nucleotides 118 to 600 of SEQ ID NO: 6), wherein the nucleic acid contains a Phosphate-starvation induced binding site and a GAREAT motif. The Phosphate-starvation induced binding site motif can be the motif at nucleotides 411 to 416 of SEQ ID NO:6 or a Phosphate-starvation induced binding site motif heterologous to that in SEQ ID NO:6. The GAREAT motif can be the motif at nucleotides 55 to 60 or 239 to 244 of SEQ ID NO:6 or a GAREAT motif heterologous to those in SEQ ID NO:6. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 466 to600 of SEQ ID NO: 6 or can be a heterologous UTR.

[0088] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 7 or a fragment thereof, wherein the nucleic acid contains a P1BS and GAREAT motif. The P IBS motif can be the motif at nucleotides 295 to 300 of SEQ ID NO: 7 or a P1BS motif heterologous to that in SEQ ID NO:7. The GAREAT can be the motif at nucleotides 123 to 128 of SEQ ID NO:7 or a GAREAT motif heterologous to that in SEQ ID NO:7. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 350 to 484 of SEQ ID NO:7 or can be a heterologous UTR.

[0089] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 8 or a fragment thereof, wherein the nucleic acid contains a TATABOX4 or TCA- element motif. The TATABOX4 motif can be the motif at nucleotides 223 to 229 of SEQ ID NO: 8 or a TATABOX4 motif heterologous to that in SEQ ID NO:8. The TCA- element motif can be the motif at nucleotides 174 to 183 of SEQ ID NO: 8 or a TCA- element motif heterologous to that in SEQ ID NO:8. In some cases, such a regulatory region can contain an intron (e.g., at nucleotides 323 to 1268 of SEQ ID NO: 8). In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 253 to 322 or 1269 to 1290 of SEQ ID NO:8 or can be a heterologous UTR.

[0090] In some embodiments, a regulatory region has a nucleotide sequence with 90%) or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 9 or a fragment thereof, wherein the nucleic acid contains a TATABOX4 and an ATHB6COREAT motif. The TATABOX4 motif can be the motif at nucleotides 1235 to 1241 of SEQ ID NO:9 or a TATABOX4 motif heterologous to that in SEQ ID NO:9. The ATHB6COREAT motif can be the motif at nucleotides 607 to 615 of SEQ ID NO:9 or an ATHB6COREAT motif heterologous to that in SEQ ID NO:9. In some cases, such a regulatory region can also include a 5 ' UTR. The 5 ' UTR can be the 5 ' UTR at nucleotides 1268 to 1400 of SEQ ID NO:9 or can be a heterologous UTR. [0091] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 10 or a fragment thereof, wherein the nucleic acid contains a TCAl Motif, TATAbox motif, and ATCT motif. The TCAlMotif can be the motif at nucleotides 589 to 598 of SEQ ID NO: 10 or a TCAlMotif heterologous to that in SEQ ID NO: 10. The TATAbox motif can be the motif at nucleotides 628 to 634 of SEQ ID NO: 10 or a TATAbox motif heterologous to that in SEQ ID NO: 10. The ATCT motif can be the motif at nucleotides 585 to 594 of SEQ ID NO: 10 or an ATCT motif heterologous to that in SEQ ID NO: 10. In some cases, such a regulatory region can also include a 5 ' UTR. The 5 ' UTR can be the 5' UTR at nucleotides 662 to 689 of SEQ ID NO: 10 or can be a heterologous UTR.

[0092] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 11 or a fragment thereof, wherein the nucleic acid contains a GATABOX and CARGCW8GAT motif. The GATABOX motif can be the motif at nucleotides 1113 to 1116 of SEQ ID NO: 11 or a GATABOX motif heterologous to that in SEQ ID NO: 11. The CARGCW8GAT motif can be the motif at nucleotides 596 to 605 of SEQ ID NO: l 1 or a CARGCW8GAT motif heterologous to that in SEQ ID NO: 11. In some cases, such a regulatory region can also include a 5 ' UTR. The 5 ' UTR can be the 5 ' UTR at nucleotides 1119 to 1200 of SEQ ID NO: 11 or can be a heterologous UTR.

[0093] In some embodiments, a regulatory region has a nucleotide sequence with 90%) or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 12 or a fragment thereof, wherein the nucleic acid contains a TATABOX4,

UP2ATMSD, and ELI-box3 motif. The TATABOX4 motif can be the motif at nucleotides 668 to 674 of SEQ ID NO: 12 or a TATABOX4 motif heterologous to that in SEQ ID NO: 12. The UP2ATMSD motif can be the motif at nucleotides 220 to 227 or 765 ti 773 of SEQ ID NO: 12 or an UP2ATMSD motif heterologous to those in SEQ ID NO: 12. The ELI-box3 motif can be the motif at nucleotides 10 to 18 or 156 to 164 of SEQ ID NO: 12 or an ELI-box3 motif heterologous to those in SEQ ID NO: 12. In some cases, such regulatory regions can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 816 to 855 of SEQ ID NO: 12 or can be a heterologous UTR. [0094] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 13 or a fragment thereof, wherein the nucleic acid contains a TATA BOX,

CTRMCAMV35S, ACE, and CACGTGMOTIF motif The TATA BOX motif can be the motif at nucleotides 280 to 298 of SEQ ID NO: 13 or a TATA BOX motif heterologous to that in SEQ ID NO: 13. The CTRMC AM V35 S motif can be the motif at nucleotides 351 to 359 of SEQ ID NO: 13 or a CTRMC AM V35 S motif heterologous to that in SEQ ID NO: 13. The ACE motif can be the motif at nucleotides 100 to 106 of SEQ ID NO: 13 or an ACE motif heterologous to that in SEQ ID NO: 13. The

CACGTGMOTIF motif can be the motif at nucleotides 102 to 107 of SEQ ID NO: 13 or a CACGTGMOTIF motif heterologous to that in SEQ ID NO: 13. In some cases, such a regulatory region can also include a 5 ' UTR. The 5 ' UTR can be the 5 ' UTR at nucleotides 325 to 429 of SEQ ID NO: 13 or can be a heterologous UTR.

[0095] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 14 or a fragment thereof (e.g., the nucleotide sequence set forth in SEQ ID NO:28, which is nucleotides 193 to 700 of SEQ ID NO: 14), wherein the nucleic acid contains a ACGTABREMOTIFAOSOSEM, ABREL ATERD 1 , and ABRE motif. The

ACGTABREMOTIFAOSOSEM motif can be the motif at nucleotides 389 to 396 of SEQ ID NO: 14 or an ACGTABREMOTIFAOSOSEM motif heterologous to that in SEQ ID NO: 14. The ABREL ATERD 1 motif can be the motif at nucleotides 305 to 309 of SEQ ID NO: 14 or an ABREL ATERD 1 motif heterologous to that in SEQ ID NO: 14. The ABRE motif can be the motif at nucleotides 269 to 275 of SEQ ID NO: 14 or an ABRE motif heterologous to that in SEQ ID NO: 14. In some cases, such regulatory regions can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 560 to 700 of SEQ ID NO: 14 or can be a heterologous UTR.

[0096] In some embodiments, a regulatory region has a nucleotide sequence with 90%) or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 15 or a fragment thereof, wherein the nucleic acid contains a TATABOX4,

UP2ATMSD, TC richVepeats, and GAGAGMGSAl motif. The TATABOX4 motif can be the motif at nucleotides 796 to 802 of SEQ ID NO: 15 or a TATABOX4 motif heterologous to that in SEQ ID NO: 15. The UP2ATMSD motif can be the motif at nucleotides 6 to 13 of SEQ ID NO: 15 or an UP2ATMSD motif heterologous to that in SEQ ID NO: 15. The TC richVepeats motif can be the motif at nucleotides 179 to 188 of SEQ ID NO: 15 or a TC richVepeats motif heterologous to that in SEQ ID NO: 15. The GAGAGMGSA1 motif can be the motif at nucleotides 725 to 742 of SEQ ID NO: 15 or a GAGAGMGSA1 motif heterologous to those in SEQ ID NO: 15. In some cases, such regulatory regions can also include a 5 ' UTR. The 5 ' UTR can be the 5 ' UTR at nucleotides 829 to 1000 of SEQ ID NO: 15 or can be a heterologous UTR.

[0097] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 16 or a fragment thereof, wherein the nucleic acid contains a PRECONSCRHSP70A, TATAbox, ABRE, and HSE motif. The PRECONSCRHSP70A motif can be the motif at nucleotides 735 to 758 of SEQ ID NO: 16 or a PRECONSCRHSP70A motif heterologous to that in SEQ ID NO: 16. The TATAbox motif can be the motif at nucleotides 723 to 727 of SEQ ID NO: 16 or a TATAbox motif heterologous to that in SEQ ID NO: 16. The ABRE motif can be the motif at nucleotides 656 to 661 or 689 to 694 of SEQ ID NO: 16 or an ABRE motif heterologous to those in SEQ ID NO: 16. The HSE motif can be the motif at nucleotides 380 to 389 of SEQ ID NO : 16 or a HSE motif heterologous to that in SEQ ID NO: 16. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 754 to 840 of SEQ ID NO: 16 or can be a heterologous UTR.

[0098] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 17 or a fragment thereof, wherein the nucleic acid contains a GT1MOTIFPSRBCS, TATAbox, and RYREPEATVFLEB4 motif. The GT1MOTIFPSRBCS motif can be the motif at nucleotides 66 to 77 of SEQ ID NO: 17 or a GT1MOTIFPSRBCS motif heterologous to that in SEQ ID NO: 17. The TATAbox motif can be the motif at nucleotides 682 to 688 of SEQ ID NO: 17 or a TATAbox motif heterologous to that in SEQ ID NO: 17. The RYREPEATVFLEB4 motif can be the motif at nucleotides 344 to 351 of SEQ ID NO: 17 or a RYREPEATVFLEB4 motif heterologous to that in SEQ ID NO: 17. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5 ' UTR at nucleotides 697 to 773 of SEQ ID NO : 17 or can be a heterologous UTR.

[0099] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 18 or a fragment thereof, wherein the nucleic acid contains an UPRMOTIFIIAT, PRECONSCRHSP70A or GCC\Box motif. The UPRMOTIFIIAT motif can be the motif at nucleotides 220 to 238 of SEQ ID NO: 18 or an UPRMOTIFIIAT motif heterologous to that in SEQ ID NO: 18. The PRECONSCRHSP70A motif can be the motif at nucleotides 213 to 236 of SEQ ID NO: 18 or a PRECONSCRHSP70A motif heterologous to that in SEQ ID NO : 18. The GCC\Box motif can be the motif at nucleotides 184 to 190 of SEQ ID NO: 18 or a GCC\Box motif heterologous to that in SEQ ID NO: 18. In some cases, such a regulatory region can contain an intron (e.g., at nucleotides 473 to 1680 of SEQ ID NO: 18). In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 329 to 472 or 1681 to 1700 of SEQ ID NO: 18 or can be a heterologous UTR.

[00100] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO: 19 or a fragment thereof, wherein the nucleic acid contains a TATABOX4,

ATHB2ATCONSENSUS, and SORLREP2AT motif. The TATABOX4 motif can be the motif at nucleotides 407 to 413 of SEQ ID NO: 19 or a TATABOX4 motif heterologous to that in SEQ ID NO: 19. The ATHB2ATCONSENSUS motif can be the motif at nucleotides 258 to 266 of SEQ ID NO: 19 or a ATHB2ATCONSENSUS motif heterologous to that in SEQ ID NO: 19. The SORLREP2AT motif can be the motif at nucleotides 304 to 312 of SEQ ID NO: 19 or a SORLREP2AT motif heterologous to that in SEQ ID NO: 19. In some cases, such a regulatory region can also include a 5' UTR.

[00101] In some embodiments, a regulatory region has a nucleotide sequence with 90%) or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:20 or a fragment thereof, wherein the nucleic acid contains a PRECONSCRHSP70A, UPRMOTIFIIAT, ABRE, and MBS motif. The PRECONSCRHSP70A motif can be the motif at nucleotides 576 to 599 of SEQ ID NO:20 or a PRECONSCRHSP70A motif heterologous to that in SEQ ID NO:20. The UPRMOTIFIIAT motif can be the motif at nucleotides 242 to 260, 384 to 402, 460 to 478, or 544 to 562 of SEQ ID NO:20 or an UPRMOTIFIIAT motif heterologous to those in SEQ ID NO:20. The ABRE motif can be the motif at nucleotides 257 to 262, 399 to 404, or 475 to 480 of SEQ ID NO:20 or an ABRE motif heterologous to that in SEQ ID NO:20. The MBS motif can be the motif at nucleotides 280 to 285 of SEQ ID NO:20 or a MBS motif heterologous to that in SEQ ID NO:20. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 637 to 814 of SEQ ID NO:20 or can be a heterologous UTR.

[00102] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:21 or a fragment thereof, wherein the nucleic acid contains a MYBPLANT motif. The MYBPLANT motif can be the motif at nucleotides 454 to 461, 509 to 516, 858 to 868 of SEQ ID NO:20 or a MYBPLANT motif heterologous to those in SEQ ID NO:21. In some cases, such a regulatory region can also include a 5' UTR.

[00103] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:22 or a fragment thereof, wherein the nucleic acid contains a PRECONSCRHSP70A, ACIIPVPAL2, and CAAT-box motif. The PRECONSCRHSP70A motif can be the motif at nucleotides 36 to 59 of SEQ ID NO:22 or a PRECONSCRHSP70A motif heterologous to that in SEQ ID NO:22. The ACIIPVPAL2 motif can be the motif at nucleotides 266 to 277 of SEQ ID NO:22 or an ACIIPVPAL2 motif heterologous to that in SEQ ID NO:22. The CAAT-box motif can be the motif at nucleotides 487 to 491 of SEQ ID NO:22 or a CAAT-box motif heterologous to that in SEQ ID NO:22. In some cases, such a regulatory region can contain an intron (e.g., at nucleotides 413 to 1500 of SEQ ID NO: 22). In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 353 to 412 of SEQ ID NO:22 or can be a heterologous UTR.

[00104] In some embodiments, a regulatory region has a nucleotide sequence with 90%) or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:23 or a fragment thereof, wherein the nucleic acid contains a TATABOX4 and ABREATCONSENSUS motif. The TATABOX4 motif can be the motif at nucleotides 153 to 159 of SEQ ID NO:23 or a TATABOX4 motif heterologous to that in SEQ ID NO:23. The ABREATCONSENSUS motif can be the motif at nucleotides 85 to 92 of SEQ ID NO:23 or an ABREATCONSENSUS motif heterologous to that in SEQ ID NO:23. In some cases, such a regulatory region can contain an intron (e.g., at nucleotides 250 to 835 of SEQ ID NO: 23). In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 184 to 249 or 836 to 880 of SEQ ID NO:23 or can be a heterologous UTR.

[00105] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:24 or a fragment thereof, wherein the nucleic acid contains a TATABOX4, TATC- box, P1BS, and OSE2ROOTNODULE motif. The TATABOX4 motif can be the motif at nucleotides 939 to 945 of SEQ ID NO:24 or a TATABOX4 motif heterologous to that in SEQ ID NO:24. The TATC-box motif can be the motif at nucleotides 941 to 947 of SEQ ID NO:24 or a TATC-box motif heterologous to that in SEQ ID NO:24. The P1BS motif can be the motif at nucleotides 493 to 500 of SEQ ID NO:24 or a P1BS motif heterologous to that in SEQ ID NO:24. The OSE2ROOTNODULE motif can be the motif at nucleotides 619 to 624 of SEQ ID NO:24 or an OSE2ROOTNODULE motif heterologous to that in SEQ ID NO:24. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 968 to 1000 of SEQ ID NO:24 or can be a heterologous UTR.

[00106] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:25 or a fragment thereof, wherein the nucleic acid contains a TATABOX2,

ABREATCONSENSUS, IBOX, ABREL ATERD 1 , and MBS motif. The TATABOX2 motif can be the motif at nucleotides 1617 to 1623 of SEQ ID NO:25 or a TATABOX2 motif heterologous to that in SEQ ID NO:25. The ABREATCONSENSUS motif can be the motif at nucleotides 710 to 717 of SEQ ID NO:25 or an ABREATCONSENSUS motif heterologous to that in SEQ ID NO:25. The IBOX motif can be the motif at nucleotides 1523 to 1528 of SEQ ID NO:25 or an IBOX motif heterologous to that in SEQ ID NO:25. The ABRELATERD 1 motif can be the motif at nucleotides 1474 to 1478, 1046 to 1050, or 1096 to 1100 of SEQ ID NO:25 or an ABRELATERD 1 motif heterologous to those in SEQ ID NO:25. The MBS motif can be the motif at nucleotides 1379 to 1375 of SEQ ID NO:25 or a MBS motif heterologous to that in SEQ ID NO:25. In some cases, such a regulatory region can also include a 5 ' UTR. The 5 ' UTR can be the 5' UTR at nucleotides 1665 to 1763 of SEQ ID NO:25 or can be a heterologous UTR.

[00107] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:26 or a fragment thereof, wherein the nucleic acid contains a MYBIAT, TATABOX, and MBS motif. The MYBIAT motif can be the motif at nucleotides 193 to 208, 340 to 345, 405 to 410, or 527 to 532 of SEQ ID NO:26 or a MYBIAT motif heterologous to those in SEQ ID NO:26. The TATABOX motif can be the motif at nucleotides 754 to 759 of SEQ ID NO:26 or a TATABOX motif heterologous to that in SEQ ID NO:26. The MBS motif can be the motif at nucleotides 672 to 677 of SEQ ID NO:26 or a MBS motif heterologous to that in SEQ ID NO:26. In some cases, such a regulatory region can also include a 5 ' UTR.

[00108] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:27 or a fragment thereof, wherein the nucleic acid contains a TATABOX5,

CARGCW8GAT, E2FCONSENSUS, LEAFYATAG, and ROOTMOTIFTAPOXl motif. The TATABOX5 motif can be the motif at nucleotides 185 to 190 of SEQ ID NO:27 or a TATABOX5 motif heterologous to that in SEQ ID NO:27. The CARGCW8GAT motif can be the motif at nucleotides 120 to 129 of SEQ ID NO:27 or a CARGCW8GAT motif heterologous to that in SEQ ID NO:27. The E2FCONSENSUS motif can be the motif at nucleotides 54 to 61 of SEQ ID NO:27 or an E2FCONSENSUS motif heterologous to that in SEQ ID NO:27. The LEAFYATAG motif can be the motif at nucleotides 57 to 63 of SEQ ID NO:27 or a LEAFYATAG motif heterologous to that in SEQ ID NO:27. The ROOTMOTIFTAPOXl motif can be the motif at nucleotides 45 to 49 of SEQ ID NO:27 or a ROOTMOTIFTAPOXl motif heterologous to that in SEQ ID NO:27. In some cases, such a regulatory region can also include a 5 ' UTR. The 5 ' UTR can be the 5 ' UTR at nucleotides 213 to 400 of SEQ ID NO:27 or can be a heterologous UTR.

[00109] In some embodiments, a regulatory region has a nucleotide sequence with 90%) or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:28 or a fragment thereof, wherein the nucleic acid contains an ABRELATERD1 motif The ABRELATERD 1 motif can be the motif at nucleotides 79 to 83, 113 to 117, 198 to 202, or 271 to 275 of SEQ ID NO:28 or an ABRELATERD 1 motif heterologous to those in SEQ ID NO:28. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 368 to506 of SEQ ID NO:28 or can be a heterologous UTR.

[00110] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:29 or a fragment thereof, wherein the nucleic acid contains an ABRELATERD 1 motif. The ABRELATERD 1 motif can be the motif at nucleotides 125 to 129 or 542 to 546 of SEQ ID NO:29 or an ABRELATERD 1 motif heterologous to those in SEQ ID NO:29. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5 ' UTR at nucleotides 1111 to 1200 of SEQ ID NO:29 or can be a

heterologous UTR.

[00111] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:30 or a fragment thereof (e.g., nucleotides 269 to 763 or 419 to 763 of SEQ ID NO: 30) wherein the nucleic acid contains a TATABOX motif. The TATABOX motif can be the motif at nucleotides 664 to 669 of SEQ ID NO:30 or a TATABOX motif heterologous to that in SEQ ID NO:30. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 698 to736 of SEQ ID NO:30 or can be a heterologous UTR.

[00112] In some embodiments, a regulatory region has a nucleotide sequence with 90%) or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:31 or a fragment thereof (e.g., the nucleotide sequence set forth in SEQ ID NO:32, which is nucleotides 1205 to 3004 of SEQ ID NO:31) that contains an UP2ATMSD and TATABOX motif. The UP2ATMSD motif can be the motif at nucleotides 407 to 414 of SEQ ID NO:32 or an UP2ATMSD motif heterologous to that in SEQ ID NO:32. The TATABOX motif can be the motif at nucleotides 381 to 388 of SEQ ID NO:32 or a TATABOX motif heterologous to that in SEQ ID NO:32. In some cases, such a regulatory region can contain an intron (e.g., at nucleotides 526 to 1699 of SEQ ID NO: 32). In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 408 to 525 of SEQ ID NO:32 or can be a heterologous UTR.

[00113] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:33 or a fragment thereof, wherein the nucleic acid contains a TATABOX4,

RGATAOS (R-GATA (GATA motif binding factor) binding site), 3-AFl\binding\site light responsive element, or P-box gibberellin-responsive element motif. The

TATABOX4 motif can be the motif at nucleotides 852 to 858 of SEQ ID NO:33 or a TATABOX4 motif heterologous to that in SEQ ID NO:33 The 3-AFl\binding\site light responsive element motif can be the motif at nucleotides 100 to 1 lOof SEQ ID NO:33 or a 3-AFl\binding\site light responsive element motif heterologous to that in SEQ ID NO:33. The P-box gibberellin-responsive element motif can be the motif at nucleotides 385 to 395 of SEQ ID NO:33 or a P-box gibberellin-responsive element motif heterologous to that in SEQ ID NO:33. The RGATAOS motif can be the motif at nucleotides 822 to 830 of SEQ ID NO:33 or a RGATAOS motif heterologous to that in SEQ ID NO:33. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 881 to 946 of SEQ ID NO:33 or can be a heterologous UTR.

[00114] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:34 or a fragment thereof. In some cases, such a regulatory region can also include a 5' UTR.

[00115] In some embodiments, a regulatory region has a nucleotide sequence with 90%) or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:35 or a fragment thereof. In some cases, such a regulatory region can also include a 5' UTR.

[00116] In some embodiments, a regulatory region has a nucleotide sequence with 90%o or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:36 or a fragment thereof. In some cases, such a regulatory region can also include a 5' UTR. [00117] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:37 or a fragment thereof, wherein the nucleic acid contains a TATAbox motif. The TATAbox motif can be the motif at nucleotides 670 to678 of SEQ ID NO:37 or a TATAbox motif heterologous to that in SEQ ID NO:37. In some cases, such a regulatory region can contain an intron (e.g., at nucleotides 741 to 823 of SEQ ID NO: 37). In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 713 to 740 or 824 to 846 of SEQ ID NO:37 or can be a heterologous UTR.

[00118] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:38 or a fragment thereof, wherein the nucleic acid contains a TATAbox or CAAT- box motif. The TATAbox motif can be the motif at nucleotides 785 to793 of SEQ ID NO :38 or a TATAbox motif heterologous to that in SEQ ID NO:38 The CAAT-box motif can be the motif at nucleotides 722 to729 of SEQ ID NO:38 or a CAAT-box motif heterologous to that in SEQ ID NO:38. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 817 to 925 of SEQ ID NO:38 or can be a heterologous UTR.

[00119] In some embodiments, a regulatory region has a nucleotide sequence with 90%) or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:39 or a fragment thereof. In some cases, such a regulatory region can also include a 5' UTR.

[00120] In some embodiments, a regulatory region has a nucleotide sequence with 90%o or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:40 or a fragment thereof, wherein the nucleic acid contains a TATAbox and enhancer motif. The TATAbox motif can be the motif at nucleotides 773 to 738 of SEQ ID NO:40 or a TATAbox motif heterologous to that in SEQ ID NO:40. The enhancer motif can be the motif at nucleotides 303 to 308 or 602 to 607 of SEQ ID NO:40 or an enhancer motif heterologous to those in SEQ ID NO:40. In some cases, such a regulatory region can also include a 5' UTR. The 5' UTR can be the 5' UTR at nucleotides 806 to 835 of SEQ ID NO:40 or can be a heterologous UTR. [00121] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:41 or a fragment thereof. In some cases, such a regulatory region can also include a 5' UTR.

[00122] In some embodiments, a regulatory region has a nucleotide sequence with 90% or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:42 or a fragment thereof. In some cases, such a regulatory region can also include a 5' UTR.

[00123] In some embodiments, a regulatory region has a nucleotide sequence with 90%) or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:43 or a fragment thereof. In some cases, such a regulatory region can also include a 5' UTR.

[00124] In some embodiments, a regulatory region has a nucleotide sequence with 90%o or greater sequence identity to the polynucleotide sequence set forth in SEQ ID NO:44 or a fragment thereof, wherein the nucleic acid contains a SP8BFIBSP8AIB, CACGCAATGMGH3, and SP8BFIBSP8AIB motif. The SP8BFIBSP8AIB motif can be the motif at nucleotides 1122 to 1140 of SEQ ID NO:44 or a SP8BFIBSP8AIB motif heterologous to that in SEQ ID NO:44. The CACGCAATGMGH3 motif can be the motif at nucleotides 1068 to 1075 of SEQ ID NO:44 or a CACGCAATGMGH3 motif heterologous to that in SEQ ID NO:44. The SP8BFIBSP8AIB motif can be the motif at nucleotides 841 to 848 of SEQ ID NO:44 or a SP8BFIBSP8AIB motif heterologous to that in SEQ ID NO:44. In some cases, such a regulatory region can also include a 5' UTR.

4. Testing of Promoters

[00125] Promoters of the document were tested for activity by cloning the sequence into an appropriate vector, transforming plants with the construct and assaying for marker gene expression. Recombinant DNA constructs were prepared which comprise the promoter sequences of the document inserted into a vector suitable for transformation of plant cells. The construct can be made using standard recombinant DNA techniques (Sambrook et al. 1989) and can be introduced to the species of interest by Agrobacterium-rnQdiatcd transformation or by other means of transformation as referenced below.

[00126] The vector backbone can be any of those typical in the art such as plasmids, viruses, artificial chromosomes, BACs, YACs and PACs and vectors of the sort described by

(a) BAC: Shizuya et al. (1992) Proc. Natl. Acad. Sci. USA 89: 8794-8797; Hamilton et al. (1996) Proc. Natl. Acad. Sci. USA 93: 9975-9979;

(b) YAC: Burke et al. (1987) Science 236:806-812;

(c) PAC:Sternberg N. et al. (1990) Proc Natl Acad Sci U S A. 87(l):103-7;

(d) Bacteria- Yeast Shuttle Vectors: Bradshaw et al. (1995) Nucl Acids Res 23: 4850-4856;

(e) Lambda Phage Vectors: Replacement Vector, e.g., Frischauf et al.

(1983) J. Mol Biol 170: 827-842; or Insertion vector, e.g., Huynh et al. (1985) In: Glover NM (ed) DNA Cloning: A practical Approach, Vol.1 Oxford: IRL Press; T-DNA gene fusion vectors :Walden et a/. (1990) Mol Cell Biol 1 : 175-194; and

(g) Plasmid vectors: Sambrook et al., infra.

[00127] Typically, the construct comprises a vector containing a promoter sequence of the present document operationally linked to any marker gene. The promoter was identified as a promoter by the expression of the marker gene. Although many marker genes can be used, Green Fluorescent Protein (GFP) is preferred. The vector may also comprise a marker gene that confers a selectable phenotype on plant cells. The marker may encode biocide resistance, particularly antibiotic resistance, such as resistance to kanamycin, G418, bleomycin, hygromycin, or herbicide resistance, such as resistance to chlorosulfuron or phosphinotricin. Vectors can also include origins of replication, scaffold attachment regions (SARs), markers, homologous sequences, introns, etc.

5. Constructing Promoters with Control Elements

5.1 Combining Promoters and Promoter Control Elements

[00128] The promoter and promoter control elements of the present document, both naturally occurring and synthetic, can be used alone or combined with each other to produce the desired preferential transcription. Also, the promoters of the document can be combined with other known sequences to obtain other useful promoters to modulate, for example, tissue transcription specific or transcription specific to certain conditions. Such preferential transcription can be determined using the techniques or assays described above.

[00129] Promoters can contain any number of control elements. For example, a promoter can contain multiple transcription binding sites or other control elements. One element may confer tissue or organ specificity; another element may limit transcription to specific time periods, etc. Typically, promoters will contain at least a basal or core promoter as described above. Any additional element can be included as desired. For example, a fragment comprising a basal or "core" promoter can be fused with another fragment with any number of additional control elements.

[00130] The following are promoters that are induced under stress conditions and can be combined with those of the present document: ldhl (oxygen stress; tomato; see Germain and Ricard (1997) Plant Mol Biol 35:949-54), GPx and CAT (oxygen stress; mouse; see Franco et al. (1999) Free Radic Biol Med 27: 1122-32), ci7 (cold stress;

potato; see Kirch et al. (1997) Plant Mol Biol. 33:897-909), Bz2 (heavy metals; maize; see Marrs and Walbot (1997) Plant Physiol 113:93-102), HSP32 (hyperthermia; rat; see Raju and Maines (1994) Biochim Biophys Acta 1217:273-80), and MAPKAPK-2 (heat shock; Drosophila; see Larochelle and Suter (1995) Gene 163:209-14).

[00131] In addition, the following examples of promoters are induced by the presence or absence of light can be used in combination with those of the present document: Topoisomerase II (pea; see Reddy et al. (1999) Plant Mol Biol 41 : 125-37), chalcone synthase (soybean; see Wingender et al. (1989) Mol Gen Genet 218:315-22) mdm2 gene (human tumor; see Saucedo et al. (1998) Cell Growth Differ 9: 119-30), Clock and BMAL1 (rat; see Namihira et al. (1999) Neurosci Lett 271 : 1-4, PHYA (Arabidopsis; see Canton and Quail (1999) Plant Physiol 121 : 1207-16), PRB-lb

(tobacco; see Sessa et al. (1995) Plant Mol Biol 28:537-47) and YprlO (common bean; see Walter et al. (1996) Eur JBiochem 239:281-93).

[00132] The promoters and control elements of the following genes can be used in combination with the present document to confer tissue specificity: MipB (iceplant; Yamada et al. (1995) Plant Cell 7:1129-42) and SUCS (root nodules; broadbean; Kuster et al. (1993) Mol Plant Microbe Interact 6:507-14) for roots, OsSUTl (rice ; Hirose et al. (1997) Plant Cell Physiol 38: 1389-96) for leaves, Msg (soybean; Stomvik et al. (1999) Plant Mol Biol 41 :217-31) for siliques, cell (Arabidopsis; Shani et al. (1997) Plant Mol Biol 34(6):837 -42) and ACT11 (Arabidopsis; Huang et al. (1997) Plant Mol Biol 33: 125-39) for inflorescence.

[00133] Still other promoters are affected by hormones or participate in specific physiological processes, which can be used in combination with those of present document. Some examples are the ACC synthase gene that is induced differently by ethylene and brassinosteroids (mung bean; Yi et al. (1999) Plant Mol Biol 41 :443-54), the TAPG1 gene that is active during abscission (tomato; Kalaitzis et al. (1995) Plant Mol Biol 28:647-56), and the 1-aminocyclopropane-l-carboxylate synthase gene

(carnation; Jones et al. (1995) Plant Mol Biol 28:505-12) and the CP-2/cathepsin L gene (rat; Kim and Wright (1997) Biol Reprod 57: 1467-77), both active during senescence.

[00134] Spacing between control elements or the configuration or control elements can be determined or optimized to permit the desired protein-polynucleotide or polynucleotide interactions to occur.

[00135] For example, if two transcription factors bind to a promoter

simultaneously or relatively close in time, the binding sites are spaced to allow each factor to bind without steric hindrance. The spacing between two such hybridizing control elements can be as small as a profile of a protein bound to a control element. In some cases, two protein binding sites can be adjacent to each other when the proteins bind at different times during the transcription process.

[00136] Further, when two control elements hybridize the spacing between such elements will be sufficient to allow the promoter polynucleotide to hairpin or loop to permit the two elements to bind. The spacing between two such hybridizing control elements can be as small as a t-RNA loop, to as large as 10 kb.

[00137] Typically, the spacing is no smaller than 5 bases; more typically, no smaller than 8; more typically, no smaller than 15 bases; more typically, no smaller than 20 bases; more typically, no smaller than 25 bases; even more typically, no smaller than 30, 35, 40 or 50 bases. [00138] Usually, the fragment size in no larger than 5 kb bases; more usually, no larger than 2 kb; more usually, no larger than 1 kb; more usually, no larger than 800 bases; more usually, no larger than 500 bases; even more usually, no more than 250, 200, 150 or 100 bases.

[00139] Such spacing between promoter control elements can be determined using the techniques and assays described above.

5.2 Vectors Used to Transform Cells/Hosts

[00140] A plant transformation construct containing a promoter of the present document may be introduced into plants by any plant transformation method. Methods and materials for transforming plants by introducing a plant expression construct into a plant genome in the practice of this document can include any of the well-known and demonstrated methods including electroporation (U.S. Pat. No. 5,384,253);

microprojectile bombardment (U.S. Pat. No. 5,015,580; U.S. Pat. No. 5,550,318; U.S. Pat. No. 5,538,880; U.S. Pat. No. 6,160,208; U.S. Pat. No. 6,399,861; and U.S. Pat. No. 6,403,865); Agrobacterium-mediatGd transformation (U.S. Pat. No. 5,824,877; U.S. Pat. No. 5,591,616; U.S. Pat. No. 5,981,840; and U.S. Pat. No. 6,384,301); and protoplast transformation (U.S. Pat. No. 5,508,184).

[00141] The present promoters and/or promoter control elements may be delivered to a system such as a cell by way of a vector. For the purposes of this document, such delivery may range from simply introducing the promoter or promoter control element by itself randomly into a cell to integration of a cloning vector containing the present promoter or promoter control element. Thus, a vector need not be limited to a DNA molecule such as a plasmid, cosmid or bacterial phage that has the capability of replicating autonomously in a host cell. All other manner of delivery of the promoters and promoter control elements of the document are envisioned. The various T-DNA vector types are a preferred vector for use with the present document. Many useful vectors are commercially available.

[00142] It may also be useful to attach a marker sequence to the present promoter and promoter control element in order to determine activity of such sequences. Marker sequences typically include genes that provide antibiotic resistance, such as tetracycline resistance, hygromycin resistance or ampicillin resistance, or provide herbicide resistance. Specific selectable marker genes may be used to confer resistance to herbicides such as glyphosate, glufosinate or bromoxynil (Comai et al. (1985) Nature 317: 741-744; Gordon-Kamm et al. (1990) Plant Cell 2: 603-618; and Stalker et al. (1988) Science 242: 419-423). Other marker genes exist which provide hormone responsiveness.

[00143] The promoter or promoter control element of the present document may be operably linked to a polynucleotide to be transcribed. In this manner, the promoter or promoter control element may modify transcription by modulating transcript levels of that polynucleotide when inserted into a genome.

[00144] However, prior to insertion into a genome, the promoter or promoter control element need not be linked, operably or otherwise, to a polynucleotide to be transcribed. For example, the promoter or promoter control element may be inserted alone into the genome in front of a polynucleotide already present in the genome. In this manner, the promoter or promoter control element may modulate the transcription of a polynucleotide that was already present in the genome. This polynucleotide may be native to the genome or inserted at an earlier time.

[00145] Alternatively, the promoter or promoter control element may be inserted into a genome alone to modulate transcription. See, for example, Vaucheret, H et al. (1998) Plant J 16: 651-659. Rather, the promoter or promoter control element may be simply inserted into a genome or maintained extrachromosomally as a way to divert transcription resources of the system to itself. This approach may be used to

downregulate the transcript levels of a group of polynucleotide(s).

[00146] The nature of the polynucleotide to be transcribed is not limited.

Specifically, the polynucleotide may include sequences that will have activity as RNA as well as sequences that result in a polypeptide product. These sequences may include, but are not limited to antisense sequences, RNAi sequences, ribozyme sequences, spliceosomes, amino acid coding sequences, and fragments thereof. Specific coding sequences may include, but are not limited to endogenous proteins or fragments thereof, or heterologous proteins including marker genes or fragments thereof.

[00147] Constructs of the present document would typically contain a promoter operably linked to a transcribable nucleic acid molecule operably linked to a 3' transcription termination nucleic acid molecule. In addition, constructs may include but are not limited to additional regulatory nucleic acid molecules from the 3 '-untranslated region (3' UTR) of plant genes (e.g., a 3' UTR to increase mRNA stability of the mRNA, such as the PI-II termination region of potato or the octopine or nopaline synthase 3' termination regions). Constructs may include but are not limited to the 5' untranslated regions (5' UTR) of an mRNA nucleic acid molecule which can play an important role in translation initiation and can also be a genetic component in a plant expression construct. For example, non-translated 5' leader nucleic acid molecules derived from heat shock protein genes have been demonstrated to enhance gene expression in plants (see for example, U.S. Pat. No. 5,659,122 and U.S. Pat. No. 5,362,865, all of which are hereby incorporated by reference). These additional upstream and downstream regulatory nucleic acid molecules may be derived from a source that is native or heterologous with respect to the other elements present on the promoter construct.

[00148] Thus, one embodiment of the document is a promoter such as provided in SEQ ID NOs: 1 - 44 or a fragment thereof, operably linked to a transcribable nucleic acid molecule so as to direct transcription of said transcribable nucleic acid molecule at a desired level or in a desired tissue or developmental pattern upon introduction of said construct into a plant cell. In some cases, the transcribable nucleic acid molecule comprises a protein-coding region of a gene, and the promoter provides for transcription of a functional mRNA molecule that is translated and expressed as a protein product. Constructs may also be constructed for transcription of antisense RNA molecules or other similar inhibitory RNA in order to inhibit expression of a specific RNA molecule of interest in a target host cell.

[00149] Exemplary transcribable nucleic acid molecules for incorporation into constructs of the present document include, for example, nucleic acid molecules or genes from a species other than the target gene species, or even genes that originate with or are present in the same species, but are incorporated into recipient cells by genetic engineering methods rather than classical reproduction or breeding techniques.

Exogenous gene or genetic element is intended to refer to any gene or nucleic acid molecule that is introduced into a recipient cell. The type of nucleic acid molecule included in the exogenous nucleic acid molecule can include a nucleic acid molecule that is already present in the plant cell, a nucleic acid molecule from another plant, a nucleic acid molecule from a different organism, or a nucleic acid molecule generated externally, such as a nucleic acid molecule containing an antisense message of a gene, or a nucleic acid molecule encoding an artificial or modified version of a gene.

[00150] The promoters of the present document can be incorporated into a construct using marker genes as described, and tested in transient analyses that provide an indication of gene expression in stable plant systems. As used herein the term "marker gene" refers to any transcribable nucleic acid molecule whose expression can be screened for or scored in some way. Methods of testing for marker gene expression in transient assays are known to those of skill in the art. Transient expression of marker genes has been reported using a variety of plants, tissues, plant cell(s), and DNA delivery systems. For example, types of transient analyses can include but are not limited to direct gene delivery via electroporation or particle bombardment of tissues in any transient plant assay using any plant species of interest. Such transient systems would include, but are not limited to, electroporation of protoplasts from a variety of tissue sources or particle bombardment of specific tissues of interest. The present document encompasses the use of any transient expression system to evaluate promoters or promoter fragments operably linked to any transcribable nucleic acid molecules, including but not limited to selected reporter genes, marker genes, or genes of agronomic interest. Examples of plant tissues envisioned to test in transients via an appropriate delivery system would include, but are not limited to, leaf base tissues, callus, cotyledons, roots, endosperm, embryos, floral tissue, pollen, and epidermal tissue.

[00151] Promoters and control elements of the present document are useful for modulating metabolic or catabolic processes. Such processes include, but are not limited to, secondary product metabolism, amino acid synthesis, seed protein storage, increased biomass, oil development, pest defense and nitrogen usage. Some examples of genes, transcripts and peptides or polypeptides participating in these processes, which can be modulated by the present document: are tryptophan decarboxylase (tdc) and strictosidine synthase (strl), dihydrodipicolinate synthase (DHDPS) and aspartate kinase (AK), 2S albumin and alpha-, beta-, and gamma-zeins, ricinoleate and 3-ketoacyl-ACP synthase (KAS), Bacillus thuringiensis (Bt) insecticidal protein, cowpea trypsin inhibitor (CpTI), asparagine synthetase and nitrite reductase. Alternatively, expression constructs can be used to inhibit expression of these peptides and polypeptides by incorporating the promoters in constructs for antisense use, co-suppression use or for the production of dominant negative mutations.

[00152] As explained above, several types of regulatory elements exist concerning transcription regulation. Each of these regulatory elements may be combined with the present vector if desired. Translation of eukaryotic mRNA is often initiated at the codon that encodes the first methionine. Thus, when constructing a recombinant polynucleotide according to the present document for expressing a protein product, it is preferable to ensure that the linkage between the 3' portion, preferably including the TATA box, of the promoter and the polynucleotide to be transcribed, or a functional derivative thereof, does not contain any intervening codons which are capable of encoding a methionine.

[00153] The vector of the present document may contain additional components.

For example, an origin of replication allows for replication of the vector in a host cell. Additionally, homologous sequences flanking a specific sequence allow for specific recombination of the specific sequence at a desired location in the target genome. T- DNA sequences also allow for insertion of a specific sequence randomly into a target genome.

[00154] The vector may also be provided with a plurality of restriction sites for insertion of a polynucleotide to be transcribed as well as the promoter and/or promoter control elements of the present document. The vector may additionally contain selectable marker genes. The vector may also contain a transcriptional and translational initiation region, and a transcriptional and translational termination region functional in the host cell. The termination region may be native with the transcriptional initiation region, may be native with the polynucleotide to be transcribed, or may be derived from another source. Convenient termination regions are available from the Ti-plasmid of A.

tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also, Guerineau et al. (1991) Mol. Gen. Genet. 262: 141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5: 141-149; Mogen et al. (1990) Plant Cell 2: 1261-1272; Munroe et al. (1990) Gene 91 : 151-158; Ballas et al. (1989) Nucleic Acids Res. 17:7891-7903; Joshi et al. (1987) Nucleic Acid Res. 15:9627-9639.

[00155] Where appropriate, the polynucleotide to be transcribed may be optimized for increased expression in a certain host cell. For example, the polynucleotide can be synthesized using preferred codons for improved transcription and translation. See U.S. Patent Nos. 5,380,831, 5,436,391; see also and Murray et al. (1989) Nucleic Acids Res. 17:477-498.

[00156] Additional sequence modifications include elimination of sequences encoding spurious polyadenylation signals, exon intron splice site signals, transposon- like repeats, and other such sequences well characterized as deleterious to expression. The G-C content of the polynucleotide may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. The polynucleotide sequence may be modified to avoid hairpin secondary mR A structures.

[00157] A general description of expression vectors and reporter genes can be found in Gruber, et al. (1993) "Vectors for Plant Transformation" In Methods in Plant Molecular Biology & Biotechnology, Glich et al. Eds. pp. 89-119, CRC Press. Moreover GUS expression vectors and GUS gene cassettes are available from Clonetech

Laboratories, Inc., Palo Alto, California while luciferase expression vectors and luciferase gene cassettes are available from Promega Corp. (Madison, Wisconsin). GFP vectors are available from Aurora Biosciences.

5.3 Polynucleotide Insertion Into A Host Cell

[00158] The promoters according to the present document can be inserted into a host cell. A host cell includes but is not limited to a plant, mammalian, insect, yeast, and prokaryotic cell, preferably a plant cell.

[00159] The method of insertion into the host cell genome is chosen based on convenience. For example, the insertion into the host cell genome may either be accomplished by vectors that integrate into the host cell genome or by vectors which exist independent of the host cell genome.

[00160] The promoters of the present document can exist autonomously or independent of the host cell genome. Vectors of these types are known in the art and include, for example, certain type of non-integrating viral vectors, autonomously replicating plasmids, artificial chromosomes, and the like.

[00161] Additionally, in some cases transient expression of a promoter may be desired.

[00162] The promoter sequences, promoter control elements or vectors of the present document may be transformed into host cells. These transformations may be into protoplasts or intact tissues or isolated cells. Preferably expression vectors are introduced into intact tissue. General methods of culturing plant tissues are provided for example by Maki et al. (1993) "Procedures for Introducing Foreign DNA into Plants" In Methods in Plant Molecular Biology & Biotechnology, Glich et al. Eds. pp. 67-88 CRC Press; and by Phillips et al. (1988) "Cell-Tissue Culture and In-Vitro Manipulation" In Corn & Corn Improvement, 3rd Edition Sprague et al. eds., pp. 345-387, American Society of

Agronomy Inc. et al.

[00163] Methods of introducing polynucleotides into plant tissue include the direct infection or co-cultivation of plant cell with Agrobacterium tumefaciens, Horsch et al. (1985) Science, 227: 1229. Descriptions of Agrobacterium vector systems and methods for Agrobacterium-mediatGd gene transfer provided by Gruber et al. supra.

[00164] Alternatively, polynucleotides are introduced into plant cells or other plant tissues using a direct gene transfer method such as microprojectile-mediated delivery, DNA injection, electroporation and the like. More preferably polynucleotides are introduced into plant tissues using the microprojectile media delivery with the biolistic device. See, for example, Tomes et al., "Direct DNA transfer into intact plant cells via microprojectile bombardment" In: Gamborg and Phillips (Eds.) Plant Cell, Tissue and Organ Culture: Fundamental Methods, Springer Verlag, Berlin (1995).

[00165] Methods for specifically transforming dicots are well known to those skilled in the art. Transformation and plant regeneration using these methods have been described for a number of crops including, but not limited to, cotton (Gossypium hirsutum), soybean (Glycine max), peanut (Arachis hypogaea), and members of the genus Brassica.

[00166] Methods for transforming monocots are well known to those skilled in the art. Transformation and plant regeneration using these methods have been described for a number of crops including, but not limited to, barley (Hordeum vulgarae); maize (Zea mays); oats (Avena sativa); orchard grass (Dactylis glomerata); rice (Oryza sativa, including indica and japonica varieties); sorghum (Sorghum bicolor); sugar cane

(Saccharum sp); tall fescue (Festuca arundinacea); turfgrass species (e.g. species:

Agrostis stolonifera, Poa pratensis, Stenotaphrum secundatum); wheat (Triticum aestivum), switchgrass (Panicum vigatum) and alfalfa (Medicago sativa). It is apparent to those of skill in the art that a number of transformation methodologies can be used and modified for production of stable transgenic plants from any number of target plants of interest.

[00167] The polynucleotides and vectors described herein can be used to transform a number of monocotyledonous and dicotyledonous plants and plant cell systems, including species from one of the following families: Acanthaceae, Alliaceae, Alstroemeriaceae, Amaryllidaceae, Apocynaceae, Arecaceae, Asteraceae,

Berberidaceae, Bixaceae, Brassicaceae, Bromeliaceae, Cannabaceae, Caryophyllaceae, Cephalotaxaceae, Chenopodiaceae, Colchicaceae, Cucurbitaceae, Dioscoreaceae, Ephedraceae, Erythroxylaceae, Euphorbiaceae, Fabaceae, Lamiaceae, Linaceae, Lycopodiaceae, Malvaceae, Melanthiaceae, Musaceae, Myrtaceae, Nyssaceae,

Papaveraceae, Pinaceae, Plantaginaceae, Poaceae, Rosaceae, Rubiaceae, Salicaceae, Sapindaceae, Solanaceae, Taxaceae, Theaceae, or Vitaceae.

[00168] Suitable species may include members of the genus Abelmoschus, Abies,

Acer, Agrostis, Allium, Alstroemeria, Ananas, Andrographis, Andropogon, Artemisia, Arundo, Atropa, Berberis, Beta, Bixa, Brassica, Calendula, Camellia, Camptotheca, Cannabis, Capsicum, Carthamus, Catharanthus, Cephalotaxus, Chrysanthemum, Cinchona, CitruUus, Coffea, Colchicum, Coleus, Cucumis, Cucurbita, Cynodon, Datura, Dianthus, Digitalis, Dioscorea, Elaeis, Ephedra, Erianthus, Erythroxylum, Eucalyptus, Festuca, Fragaria, Galanthus, Glycine, Gossypium, Helianthus, Hevea, Hordeum, Hyoscyamus, Jatropha, Lactuca, Linum, Lolium, Lupinus, Lycopersicon, Lycopodium, Manihot, Medicago, Mentha, Miscanthus, Musa, Nicotiana, Oryza, Panicum, Papaver, Parthenium, Pennisetum, Petunia, Phalaris, Phleum, Pinus, Poa, Poinsettia, Populus, Rauwolfia, Ricinus, Rosa, Saccharum, Salix, Sanguinaria, Scopolia, Secale, Solanum, Sorghum, Spartina, Spinacea, Tanacetum, Taxus, Theobroma, Triticosecale, Triticum, Uniola, Veratrum, Vinca, Vitis, and Zea.

[00169] Suitable species include Panicum spp. or hybrids thereof, Sorghum spp. or hybrids thereof, sudangrass, Miscanthus spp. or hybrids thereof, Saccharum spp. or hybrids thereof, Erianthus spp., Populus spp., Andropogon gerardii (big bluestem), Pennisetum purpureum (elephant grass) or hybrids thereof (e.g., Pennisetum purpureum x Pennisetum typhoidum), Phalaris arundinacea (reed canarygrass), Cynodon dactylon (bermudagrass), Festuca arundinacea (tall fescue), Spartina pectinata (prairie cord- grass), Medicago sativa (alfalfa), Arundo donax (giant reed) or hybrids thereof, Secale cereale (rye), Salix spp. (willow), Eucalyptus spp. (eucalyptus), Triticosecale {Triticum - wheat X rye), Tripsicum dactyloides (Eastern gammagrass), Leymus cinereus (basin wildrye), Leymus condensatus (giant wildrye), and bamboo.

[00170] In some embodiments, a suitable species can be a wild, weedy, or cultivated sorghum species such as, but not limited to, Sorghum almum, Sorghum amplum, Sorghum angustum, Sorghum arundinaceum, Sorghum bicolor (such as bicolor, guinea, caudatum, kafir, and durra), Sorghum brachypodum, Sorghum bulbosum, Sorghum burmahicum, Sorghum controversum, Sorghum drummondii, Sorghum ecarinatum, Sorghum exstans, Sorghum grande, Sorghum halepense, Sorghum interjectum, Sorghum intrans, Sorghum laxiflorum, Sorghum leiocladum, Sorghum macrospermum, Sorghum matarankense, Sorghum miliaceum, Sorghum nigrum, Sorghum nitidum, Sorghum plumosum, Sorghum propinquum, Sorghum

purpureosericeum, Sorghum stipoideum, Sorghum sudanensese, Sorghum timorense, Sorghum trichocladum, Sorghum versicolor, Sorghum virgatum, Sorghum vulgare, or hybrids such as Sorghum x almum, Sorghum x sudangrass or Sorghum x drummondii.

[00171] Suitable species also include Helianthus annuus (sunflower), Carthamus tinctorius (safflower), Jatropha curcas (jatropha), Ricinus communis (castor), Elaeis guineensis (palm), Linum usitatissimum (flax), and Brassica juncea.

[00172] Suitable species also include Beta vulgaris (sugarbeet), and Manihot esculenta (cassava).

[00173] Suitable species also include Lycopersicon esculentum (tomato),

Lactuca sativa (lettuce), Musa paradisiaca (banana), Solanum tuberosum (potato), Brassica oleracea (broccoli, cauliflower, brusselsprouts), Camellia sinensis (tea), Fragaria ananassa (strawberry), Theobroma cacao (cocoa), Coffea arabica (coffee), Vitis vinifera (grape), Ananas comosus (pineapple), Capsicum annum (hot & sweet pepper), Allium cepa (onion), Cucumis melo (melon), Cucumis sativus (cucumber), Cucurbita maxima (squash), Cucurbita moschata (squash), Spinacea oleracea (spinach), Citrullus lanatus (watermelon), Abelmoschus esculentus (okra), and Solanum melongena (eggplant).

[00174] Suitable species also include Papaver somniferum (opium poppy),

Papaver orientale, Taxus baccata, Taxus brevifolia, Artemisia annua, Cannabis sativa, Camptotheca acuminate, Catharanthus roseus, Vinca rosea, Cinchona officinalis, Colchicum autumnale, Veratrum californica, Digitalis lanata, Digitalis purpurea, Dioscorea spp., Andrographis paniculata, Atropa belladonna, Datura stomonium, Berberis spp., Cephalotaxus spp., Ephedra sinica, Ephedra spp., Erythroxylum coca, Galanthus wornorii, Scopolia spp., Lycopodium serratum (= Huperzia errata), Lycopodium spp., Rauwolfia serpentina, Rauwolfia spp., Sanguinaria canadensis, Hyoscyamus spp., Calendula officinalis, Chrysanthemum parthenium, Coleus forskohlii, and Tanacetum parthenium.

[00175] Suitable species also include Parthenium argentatum (guayule), Hevea spp. (rubber), Mentha spicata (mint), Mentha piperita (mint), Bixa orellana, and Alstroemeria spp.

[00176] Suitable species also include Rosa spp. (rose), Dianthus caryophyllus

(carnation), Petunia spp. (petunia) and Poinsettia pulcherrima (poinsettia).

[00177] Suitable species also include Nicotiana tabacum (tobacco), Lupinus albus (lupin), Uniola paniculata (oats), bentgrass (Agrostis spp.), Populus tremuloides (aspen), Pinus spp. (pine), Abies spp. (fir), Acer spp. (maple, Hordeum vulgare (barley), Poa pratensis (bluegrass), Lolium spp. (ryegrass) and Phleum pratense (timothy).

[00178] Thus, the methods and compositions can be used over a broad range of plant species, including species from the dicot genera Brassica, Carthamus, Glycine, Gossypium, Helianthus, Jatropha, Parthenium, Populus, and Ricinus; and the monocot genera Elaeis, Festuca, Hordeum, Lolium, Oryza, Panicum, Pennisetum, Phleum, Poa, Saccharum, Secale, Sorghum, Triticosecale, Triticum, and Zea. In some embodiments, a plant is a member of the species Panicum virgatum (switchgrass), Sorghum bicolor (sorghum, sudangrass), Miscanthus giganteus (miscanthus), Saccharum sp. (energycane), Populus balsamifera (poplar), Zea mays (corn), Glycine max (soybean), Brassica napus (canola), Triticum aestivum (wheat), Gossypium hirsutum (cotton), Oryza sativa (rice), Helianthus annuus (sunflower), Medicago sativa (alfalfa), Beta vulgaris (sugarbeet), or Pennisetum glaucum (pearl millet).

[00179] In certain embodiments, the polynucleotides and vectors described herein can be used to transform a number of monocotyledonous and dicotyledonous plants and plant cell systems, wherein such plants are hybrids of different species or varieties of a specific species (e.g., Saccharum sp. x Miscanthus sp., Panicum virgatum x Panicum amarum, Panicum virgatum x Panicum amarulum, and Pennisetum purpureum x Pennisetum typhoidum).

[00180] In another embodiment of the current document, expression constructs can be used for gene expression in callus culture for the purpose of expressing marker genes encoding peptides or polypeptides that allow identification of transformed plants. Here, a promoter that is operatively linked to a polynucleotide to be transcribed is transformed into plant cells and the transformed tissue is then placed on callus-inducing media. If the transformation is conducted with leaf discs, for example, callus will initiate along the cut edges. Once callus growth has initiated, callus cells can be transferred to callus shoot-inducing or callus root-inducing media. Gene expression will occur in the callus cells developing on the appropriate media: callus root-inducing promoters will be activated on callus root-inducing media, etc. Examples of such peptides or polypeptides useful as transformation markers include, but are not limited to barstar, glyphosate, chloramphenicol acetyltransferase (CAT), kanamycin, spectinomycin, streptomycin or other antibiotic resistance enzymes, green fluorescent protein (GFP), and β-glucuronidase (GUS), etc. Some of the promoters provided in SEQ ID NOs: 1 - 18 will also be capable of sustaining expression in some tissues or organs after the initiation or completion of regeneration. Examples of these tissues or organs are somatic embryos, cotyledon, hypocotyl, epicotyl, leaf, stems, roots, flowers and seed.

[00181] Integration into the host cell genome also can be accomplished by methods known in the art, for example, by the homologous sequences or T-DNA discussed above or using the Cre-lox system (A.C. Vergunst et al. (1998) Plant Mol. Biol. 38:393).

6. Uses of the Promoters

6.1 Use of the Promoters to Study and Screen for Expression

[00182] The promoters of the present application can be used to further understand developmental mechanisms. For example, promoters that are specifically induced during callus formation, somatic embryo formation, shoot formation or root formation can be used to explore the effects of overexpression, repression or ectopic expression of target genes, or for isolation of trans-acting factors.

[00183] The vectors of the present application can be used not only for expression of coding regions but may also be used in exon-trap cloning, or promoter trap procedures to detect differential gene expression in various tissues (see Lindsey et al. (1993) Transgenic Research 2:3347. Auch and Reth (1990) Nucleic Acids Research 18: 6743).

[00184] Entrapment vectors, first described for use in bacteria (Casadaban and

Cohen (1979) Proc. Nat. Aca. Sci. U.S.A. 76: 4530; Casadaban et al. (1980) J. Bacteriol. 143: 971) permit selection of insertional events that lie within coding sequences.

Entrapment vectors can be introduced into pluripotent ES cells in culture and then passed into the germline via chimeras (Gossler et al. 1989) Science 244: 463; Skarnes (1990) Biotechnology 8: 827). Promoter or gene trap vectors often contain a reporter gene, e.g., lacZ, lacking its own promoter and/or splice acceptor sequence upstream. That is, promoter gene traps contain a reporter gene with a splice site but no promoter. If the vector lands in a gene and is spliced into the gene product, then the reporter gene is expressed.

[00185] Recently, the isolation of preferentially-induced genes has been made possible with the use of sophisticated promoter traps (e.g. IVET) that are based on conditional auxotrophy complementation or drug resistance. In one IVET approach, various bacterial genome fragments are placed in front of a necessary metabolic gene coupled to a reporter gene. The DNA constructs are inserted into a bacterial strain otherwise lacking the metabolic gene, and the resulting bacteria are used to infect the host organism. Only bacteria expressing the metabolic gene survive in the host organism; consequently, inactive constructs can be eliminated by harvesting only bacteria that survive for some minimum period in the host. At the same time, broadly active constructs can be eliminated by screening only bacteria that do not express the reporter gene under laboratory conditions. The bacteria selected by such a method contain constructs that are selectively induced only during infection of the host. The IVET approach can be modified for use in plants to identify genes induced in either the bacteria or the plant cells upon pathogen infection or root colonization. For information on IVET see the articles by Mahan et al. (1993) Science 259:686-688, Mahan et al. (1995) Proc. Natl. Acad. Sci. USA 92:669-673, Heithoff et al. (1997) Proc. Natl. Acad. Sci USA 94:934-939, and Wang et al. (1996) Proc. Natl. Acad. Sci USA 93: 10434.

6.2 Use of the Promoters to Transcribe Genes of Interest

[00186] In one embodiment of the document, a nucleic acid molecule as shown in SEQ ID NOs: 1 - 44 is incorporated into a construct such that a promoter of the present document is operably linked to a transcribable nucleic acid molecule that is a gene of agronomic interest. As used herein, the term "gene of agronomic interest" refers to a transcribable nucleic acid molecule that includes but is not limited to a gene that provides a desirable characteristic associated with plant morphology, physiology, growth and development, yield, nutritional enhancement, disease or pest resistance, or environmental or chemical tolerance. The expression of a gene of agronomic interest is desirable in order to confer an agronomically important trait. A gene of agronomic interest that provides a beneficial agronomic trait to crop plants may be, for example, including, but not limited to genetic elements comprising herbicide resistance, increased yield, increased biomass, insect control, fungal disease resistance, virus resistance, nematode resistance, bacterial disease resistance, starch production, modified oils production, high oil production, modified fatty acid content, high protein production, fruit ripening, enhanced animal and human nutrition, biopolymers, environmental stress resistance, pharmaceutical peptides, improved processing traits, improved digestibility, industrial enzyme production, improved flavor, nitrogen fixation, hybrid seed production, and biofuel production. The genetic elements, methods, and transgenes described in the patents listed above are hereby incorporated by reference.

[00187] Alternatively, a transcribable nucleic acid molecule can effect the above mentioned phenotypes by encoding a RNA molecule that causes the targeted inhibition of expression of an endogenous gene, for example via antisense, inhibitory RNA (RNAi), or cosuppression-mediated mechanisms. The RNA could also be a catalytic RNA molecule (i.e., a ribozyme) engineered to cleave a desired endogenous mRNA product. Thus, any nucleic acid molecule that encodes a protein or mRNA that expresses a phenotype or morphology change of interest may be useful for the practice of the present document.

6.3. Stress Induced Preferential Transcription

[00188] Promoters and control elements providing modulation of transcription under oxidative, drought, oxygen, wound, and methyl jasmonate stress are particularly useful for producing host cells or organisms that are more resistant to biotic and abiotic stresses. In a plant, for example, modulation of genes, transcripts, and/or polypeptides in response to oxidative stress can protect cells against damage caused by oxidative agents, such as hydrogen peroxide and other free radicals.

[00189] Drought induction of genes, transcripts, and/or polypeptides are useful to increase the viability of a plant, for example, when water is a limiting factor. In contrast, genes, transcripts, and/or polypeptides induced during oxygen stress can help the flood tolerance of a plant.

[00190] The promoters and control elements of the present document can modulate stresses similar to those described in, for example, stress conditions are VuPLDl (drought stress; Cowpea; see Pham-Thi et al. (1999) Plant Mol Biol 39: 1257- 65), pyruvate decarboxylase (oxygen stress; rice; see Rivosal et al. (1997) Plant Physiol 114(3): 1021-29), chromoplast specific carotenoid gene (oxidative stress; Capsicum; see Bouvier et al. (1998) J Biol Chem 273: 30651-59).

[00191] Promoters and control elements providing preferential transcription during wounding or induced by methyl jasmonate can produce a defense response in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptides under such conditions is useful to induce a defense response to mechanical wounding, pest or pathogen attack or treatment with certain chemicals.

[00192] Promoters and control elements of the present document also can trigger a response similar to those described for cf9 (viral pathogen; tomato; see O'Donnell et al. (1998) Plant J 14(1): 137-42), hepatocyte growth factor activator inhibitor type 1 (HAI- 1), which enhances tissue regeneration (tissue injury; human; Koono et al. (1999) J Histochem Cytochem 47: 673-82), copper amine oxidase (CuAO), induced during ontogenesis and wound healing (wounding; chick-pea; Rea et al. (1998) FEBS Lett 437: 177-82), proteinase inhibitor II (wounding; potato; see Pena-Cortes et al. (1988) Planta 174: 84-89), protease inhibitor II (methyl jasmonate; tomato; see Farmer and Ryan (1990) Proc Natl Acad Sci USA 87: 7713-7716), two vegetative storage protein genes VspA and VspB (wounding, jasmonic acid, and water deficit; soybean; see Mason and Mullet (1990) Plant Cell 2: 569-579).

[00193] Up-regulation and down-regulation of transcription are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase oxidative, flood, or drought tolerance may require up-regulation of transcription.

[00194] Typically, promoter or control elements, which provide preferential transcription in wounding or under methyl jasmonate induction, produce transcript levels that are statistically significant as compared to cell types, organs or tissues under other conditions.

[00195] For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.

6.4. Light Induced Preferential Transcription

[00196] Promoters and control elements providing preferential transcription when induced by light exposure can be utilized to modulate growth, metabolism, and development; to increase drought tolerance; and decrease damage from light stress for host cells or organisms. In a plant, for example, modulation of genes, transcripts, and/or polypeptides in response to light is useful

(1) to increase the photosynthetic rate; (2) to increase storage of certain molecules in leaves or green parts only, e.g. silage with high protein or starch content;

(3) to modulate production of exogenous compositions in green tissue, e.g. certain feed enzymes;

(4) to induce growth or development, such as fruit development and maturity, during extended exposure to light;

(5) to modulate guard cells to control the size of stomata in leaves to prevent water loss, or

(6) to induce accumulation of beta-carotene to help plants cope with light induced stress.

[00197] The promoters and control elements of the present document also can trigger responses similar to those described in: abscisic acid insensitive3 (ABI3) (dark- grown Arabidopsis seedlings, see Rohde et al. (2000) Plant Cell 12: 35-52), asparagine synthetase (pea root nodules, see Tsai and Coruzzi (1990) EMBO J9: 323-32), mdm2 gene (human tumor, see Saucedo et al. (1998) Cell Growth Differ 9: 119-30).

[00198] Up-regulation and down-regulation of transcription are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase drought or light tolerance may require up-regulation of transcription.

[00199] Typically, promoter or control elements, which provide preferential transcription in cells, tissues or organs exposed to light, produce transcript levels that are statistically significant as compared to cells, tissues, or organs under decreased light exposure (intensity or length of time).

[00200] For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.

6.5. Dark Induced Preferential Transcription

[00201] Promoters and control elements providing preferential transcription when induced by dark or decreased light intensity or decreased light exposure time can be utilized to time growth, metabolism, and development, to modulate photosynthesis capabilities for host cells or organisms. In a plant, for example, modulation of genes, transcripts, and/or polypeptides in response to dark is useful, for example, (1) to induce growth or development, such as fruit development and maturity, despite lack of light;

(2) to modulate genes, transcripts, and/or polypeptide active at night or on cloudy days; or

(3) to preserve the plastid ultra structure present at the onset of darkness.

[00202] The present promoters and control elements can also trigger response similar to those described in the section above.

[00203] Up-regulation and down-regulation of transcription are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase or decrease growth and development may require up-regulation of transcription.

[00204] Typically, promoter or control elements, which provide preferential transcription under exposure to dark or decrease light intensity or decrease exposure time, produce transcript levels that are statistically significant.

[00205] For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.

6.6. Leaf Preferential Transcription

[00206] Promoters and control elements providing preferential transcription in a leaf can modulate growth, metabolism, and development or modulate energy and nutrient utilization in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptide in a leaf, is useful, for example,

(1) to modulate leaf size, shape, and development;

(2) to modulate the number of leaves ; or

(3) to modulate energy or nutrient usage in relation to other organs and tissues

[00207] Up-regulation and down-regulation of transcription are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase growth, for example, may require up-regulation of transcription.

[00208] Typically, promoter or control elements, which provide preferential transcription in the cells, tissues, or organs of a leaf, produce transcript levels that are statistically significant as compared to other cells, organs or tissues. [00209] For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.

6.7. Root Preferential Transcription

[00210] Promoters and control elements providing preferential transcription in a root can modulate growth, metabolism, development, nutrient uptake, nitrogen fixation, or modulate energy and nutrient utilization in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptide in a root, is useful,

(1) to modulate root size, shape, and development;

(2) to modulate the number of roots, or root hairs;

(3) to modulate mineral, fertilizer, or water uptake;

(4) to modulate transport of nutrients; or

(4) to modulate energy or nutrient usage in relation to other cells, organs and tissues.

[00211] Up-regulation and down-regulation of transcription are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase or decrease growth, for example, may require up-regulation of transcription.

[00212] Typically, promoter or control elements, which provide preferential transcription in cells, tissues, or organs of a root, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.

[00213] For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.

6.8. Stem/Shoot Preferential Transcription

[00214] Promoters and control elements providing preferential transcription in a stem or shoot can modulate growth, metabolism, and development or modulate energy and nutrient utilization in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptide in a stem or shoot, is useful, for example,

(1) to modulate stem/shoot size, shape, and development; or (2) to modulate energy or nutrient usage in relation to other organs and tissues

[00215] Up-regulation and down-regulation of transcription are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase growth, for example, may require up-regulation of transcription.

[00216] Typically, promoter or control elements, which provide preferential transcription in the cells, tissues, or organs of a stem or shoot, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.

[00217] For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.

6.9. Fruit and Seed Preferential Transcription

[00218] Promoters and control elements providing preferential transcription in a silique or fruit can time growth, development, or maturity; or modulate fertility; or modulate energy and nutrient utilization in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptides in a fruit, is useful

(1) to modulate fruit size, shape, development, and maturity;

(2) to modulate the number of fruit or seeds;

(3) to modulate seed shattering;

(4) to modulate components of seeds, such as, storage molecules, starch, protein, oil, vitamins, anti-nutritional components, such as phytic acid;

(5) to modulate seed and/or seedling vigor or viability;

(6) to incorporate exogenous compositions into a seed, such as lysine rich proteins;

(7) to permit similar fruit maturity timing for early and late blooming flowers; or

(8) to modulate energy or nutrient usage in relation to other organs and tissues. [00219] Up-regulation and down-regulation of transcription are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase or decrease growth, for example, may require up-regulation of transcription.

[00220] Typically, promoter or control elements, which provide preferential transcription in the cells, tissues, or organs of siliques or fruits, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.

[00221] For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.

6.10. Callus Preferential Transcription

[00222] Promoters and control elements providing preferential transcription in a callus can be useful to modulating transcription in dedifferentiated host cells. In a plant transformation, for example, preferential modulation of genes, transcripts, in callus is useful to modulate transcription of a marker gene, which can facilitate selection of cells that are transformed with exogenous polynucleotides.

[00223] Up-regulation and down-regulation of transcription are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase marker gene detectability, for example, may require up-regulation of transcription.

[00224] For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.

6.11. Flower Specific Transcription

[00225] Promoters and control elements providing preferential transcription in flowers can modulate pigmentation; or modulate fertility in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptides in a flower, is useful,

(1) to modulate petal color; or

(2) to modulate the fertility of pistil and/or stamen.

[00226] Up-regulation and down-regulation of transcription are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase or decrease pigmentation, for example, may require up-regulation of transcription [00227] Typically, promoter or control elements, which provide preferential transcription in flowers, produce transcript levels that are statistically significant as compared to other cells, organs or tissues.

[00228] For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.

6.12. Immature Bud/Floret and Inflorescence Preferential Transcription

[00229] Promoters and control elements providing preferential transcription in an immature bud/floret or inflorescence can time growth, development, or maturity; or modulate fertility or viability in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptide in an immature bud and/or inflorescence, is useful,

(1) to modulate embryo development, size, and maturity;

(2) to modulate endosperm development, size, and composition;

(3) to modulate the number of seeds and fruits; or

(4) to modulate seed development and viability.

[00230] Up-regulation and down-regulation of transcription are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase or decrease growth, for example, may require up-regulation of transcription.

[00231] Typically, promoter or control elements, which provide preferential transcription in immature buds/florets and inflorescences, produce transcript levels that are statistically significant as compared to other cell types, organs or tissues.

[00232] For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.

6.13. Senescence Preferential Transcription

[00233] Promoters and control elements providing preferential transcription during senescence can be used to modulate cell degeneration, nutrient mobilization, and scavenging of free radicals in host cells or organisms. Other types of responses that can be modulated include, for example, senescence associated genes (SAG) that encode enzymes thought to be involved in cell degeneration and nutrient mobilization (Arabidopsis; see Hensel et al. (1993) Plant Cell 5: 553-64), and the CP-2/cathepsin L gene (rat; Kim and Wright (1997) Biol Reprod 57: 1467-77), both induced during senescence.

[00234] In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptides during senescencing is useful to modulate fruit ripening.

[00235] Up-regulation and down-regulation of transcription are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase or decrease scavenging of free radicals, for example, may require up-regulation of transcription.

[00236] Typically, promoter or control elements, which provide preferential transcription in cells, tissues, or organs during senescence, produce transcript levels that are statistically significant as compared to other conditions.

[00237] For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.

6.14. Germination Preferential Transcription

[00238] Promoters and control elements providing preferential transcription in a germinating seed can time growth, development, or maturity; or modulate viability in host cells or organisms. In a plant, for example, preferential modulation of genes, transcripts, and/or polypeptide in a germinating seed, is useful,

(1) to modulate the emergence of the hypocotyls, cotyledons and radical; or

(2) to modulate shoot and primary root growth and development;

[00239] Up-regulation and down-regulation of transcription are useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase or decrease growth, for example, may require up-regulation of transcription.

[00240] Typically, promoter or control elements, which provide preferential transcription in a germinating seed, produce transcript levels that are statistically significant as compared to other cell types, organs or tissues.

[00241] For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay. EXPERIMENTAL PROCEDURES AND RESULTS

Agi'obactei'ium-Med ated Transformation of Arabidopsis

[00242] Host Plants and Transgenes: Wild-type Arabidopsis thaliana

Wassilewskija (WS) plants are transformed with Ti plasmids containing nucleic acid sequences to be expressed, as noted in the respective examples, in the sense orientation relative to the 35S promoter in a Ti plasmid. A Ti plasmid vector useful for these constructs, CRS 338, contains the Ceres-constructed, plant selectable marker gene phosphinothricin acetyltransferase (PAT), which confers herbicide resistance to transformed plants.

[00243] Ten independently transformed events are typically selected and evaluated for their qualitative phenotype in the Ti generation.

[00244] Preparation of Soil Mixture: 24L Sunshine Mix #5 soil (Sun Gro

Horticulture, Ltd., Bellevue, WA) is mixed with 16L Therm-O-Rock vermiculite (Therm- O-Rock West, Inc., Chandler, AZ) in a cement mixer to make a 60:40 soil mixture. To the soil mixture is added 2 Tbsp Marathon 1% granules (Hummert, Earth City, MO), 3 Tbsp OSMOCOTE® 14-14-14 (Hummert, Earth City, MO) and 1 Tbsp Peters fertilizer 20-20-20 (J.R. Peters, Inc., Allentown, PA), which are first added to 3 gallons of water and then added to the soil and mixed thoroughly. Generally, 4-inch diameter pots are filled with soil mixture. Pots are then covered with 8-inch squares of nylon netting.

[00245] Planting: Using a 60 mL syringe, 35 mL of the seed mixture is aspirated. 25 drops are added to each pot. Clear propagation domes are placed on top of the pots that are then placed under 55% shade cloth and subirrigated by adding 1 inch of water.

[00246] Plant Maintenance: 3 to 4 days after planting, lids and shade cloth are removed. Plants are watered as needed. After 7-10 days, pots are thinned to 20 plants per pot using forceps. After 2 weeks, all plants are subirrigated with Peters fertilizer at a rate of 1 Tsp per gallon of water. When bolts are about 5-10 cm long, they are clipped between the first node and the base of stem to induce secondary bolts. Dipping

infiltration is performed 6 to 7 days after clipping.

[00247] Preparation of Agrobacterium: To 150 mL fresh YEB is added 0.1 mL each of carbenicillin, spectinomycin and rifampicin (each at 100 mg/ml stock

concentration). Agrobacterium starter blocks are obtained (96-well block with

Agrobacterium cultures grown to an OD₆₀o of approximately 1.0) and inoculated one culture vessel per construct by transferring 1 mL from appropriate well in the starter block. Cultures are then incubated with shaking at 27°C. Cultures are spun down after attaining an OD₆oo of approximately 1.0 (about 24 hours). 200 mL infiltration media is added to resuspend Agrobacterium pellets. Infiltration media is prepared by adding 2.2 g MS salts, 50 g sucrose, and 5 2 mg/ml benzylaminopurine to 900 ml water.

[00248] Dipping Infiltration: The pots are inverted and submerged for 5 minutes so that the aerial portion of the plant is in the Agrobacterium suspension. Plants are allowed to grow normally and seed is collected.

[00249] High-throughput Screening of Ti Transgenic Plants: Seed is evenly dispersed into water-saturated soil in pots and placed into a dark 4°C cooler for two nights to promote uniform germination. Pots are then removed from the cooler and covered with 55% shade cloth for 4-5 days. Cotyledons are fully expanded at this stage. FINALE^® (Sanofi Aventis, Paris, France) is sprayed on plants (3 ml FINALE^® diluted into 48 oz. water) and repeated every 3-4 days until only transformants remain.

GFP Assay

[00250] Tissues are dissected by eye or under magnification using INOX 5 grade forceps and placed on a slide with water and coversliped. An attempt is made to record images of observed expression patterns at earliest and latest stages of development of tissues listed below. Specific tissues will be preceded with High (H), Medium (M), Low (L) designations. Flower Pedicel, receptacle, nectary, sepal, petal, filament, anther, pollen, carpel, style, papillae, vascular, epidermis, stomata, trichome

Silique Stigma, style, carpel, septum, placentae, transmitting tissue, vascular,

epidermis, stomata, abscission zone, ovule

Ovule Pre- fertilization: inner integument, outer integument, embryo sac,

funiculus, chalaza, micropyle, gametophyte

Post- fertilization: zygote, inner integument, outer integument, seed coat, primordia, chalaza, micropyle, early endosperm, mature endosperm, embryo

Embryo Suspensor, preglobular, globular, heart, torpedo, late mature, pro vascular, hypophysis, radicle, cotyledons, hypocotyl

Stem Epidermis, cortex, vascular, xylem, phloem, pith, stomata, trichome

Leaf Petiole, mesophyll, vascular, epidermis, trichome, primordia, stomata, stipule, margin

[00251] Tl Mature: These are the Tl plants resulting from independent transformation events. These are screened between stage 6.50-6.90 (i.e. the plant is flowering and 50-90% of the flowers that the plant will make have developed), which is 4-6 weeks of age. At this stage the mature plant possesses flowers, siliques at all stages of development, and fully expanded leaves. The plants are initially imaged under UV with a Leica Confocal microscope to allow examination of the plants on a global level. If expression is present, they are re -imaged using scanning laser confocal microscopy.

[00252] T2 Seedling: Progeny are collected from the Tl plants giving the same expression pattern and the progeny (T2) are sterilized and plated on agar-solidified medium containing M&S salts. In the event that there is no expression in the Tl plants, T2 seeds are planted from all lines. The seedlings are grown in Percival incubators under continuous light at 22°C for 10-12 days. Cotyledons, roots, hypocotyls, petioles, leaves, and the shoot meristem region of individual seedlings were screened until two seedlings were observed to have the same pattern. In general, the same expression pattern was found in the first two seedlings. However, up to 6 seedlings were screened before "no expression pattern" was recorded. All constructs are screened as T2 seedlings even if they did not have an expression pattern in the Tl generation.

[00253] T2 Mature: The T2 mature plants were screened in a similar manner to the Tl plants. The T2 seeds were planted in the greenhouse, exposed to selection and at least one plant screened to confirm the Tl expression pattern. In instances where there were any subtle changes in expression, multiple plants were examined and the changes noted in the tables.

[00254] T3 Seedling: This was done similar to the T2 seedlings except that only the plants for which we are trying to confirm the pattern are planted.

Agrobacterium-Mediated Transformation of Rice

Induce calli formation from mature rice seeds

[00255] De-husk mature seeds using de-husker (Kett; Cat # TR120) and discard spotted ones if present. Transfer 100 de-husked seeds to a 50 mL conical tube. Add 24mL autoclaved distilled water and then 6ml Clorox™ (Clorox contains 5.25% sodium hypochlorite so final concentration is 1.05%) and 2-3 drops of Liqui-Nox^®. Shake the tube occasionally for 30min. Pour out Clorox™ solution and rinse seeds 5 times with sterile water. Dry the seeds on autoclaved Kimwipes™ for a few minutes. Transfer seeds on the semi-solid N6-P medium (3.98 g/L N6 basal salt mixture, 0.8 mg/L KI, 0.025 mg/L CoCl₂.6H₂0, 0.025 mg/L CuSO₄.5H₂0, 0.25 mg/L NaMoO₄.2H₂0, 2 mg/L Glycine, 100 mg/L Myo-inositol, 5 mg/L Thiamine. HC1, 1 mg/L Pyridoxine.HCl, 1 mg/L

Nicotinic acid, 2.8 g/L Proline, 300 mg/L Casamino acid, 30 g/L Sucrose, 2 mg/L 2, 4- Dichloro-Phenoxyacetic Acid, 4g/L Gel rite, pH 5.6); 10 seeds each Petri dish. Each Petri dish contains 30 ml N6-P medium. Dishes are sealed with antifungal tape to allow air exchange. Place the plates at 28°C under cold fluorescent light. Many granular calli should be formed within 4 weeks. Calli of good quality consist of small and spherical cells with dense cytoplasm, which are competent for transformation. The calli can be used directly for Agrobacterium infection, or subculture them for later use. Infection and co-cultivation of calli with Agrobacterium cells

[00256] Pick up a single Agrobacterium clone from stock and culture it in 2 mL

YEB liquid medium by growing it overnight in a shaker. Appropriate antibiotics are included at 50 mg/L or higher. Put on 28°C shaker overnight. The next day, reinoculate 25 xL of overnight culture into 5 mL of liquid YEB with selection and grow overnight at 28°C. The next day, use this culture for transformation. Transfer the liquid culture to 1.5 mL microtube and centrifuge it at 10,000 RPM for 2 minutes. Discard the supernatant and resuspend cells in 15mL N6-AS liquid medium (3.98g/L N6 basal salt mixture, 0.8 mg/L KI, 0.025 mg/L CoCl₂.6H₂0, 0.025 mg/L CuSO₄.5H₂0, 0.25 mg/L NaMoO₄.2H₂0, 2 mg/L Glycine, lOOmg/L Myo-inositol, 5 mg/L Thiamine.HCl, 1 mg/L Pyridoxine.HCl, 1 mg/L Nicotinic acid, 1 g/L Casamino acid, 30 g/L Sucrose, 10 g/L Glucose, 2 mg/L 2, 4- Dichloro-Phenoxyacetic Acid, pH 5.6). Adjust cell density with the N6-AS medium. The density can be measured by a spectrophotometer (use 750 aliquot for reading). The optimal OD₆oo reading varies significantly depending on Agrobacterium strains and sometimes vectors. The optimal reading means that there is no over-growth of

Agrobacterium cells in at least 3 day co-cultivation. The optimum OD₆oo for rice is 0.2. Mix rice calli with Agrobacterium cells. This is done in a 50 mL sterile conical tube. Place tubes in a sterile 1 gallon plastic bag and place horizontally on a shaker for 30 minutes. Pipette out solution with 10-mL pipette. Transfer calli onto autoclaved Kimwipes™ to remove excess solution. Remove any agar media if present, since Agrobacterium will grow faster in agar. Culture calli on autoclaved filter paper placed on the N6-AS semi-solid medium (N6-AS medium containing 4g/L Gel rite). Each 100 mm x 20 mm dish contains 10-20 mL N6-AS media. Seal the dish with antifungal tape. Cover plates with aluminum foil because acetosyringone present in the media is light sensitive. Co-culture calli and Agrobacterium cells at 22°C in the dark until

Agrobacterium mass can be seen by the naked eye.

Selection of transformed calli

[00257] Transfer the infected calli with a sterile, disposable spatula to a sterile 50 mL tube containing 35 mL sterile distilled water. Shake the tube for a few seconds and pipette out the water. Repeat washing 3 times or more if necessary, until solution becomes clear. For the final wash, add carbenicillin at the concentration of 500 mg/L. Transfer calli with a disposable blue ino-loop onto 2 layers thick of autoclaved

Kimwipes™ paper in a large spherical Petri plate to blot. Culture calli on dishes containing semisolid N6-P medium with 250mg/L carbenicillin at 28°C under cold fluorescent light for 6 days. Each 100mm x 20mm dish contains 30 mL N6-P medium, use approximately 4 dishes of calli for each construct. Dishes are sealed with antifungal tape. Transfer calli from the resting media on to the selection media containing 250mg/L carbenicillin and 5 mg/L purified Bialaphos™ (for selection of BAR gene) or 100 mg/L Paromomycin sulfate (for seclection of NPTII gene) for 14 days. For second round of selection, subculture calli for another 14 days. Transformed calli can typically be seen clearly at the end of this selection. Third selection is done if the second selection does not produce enough resistant calli.

Regeneration of transgenic plants

[00258] Transfer independent resistant calli to the N6-R plant regeneration medium (3.98 g/L N6 basal salt mixture, 0.8 mg/L KI, 0.025 mg/L CoCL₂.6H₂0, 0.025 mg/L CuSO₄.5H₂0, 0.25 mg/L NaMoO₄.2H₂0, 2 mg/L Glycine, 100 mg/L Myo-inositol, 5 mg/L Thiamine.HCl, 1 mg/L Pyridoxine.HCl, 1 mg/L Nicotinic acid, 1 g/L Casamino acid, 25 g/L Sucrose, 25 g/L Sorbitol, 2 mg/L 6-Benzylaminopurine, 0.05 mg/L 1- Naphthaleneacetic acid, 7 g/L Agarose (Omnipur), pH 5.6). Each 100mm x 20mnm dish contains 30 mL N6-R medium, 4 or 6 callus lines on each dish. Dishes are sealed with antifungal tape. Culture calli at 28°C under cold fluorescent light until shoots and roots are formed. Typically, shoots should be seen within 3 weeks. Transfer plantlets to Magenta boxes containing 30 mL ½ MSI A (2.165 g/L MS salts, lml/L of lOOOx B5 vitamins stock, 15 g/L Sucrose, 5 g/L Agar, pH 5.7). Grow plantlets at 28°C under old fluorescent light for 10-14 days.

[00259] Ten independently transformed events (plantlets) are selected with one tiller from each event evaluated for GFP Expression in the TO generation.

[00260] Preparation of Soil Mixture: 6L Potting Soil (Farmers Organic Potting

Soil, Chino, CA) is mixed with 4L Turface in a cement mixer to make a 60:40 soil mixture. To the soil mixture is added 1 tsp Marathon 1% granules (Hummert, Earth City, MO), 2 Tbsp OSMOCOTE® 14-14-14 (Hummert, Earth City, MO). Once a month 1 Tbsp Peters fertilizer 20-20-20 (J.R. Peters, Inc., Allentown, PA) is mixed well in 3 gallons of water and poured into the bottom flat to fertilize. 6-inch diameter Azalea pots are used for transplanting with 1-2 plants per pot.

[00261] Planting: Plants growing in magenta boxes are carefully pulled from

MS agar rice media. Plant roots are cleaned and divided into single tillers ensuring that each tiller has a viable root and no residual callus material. The tillers are screened for GFP expression and one positively expressing tiller per independently transformed event is transplanted to soil and grown to maturity for further analysis.

[00262] Plant Maintenance: Plants are well watered throughout the duration of the lifecycle. The bottom of the flat is cleaned and new water added twice a week.

Approximately 21 days after planting, rice is sub-irrigated with Peter's fertilizer at a concentration of 1 Tsp per 3 gallons of water. Plants are analyzed for GFP expression at the TO seedling, TO mature and Tl generations.

GFP Assay and Imaging

[00263] The polynucleotide sequences of the present document were tested for promoter activity using Green Fluorescent Protein (GFP) assays in the following manner.

[00264] Each isolated nucleic acid described in the Sequence Listing was cloned into a Ti plasmid vector, CRS380_Binary_DF_EGFP using appropriate primers tailed with Sfil restriction sites. Standard PCR reactions using these primers and genomic DNA were conducted. The resulting product was isolated, cleaved with Sfil and cloned into the Sfil site of an appropriate vector, such as, CRS380_Binary_DF_EGFP (see Figure 1). GFP assay in rice Callus

[00265] GFP expression in rice callus can be observed as early as 4-7 days after co-cultivation. The rice callus used for co-cultivation is observed under Zeiss Stemi SVII APO dissecting microscope for GFP expression. For viewing GFP expression we use GFP 500 filter in the microscope. The images observed under the microscope can be transferred, captured and stored to a computer using the Axiocam (Zeiss) camera and Axiovision software.

GFP assay in TO Seedling

[00266] Each independently transformed event is divided into single tillers which then undergo Typhoon scanner laser imaging. One positively GFP-expressing tiller per event is selected for subsequent GFP analysis by Confocal microscopy and ultimately for transplantation for further mature tissue analysis.

[00267] Typhoon Scan: Plants are initially scanned with a Typhoon Scanner to examine the GFP expression of the plants on a global level. If expression is present, images are collected by Typhoon scanning laser imaging and scanning laser confocal microscopy. Scanned images from the Typhoon scanner are taken as 2-D images of the entire plant and can be opened using the program ImageQuant.

[00268] Confocal Microscopy: Tissues are dissected by eye or under

magnification using INOX 5 grade forceps and placed on a slide with water and coversliped. An attempt is made to record images of observed expression patterns at earliest and latest stages of development of tissues listed below. Specific tissues will be defined as having positive expression or no expression.

[00269] Ziess UV stereoscope: Reproductive tissues that are too large to use with the confocal microscope are prepared using a dissection microscope under high magnification using INOX 5 grade forceps and placed on a slide. An attempt is made to record images of observed expression patterns in mature rice reproductive tissues.

Auxio vision is the program used for capturing GFP images under the following settings: GFP: 4900ms, gain=3, resolution^ 300 x 1030 interpolated

Bright field: 100ms, conversion=square root, resolution=1300 x 1030 interpolated.

TO Mature

[00270] These are the TO plants resulting from a single tiller from each independent transformation event having predetermined positive GFP expression. These are screened between stage 3-5 (i.e. between late vegetative to panicle initiation and floral maturation), which is 6-8 weeks of age. At this stage the mature plant possesses young panicle inflorescence to adolescent flowers, fully expanded leaves, multiple nodes and mature stem and root tissue. The plants are initially imaged using the Typhoon scanner and then imaged in detail using the Leica Confocal microscope and Ziess UV Stereoscope to allow examination of the mature plants on a global level.

Tl Seedling

[00271] Seed is collected from the TO plants and stored for further use in induction experiments.

RESULTS

[00272] The Promoter Expression Reports of the Tables present the results of the

GFP assays as reported by their corresponding construct number and line number.

[00273]

Analysis of Promoter PD3485 activity

Promoter Expression Report for PD3485 (SEQ ID NO:36)

Organism Evaluated: Arabidopsis thaliana

Construct: PD3485

SR/OS Line: SR05899

Promoter candidate I.D: 61035560

Events expressing: -02-06-09-11-12-13-15

Spatial expression summary:

Tl Mature

Events Screened: n = 16 Events Expressing: n = 7 (02, 06, 09, 11-13, 15)

FLOWER

0 SILIQUE

OVULE

0 MICROPYLE 0 SEED COAT

SILIQUE

0 OVULE

Observed expression pattern:

Tl Mature expression: Expression is observed specifically from the ovule.

Selection Criteria: p450 project

GenBank: At5g24910 similar to Cytochrome P450 72A1 (SP:Q05047) [Catharanthus roseus]; similar to fatty acid omega-hydroxylase cytochrome P450 4A11 - Homo sapiens, PIRT53015; supported by cDNA: gi_16604323_gb_AY058060.1_; go function: cytochrome P450 activity

[goid 0015034]; go function: oxygen binding [goid 0019825]

protein id NP 568463.1

PFAM p450;

Source Promoter Organism: Arabidopsis thaliana

Vector: Binary DF EGFP

Marker Type: EGFP

Generation Screened: Tl Mature

Promoter utility

Trait Area: Seed enhancement, Sterility

Sub-trait Area:

Utility: Among other uses, this promoter sequence could be useful to engineer enhancements to seed, including, but not limited to, alterations in germination timing, abiotic and biotic tolerances, and seed size, and to engineer seed sterility. Analysis of Promoter PD3536 activity

Promoter Expression Report PD3536 (SEQ ID NO:35)

Organism Evaluated: Arabidopsis thaliana

Construct: PD3536

SR/OS Line: SR05941

Promoter candidate I.D: 72581207

Events expressing: ND - no expression on whole-plant scan. Confocal analysis revealed expression, and not all events were analyzed

Spatial expression summary:

TO Mature

FLOWER

0 ANTHER 0 POLLEN 0 SILIQUE

EMBRYO

0 COTYLEDONS 0 RADICLE 0 ROOT MERISTEM 0 TORPEDO STAGE

OVULE

0 EMBRYO (EARLY) 0 EMBRYO (LATE) 0 ENDOSPERM (CELLULARIZED)

SILIQUE

0 CARPEL 0 EPIDERMIS 0 FUNICULUS 0 OVULE

Observed expression pattern:

Tl Mature expression: Expression observed in embryos

Selection Criteria: AGL55. Part of Malpha MADS box family.

7x enriched in closed flower

Gene: Arabidopsis thaliana AT1G60920

cDNA LD: 23520899

GenBank: contains SRF-type transcription factor (DNA-binding and dimerisation domain); go function: DNA binding [goid 0003677]; go function: transcription factor activity [goid

0003700]

protein id NP 176288.1

PFAM SRF-TF;

Source Promoter Organism: Arabidopsis thaliana

Vector: Binary DF EGFP

Marker Type: EGFP

Generation Screened: Tl Mature

Promoter utility

Trait Area: Early growth and development

Sub-trait Area:

Utility: Among other uses, this promoter sequence could be useful to engineer modifications to early embryo and seedling development. Analysis of Promoter PD3558 activity

Promoter Expression Report PD3558 (SEQ ID NO:34) j

Organism Evaluated: Arabidopsis thaliana

Construct: PD3558

SR/OS Line: SR05955

Promoter candidate LP: 71811437

Events expressing: 01, 05, 07-10, 13-15

Spatial expression summary:

Tl Mature

Events Screened: n = 15 Events Expressing: n = 9 (01, 05, 07-10, 13-15)

FLOWER

0 ANTHER 0 EPIDERMIS 0 PEDICEL 0 POLLEN 0 SEPAL EMBRYO

0 COTYLEDONS 0 RADICLE 0 ROOT MERISTEM LEAF

0 EPIDERMIS 0 MESOPHYLL 0 LEAF BLADE 0 TRICHOME 0 VASCULATURE

SILIQUE

0 EPIDERMIS

STEM

0 CORTEX 0 EPIDERMIS Observed expression pattern:

Tl Mature expression: Expression observed in green tissues.

Selection Criteria: Poplar ortholog of Arabidopsis gene Atlg55670

Gene: Populus balsamifera subsp. trichocarpa annot ID: 1533924

cDNA LD: 37152565

GenBank: Photosystem I reaction center subunit V, chloroplast precursor (PSI-G) (Photosystem

1 9 kDa protein) {Hordeum vulgare}; contains Pfam profile PF01241 : Photosystem I psaG / psaK; go component: photosystem I [goid 0009522]; go component: membrane [goid 0016020];

go_process: photosynthesis [goid 0015979]

protein id NP l 75963.1

Source Promoter Organism: Populus balsamifera subsp. trichocarpa

Vector: Binary DF EGFP

Marker Type: EGFP

Generation Screened: Tl Mature

Promoter utility

Trait Area: Growth, Photosynthesis, Carbon Utilization

Sub-trait Area:

Utility: Among other uses, this promoter sequence could be useful to engineer increased biomass , among other things, increasing photosynthetic efficiency.

Analysis of Promoter PD3801 activity

Promoter Expression Report PD3801 (SEQ ID NO:43) |

Organism Evaluated: Panicum virgatum

Construct: PD3801

SR/OS Line: PV00325

Promoter candidate LP: 75181013

Events expressing: 02, 05, 07-09, 12

Spatial expression summary:

TO Seedling

Events Screened: n = 20 Events Expressing: n = 0 ()

No expression detected

TO Mature

Events Screened: n = 14 Events Expressing: n = 6 (02, 05, 07-09, 12) MAIN CULM

0 ENDODERMIS 0 EPIDERMIS 0 INTERNODE 0 VASCULATURE

Observed expression pattern:

Tl Mature expression: Expression was detected in a stem-specific manner, in all tissues, in the mature plant.

Selection Criteria: Predicted to be stem-specific.

GenBank: Pv clone 1806607 cellulose synthase-like family C; pfam: Glycosyl transferase family 2

Source Promoter Organism: Panicum virgatum

Vector: Binary Direct Fusion EGFP

Marker Type: EGFP

Generation Screened: Tl Mature

Promoter utility

Trait Area: Nutrient Use Efficiency, Cell-wall modification, Drought Tolerance

Sub-trait Area: Nitrogen use efficiency, phosphate use efficiency, Increased sugar accessibility,

Lignin modulation, Water Use Efficiency

Utility: Among other uses, this promoter sequence could be useful to engineer pathways that enhance the distribution of nutrients and/or water from the roots to the green tissues of the plant. It could also be used to specifically target the modulation of cell-wall genes to, among other things, modulate components involved in regulating energy production from the plant, such as, for example, enhancing accessible sugars. Analysis of Promoter PD3421 activity

Promoter Expression Report PD3421 (SEQ ID NO:40)

Organism Evaluated: Arabidopsis thaliana

Construct: PD3421

SR/OS Line: SR05782

Promoter candidate LP: 58417441

Events expressing: 09-10-11-12-13-14-15-16

Spatial expression summary:

Tl Mature

Events Screened: n = 16 Events Expressing: n = 8 (09-16)

Events 1-8 were screened for above ground tissues only, and the low-level of stem expression was not observed by the whole-plant scanner. Events 9-16 were screened for above and below ground expression, and the strength of the root-expression lead to confocal screening of the stem.

MATURE ROOT

0 ENDODERMIS 0 PERICYCLE

STEM

0 PITH

Observed expression pattern:

Tl Mature expression: Expression was detected in the vasculature of the root and stem, but not in the leaves.

Selection Criteria: high stem expression by microarray data

GenBank: locus tag At3g 16920

note similar to class I chitinase GL7798670 from [Arabis microphylla]; go function: chitinase activity [goid 0004568]

protein_id NP_188317.1

PFAM Glyco_hydro_19;

Source Promoter Organism: Arabidopsis thaliana

Vector: Binary Direct Fusion EGFP

Marker Type: EGFP

Generation Screened: Tl Mature Analysis of Promoter PD3540 activity

Promoter Expression Report PD3540 (SEQ ID NO:39) J

Organism Evaluated: Arabidopsis thaliana

Construct: PD3540

SR/OS Line: SR05945

Promoter candidate I.D: 72581086

Events expressing: -01-02-04-05-06-08-09-10-11-12-13-14-15-16

Spatial expression summary:

Tl Mature

Events Screened: n = 16 Events Expressing: n = 14 (1-2,4-6,8-16) FLOWER

0 ANTHER 0 CARPEL 0 SEPAL 0 PEDICEL 0 PETAL 0 SILIQUE 0 TRICHOME

MERISTEM

0 FLORAL MERISTEM

LEAF

0 EPIDERMIS 0 MESOPHYLL 0 TRICHOME 0 VASCULATURE MATURE ROOT

0 PERICYCLE 0 CORTEX 0 EPIDERMIS SILIQUE

0 SEPTUM 0 EPIDERMIS 0 FUNICULUS STEM

0 CORTEX 0 EPIDERMIS Observed expression pattern:

Tl Mature expression: Expression was detected in both above ground and below ground vegetative tissues, in both the epidermal, cortical, and vasculature tissues. No expression detected in pollen or seed.

Selection Criteria: At4g30650 low-temp and salt responsive homolog.Upregulated in cold at 2hr - 24 hr by Riken microarray.Upregulated in cold at 40 x induction at 4°C 6 hr by Ceres microarray.Also predicted to be induced by Salt.

Gen Bank: At4g30650 similar to SP|Q9ZNQ7 Hydrophobic protein RCI2A (Low temperature and salt responsive protein LTI6A) {Arabidopsis thaliana}; contains Pfam profile PF01679:

Uncharacterized protein family; go_process: response to cold [goid 0009409]; go_process:

hyperosmotic salinity response [goid 0042538]

protein id NP l 94794.1

PFAM UPF0057;

Source Promoter Organism: Arabidopsis thaliana

Vector: Binary Direct Fusion EGFP Marker Type: EGFP

Generation Screened: Tl Mature

Promoter utility

Trait Area: Growth and Development, Plant Architecture, Nutrient Use Efficiency, Water Use Efficiency, Photosynthetic Efficiency

Sub-trait Area

Utility: Among other uses, this promoter sequence could be useful to engineer agronomic trait improvements in both above ground (plant architecture, biomass yield, photosynthetic efficiency, herbivory resistance and disease resistance, among others) and below ground tissues (root architecture, insect and disease resistance, and water and nutrient uptake from soils, among others) while minimizing expression in gametes and germplasm, thus minimizing the exposure of expressed trait protein to the environment

Analysis of Promoter PD3422 activity

Promoter Expression Report PD3422 (SEQ ID NO:38) ^~|

Organism Evaluated: Arabidopsis thaliana

Construct: PD3422

SR/OS Line: SR05783

Promoter candidate LP: 58417447

Events expressing: 9,10, 12-16

Spatial expression summary:

Tl Mature

Events Screened: n = 16 Events Expressing: n = 7 (9,10, 12-16)

Note: Events 1-8 were analyzed for above-ground expression only. Events 9-16 were analyzed for whole-plant expression.

MATURE ROOT

0 STELE 0 VASCULATURE

Observed expression pattern:

Tl Mature expression: Expression was detected within the vasculature of the root

Selection Criteria: Nominated based upon microarray data. The cDNA downstream of this promoter element is predicted to be highly expressed in stems.

GenBank: At4g27435 protein_id NP_567774.1

PFAM DUF1218;

Source Promoter Organism: Arabidopsis thaliana

Vector: Binary Direct Fusion EGFP

Marker Type: EGFP

Generation Screened: Tl Mature

Promoter utility:

Trait Area: Nutrient Use Efficiency and Water Use Efficiency

Sub-trait Area: Nitrogen Uptake, Phosphorous Uptake, Water Uptake

Utility: Among other uses, this promoter sequence could be useful to engineer increased volume or efficiency of nutrient and/or water uptake and transport from soil and into the above ground regions of the plant. Analysis of Promoter PD3333 activity

Promoter Expression Report PD3333 (SEQ ID NO:40) j

Organism Evaluated: Arabidopsis thaliana

Construct: PD3333

SR/OS Line: SR05688

Promoter candidate LP: 57007779

Events expressing: 09-15

Spatial expression summary:

Tl Mature

Events Screened: n = 15 Events Expressing: n = 7 (09-15)

Note: Events 1-8 were screened for above ground expression only. Events 9-15 were scored for root expression.

MATURE ROOT

0 EPIDERMIS 0 EXODERMIS 0 ROOT CAP

Observed expression pattern:

Tl Mature expression: Expression was detected exclusively in the root; specifically in the outer layers of root tissue, including the epidermis and exodermis.

Selection Criteria: microarray data suggest root-specific expression of the mRNA downstream of this promoter element.

GenBank: AT3G16450 similar to SP|Q9SAV1 Myrosinase binding protein-like Atlg52030

{Arabidopsis thaliana}; contains Pfam profile: PF01419 jacalin-like lectin domain

protein_id NP_188266.1

PFAM Jacalin;

Source Promoter Organism: Arabidopsis thaliana

Vector: Binary Direct Fusion EGFP

Marker Type: EGFP

Generation Screened: Tl Mature

Promoter utility

Trait Area: Plant growth and development, Water Use Efficiency, Nutrient Use Efficiency, Pathogen Sub-trait Area: Root architecture, Water Uptake, Nutrient Uptake

Utility: Among other uses, this promoter sequence could be useful to engineer pathways to modulate root growth and the uptake of substances from the soil, including, but not limited to, water, nitrogen, phosphorous, and other minerals. It could also be used to engineer traits that minimize pathogen invasion, including microbial and nematode infections. Analysis of Promoter PD3407 activity

Promoter Expression Report PD3407 (SEQ ID NO: 19) |

Organism Evaluated: Oryza sativa

Construct: PD3407

SR/OS Line: OS00704

Promoter candidate I.D: 57384177

Events expressing: 01, 02, 03, 06, 07, 10, 13, 14, 17, 21

Spatial expression summary:

TO Seedling

Events Screened: n = 10 Events Expressing: n = 7 (01-03, 06, 07, 10, 13)

ROOT

□^■CORTEX □ ENDODERMIS □ EPIDERMIS □ EXODERMIS □ LATERAL ROOT 0 NOT-SPECIFIC □ ROOT CAP AVASCULAR

TO Mature

Events Screened: n = 7 Events Expressing: n = 7 (01-03, 06, 07, 10, 13)

ROOT

0 CORTEX 0 ENDODERMIS □ EPIDERMIS □ EXODERMIS □ LATERAL ROOT

□ NOT-SPECIFIC □ ROOT CAP A VASCULAR

Observed expression pattern:

TO Seedling: GFP expression was detected in root tissues only.

TO Mature expression: GFP expression was detected in the cortical fiber cells, the endodermis, and the vasculature of the root.

Selection Criteria: Putative homolog of Arabidopsis gene AT3G09925, which gave rise to a promoter that expressed specifically in the roots in Arabidopsis

Gene: OS01G07060

cDNA LD: 6798740

GenBank: Ole e I family protein

Source Promoter Organism:

Vector: CRS830 Binary DF EGFP

Marker Type: EGFP

Generation Screened: TO Seedling and TO Mature

Promoter utility

Trait Area: Water Use Efficiency, Nutrient Use Efficiency

Sub-trait Area: Enhanced water uptake, Enhanced nitrogen uptake

Utility: Among other uses, this promoter sequence could be useful to improve: the growth and architecture of roots, the strength of the root system, and the transport of water and nutrients into the above ground portion of the plant for enhanced biomass. Analysis of Promoter PD3389 activity

Table 1. TO Seedling Expression Organs/Tissues screened

Events Screened: n = 16 Events Expressing : n = 3 (01, 05,13)

Organs

Root

0 CORTEX 0 EPIDERMIS 0 ROOT CAP

Table 2. TO Mature Plant Expression Organs/Tissues screened

Events Screened: n = 4 Events Expressing: n = 2 (05,13)

Organs

Root

0 NOT-SPECIFIC

Promoter utility

Trait Area: Salt tolerance, Drought Tolerance, Nutrient Use Efficiency, Nutrient

Utilization

Sub-trait Area: Salt tolerance, Drought tolerance, Phosphate and Nitrate Use Efficiency, Phosphate and Nitrate Utilization

Utility: Among other uses, this promoter sequence could be useful to improve: the biomass of the plants under normal and stressful conditions through the overexpression of trait- specific transgenes.

Construct: PD3389

SR OS Line: OS00605

Promoter candidate I.D: 58350521

cDNA I.D: 41681782

Events expressing: 01, 05, 13

Analysis of Promoter PD3812 activity

Promoter Expression Report PD3812 (SEQ ID NO:44)

Organism Evaluated: Oryza sativa

Construct: PD3812

SR/OS Line: OS00867

Promoter candidate LP: 89744767

Events expressing: 01,02, 04-09

Spatial expression summary:

TO Seedling

Events Screened: n = 9 Events Expressing: n = 8 (01,02, 04-09)

LEAF

0 EPIDERMIS 0 FIBER CELLS 0 FLAG LEAF 0 GUARD CELL

0 LEAF BLADE DLEAF SHEATH □ MARGIN 0MESOPHYLL DNOT-SPECIFIC

□ PETIOLE □ PRIMORDIA □ STIPULE 0 STOMATA □ TRICHOME

0 VASCULATURE

ROOT

0 CORTEX DENDODERMIS 0 EPIDERMIS □ EXODERMIS □ LATERAL ROOT

□ NOT-SPECIFIC 0 ROOT CAP AVASCULAR

TO Mature

Events Screened: n = 7 Events Expressing: n = 7 (02, 04-09)

LEAF

0 EPIDERMIS 0 FIBER CELLS 0 FLAG LEAF 0 GUARD CELL

0 LEAF BLADE □ LEAF SHEATH □ MARGIN 0 MESOPHYLL

□ NOT-SPECIFIC □ PETIOLE □ PRIMORDIA □ SITIPULE 0 STOMATA

□ TRICHOME 0 VASCULATURE

SPIKELET

0 ALEURONE LAYER 0 ANTHER 0 CARPEL DEMBRYO □ ENDOSPERM 0 FILAMENT 0 LEMMA □ NOT-SPECIFIC □ OVULE □ PALEA □ PEDICEL

□ POLLEN □ SEED 0 STIGMA

PANICLE

□ NOT-SPECIFIC □ OVARY 0 PEDUNCLE 0 PRIMARY BRANCH□ RACHILLA 0 RACHIS 0 SPIKELET

ROOT

0 CORTEX DENDODERMIS 0 EPIDERMIS □ EXODERMIS□ LATERAL ROOT

□ NOT-SPECIFIC 0 ROOT CAP 0 VASCULAR

MAIN CULM

0 BUNDLE SHEATH 0 ENDODERMIS 0 EPIDERMIS □ INTERNODE

□ LIGULE □ NODE □ NOT-SPECIFIC □ PERICYCLE DPHLOEM

□ SCLERENCHYMA LAYER 0 VASCULATURE □ XYLEM Observation expression pattern:

TO Seedling: Strong expression in all tissues analyzed

TO Mature: Strong expression in all tissues analyzed

Selection Criteria: Ubiquitin promoter homolog from Sorghum

Gene: Sorghum annot ID: 7953526

cDNA LD: 88923100

GenBank: pfam: Ubiquitin; go function: protein degradation;

Source Promoter Organism: Sorghum bicolor

Vector: NB4_Kan

Marker Type: EGFP

Generation Screened: TO Seedling and TO Mature

Promoter utility

Trait Area: Salt tolerance, Water Use Efficiency, Nutrient Use Efficiency, Nutrient Utilization, Increased Biomass, BioConfmement

Sub-trait Area: Salt tolerance, Drought tolerance, Phosphate and Nitrate Use Efficiency, Phosphate and Nitrate Utilization, Plant Architecture, Enhanced Photosynthesis, Cell-wall composition and conversion, Male sterility, Female sterility, Total sterility

Utility: Among other uses, this promoter sequence could be useful to improve: the biomass of the plants under normal and stressful conditions through the overexpression of transgenes that improve water use, nutrient use, alter composition, alter plant architecture, disrupt reproductive biology, and improve the carbon-nitrogen balance.

Notes: Contains a putative cis-acting heat stress response element aaAAAATTTc (ref: Plant Care database: http at bioinformatics.psb.ugent.be/webtools/plantcare/html/).

qPvT-PCR results suggest that this promoter element is not induced to a higher level of

expression by heat-shock at 4 hrs or 24 hrs at 42°C relative to controls grown at 28°C.

Analysis of Promoter PD3800 activity

Promoter Expression Report PD3800 (SEP ID NO:2)

Organism Evaluated: Panicum virgatum

Construct: PD3800

SR/OS Line: PV00323

Promoter candidate I.D: 75273274

Events expressing:

Spatial expression summary:

TO Seedling

Events Screened: n = 15 Events Expressing: n = 0

TO Mature

Events Screened: n = 11 Events Expressing: n = 1 (11)

MERISTEM

0 REPRODUCTIVE MERISTEM Observed expression pattern:

TO Seedling: No expression detected.

TO Mature expression: expression was detected in a circular pattern at the base of the panicle branch meristem.

Selection Criteria: Ortholog of FZP

Gene: Sorghum annot ID: 6086826

cDNA LD: 71605027

GenBank: PFAM AP2; Herpes_gp2;

Source Promoter Organism: Sorghum bicolor

Vector: NB4_Kan

Marker Type: EGFP

Generation Screened: TO Seedling and TO Mature

Promoter utility

Trait Area: BioConfmement

Sub-trait Area: Total sterility

Utility: Among other uses, this promoter sequence could be useful to engineer sterility through the expression of genes that regulate floral development. Reduced fertility may also lead to increased biomass, increased sugar content and inhibit ergot infection in sorghum.

Analysis of Promoter PD3796 activity

Promoter Expression Report PD3796 (SEP ID NO: 1) |Γ ^~

Organism Evaluated: Panicum virgatum

Construct: PD3796

SR/OS Line: PV00327

Promoter candidate LP: 75273275

Events expressing: 04,07

Spatial expression summary:

TO Seedling

Events Screened: n = 15 Events Expressing: n = 0

TO Mature

Events Screened: n = 6 Events Expressing: n = 2 (04,07)

MERISTEM

0 REPRODUCTIVE MERISTEM 0 SPIKELET MERISTEM 0 FLORET MERISTEM

Observed expression pattern:

TO Seedling: No expression detected.

TO Mature expression: Expression observed strongly in the emerging panicle meristem, the spikelet meristem, and the floret meristem

Selection Criteria: Ortholog of LFY

Gene: Sorghum annot ID: 6007109

cDNA LD: 36980280

GenBank: PFAM FLO LFY; LFY floral meristem identity control protein Source Promoter Organism: Sorghum bicolor

Vector: NB4_Kan

Marker Type: EGFP

Generation Screened: TO Seedling and TO Mature

Promoter utility

Trait Area: BioConfmement

Sub-trait Area: Male sterility, Female sterility, Total sterility

Utility: Among other uses, this promoter sequence could be useful to engineer sterility through the expression of genes that regulate floral development. Reduced fertility may also lead to increased biomass, increased sugar content and inhibit ergot infection in sorghum.

Analysis of Promoter PD3777 activity

Promoter Expression Report PD3777 (SEQ ID NO:22) |^{~ ~}

Organism Evaluated: Oryza sativa

Construct: PD3777

SR/OS Line: OS00865

Promoter candidate LP: 89744768

Events expressing: 2-7

Spatial expression summary:

TO Seedling

Events Screened: n = 7 Events Expressing: n = 6 (02-07)

LEAF

0 EPIDERMIS 0 FIBER CELLS 0 FLAG LEAF □ GUARD CELL 0 LEAF BLADE

□ LEAF SHEATH □ MARGIN □ MESOPHYLL □ NOT-SPECIFIC □ PETIOLE

□ PRIMORDIA □ STIPULE 0 STOMATA □ TRICHOME 0 VASCULATURE

ROOT

0 CORTEX 0 ENDODERMIS 0 EPIDERMIS 0 EXODERMIS 0 LATERAL ROOT

□ NOT-SPECIFIC 0 ROOT CAP 0 VASCULAR

TO Mature

Events Screened: n = 4 Events Expressing: n = 4 (03-05, 07)

LEAF

0 EPIDERMIS □ FIBER CELLS 0 FLAG LEAF 0 GUARD CELL 0 LEAF BLADE

□ LEAF SHEATH □ MARGIN □ MESOPHYLL □ NOT-SPECIFIC DPETIOLE

□ PRIMORDIA □ STIPULE 0 STOMATA 0 TRICHOME □ VASCULATURE

SPIKELET

□ ALEURONE LAYER 0 ANTHER 0 CARPEL □ EMBRYO □ ENDOSPERM

0 FILAMENT 0 LEMMA □ NOT-SPECIFIC □ OVULE □ PALEA□ PEDICEL

0 POLLEN □ SEED 0 STIGMA

PANICLE

□ NOT-SPECIFIC □ OVARY □ PEDUNCLE □ PRIMARY BRANCH □ RACHILLA □ RACHIS 0 SPIKELET

ROOT

□ CORTEX 0 ENDODERMIS 0 EPIDERMIX □ EXODERMIS □ LATERAL ROOT

□ NOT-SPECIFIC 0 ROOT CAP A VASCULAR

MAIN CULM

0 BUNDLE SHEATH 0 ENDODERMIS 0 EPIDERMIS 0 INTERNODE 0 LIGULE

□ NODE □ NOT-SPECIFIC □ PERICYCLE □ PHLOEM 0 SCLERENCHYMA LAYER

□ VASCULATURE □ XYLEM

Observed expression pattern:

TO Seedling: Expression observed strongly throughout all tissues of the seedling.

TO Mature expression: Expression observed strongly throughout all tissues of the mature plant.

Selection Criteria: Deletion of previously described promoter PD3580

Gene: Sorghum annot ID: 8744325

cDNA LD: 88993479

GenBank: pfam: Ubiquitin; go function: protein degradation;

Source Promoter Organism: Sorghum bicolor

Vector: NB4_Kan

Marker Type: EGFP

Generation Screened: TO Seedling and TO Mature

Promoter utility

Trait Area: Salt tolerance, Water Use Efficiency, Nutrient Use Efficiency, Nutrient Utilization, Increased Biomass, BioConfmement

Sub-trait Area: Salt tolerance, Drought tolerance, Phosphate and Nitrate Use Efficiency, Phosphate and Nitrate Utilization, Plant Architecture, Enhanced Photosynthesis, Cell- wall composition and conversion, Male sterility, Female sterility, Total sterility

Utility: Among other uses, this promoter sequence could be useful to improve: the biomass of the plants under normal and stressful conditions through the overexpression of transgenes that improve water use, nutrient use, alter composition, alter plant architecture, disrupt reproductive biology, and improve the carbon-nitrogen balance.

Notes: Does not contain a putative HSE (ref: Plant Care database: http at

bioinformatics.psb.ugent.be/webtools/plantcare/html/).

qRT-PCR results suggest that this promoter element is not induced to a higher level of expression by heat-shock at 4 hrs or 24 hrs at 42°C relative to controls grown at 28°C.

[00274] For promoter PD3423 (SEQ ID NO:33), expression in Arabidopsis was characterized as above ground, vegetative. For promoter PD3801 (SEQ ID NO:43),

expression in Panicum virgatum was stem-specific.

[00275] The following Table summarizes the results of the GFP assays for

PD3395, PD3623, PD3716, PD3428, PD3343, P02916, PD3701, PD3304, PD3684,

PD3695, PD2946, PD3408, PD3607, PD3583, PD3256, PD3201, PD3490, PD3505 (P02916), PD3324, PD2195, PD3548, YP2959, PD3492, PD2998, PD2695, PD3689, and PD3092.

Promoter SEQ ID Expression GFP Expression description Induction Useful for traits ID NO: organism description

PD3395 12 Oryza sativa MERISTEM Biomass

PD3623 16 Oryza sativa EXPRESSION INDUCED BY DROUGHT IN STEM DROUGHT Drought

EPIDERMIS

PD3716 15 Oryza sativa SPIKELET Biomass, yield

PD3428 1 1 Arabidopsis EMBRYO,OVULE,MATURE ROOT, LEAF, STEM, Biomass, yield

thaliana - FLOWER, SILIQUE

WS

PD3343 23 Oryza sativa TILLER,MERISTEM,ROOT,LEAF,PANICLE,SPIK Biomass, yield

ELET,MAIN CULM

P02916 31 Oryza sativa PANICLE,SPIKELET,TILLER,LEAF,ROOT,MAIN Nitrogen use efficiency, drought,

CULM,MERISTEM biomass

PD3701 21 Oryza sativa ROOT,LEAF,MERISTEM,SPIKELET biomass, yield PD3304 29 Oryza sativa MAIN CULM,LEAF,ROOT Acute drought, Chronic drought

PD3684 41 Oryza sativa PANICLE,TILLER,LEAF,MAIN CULM,SPIKELET Biomass, yield

PD3695 30 Oryza sativa SPIKELET,LEAF,MAIN CULM,ROOT Plant size, Low nitrogen tolerance,

Nitrogen use efficiency, Nitrogen utilization, Biomass, Disease resistance

PD2946 25 Arabidopsis SILIQUE,FLOWER COLD,HEAT, Drought, biomass, cold, heat, yield thaliana - DROUGHT

WS

PD3408 8 Oryza sativa MAIN CULM, SPIKELET, ROOT, PANICLE, Photosynthetic efficiency, C/N

LEAF, MERISTEM, TILLER Partitioning, Amino acids,

Carbohydrate,

Protein, Total oil, Total composition, Sterility, Shade, Biomass, Sodium chloride, yield

Panicum ROOT Drought, biomass virgatum

Oryza sativa TILLER,PANICLE,ROOT,MERISTEM,LEAF,SPIK Stay Green, Plant size, Nitrogen use

ELET,MAIN CULM efficiency, Nitrogen utilization, biomass

Photosynthetic efficiency, C/N Partitioning, Chronic drought, Growth rate, Plant architecture, , yield

Early flowering, Sterility, Late flowering, Phosphate use efficiency, Shade, Seed, Biomass, Chronic heat, Sodium chloride, Disease resistance

Oryza sativa LEAF,MAIN CULM, SPIKELET,TILLER Plant size, total composition, Growth rate, Biomass, Carbohydrate, yield

Oryza sativa ROOT Nitrogen use efficiency, drought, biomass

Oryza sativa ROOT Nitrogen use efficiency, drought, biomass

Oryza sativa MAIN Nitrogen use efficiency, drought,

CULM,TILLER,MERISTEM,PANICLE,SPIKELET, biomass, yield LEAF,ROOT

Arabidopsis FLOWER,LEAF,MATURE ROOT, OVULE, DROUGHT Drought, biomass, yield thaliana - SILIQUE, STEM

WS

Arabidopsis HYPOCOTYL, COTYLEDONS, AND ROOT OF Biomass, yield thaliana - SEEDLNG. EXPRESSED IN LEAF, STEM AND

WS FLOWERS IN MATURE.

Oryza sativa LEAF,SPIKELET,ROOT Biomass, yield

Arabidopsis SILIQUE,MATURE ROOT Stay Green, yield thaliana - WS

Oryza sativa LEAF,MERISTEM,ROOT,MAIN Stay Green, Early Maturity, Plant

CULM,TILLER,PANICLE,SPIKELET size, Low nitrogen tolerance,

Nitrogen use efficiency, yield Nitrogen utilization, Photosynthetic efficiency, biomass C/N Partitioning, Cold growth, Freezing tolerance, Chronic drought, Growth rate, Plant architecture, Early flowering,

Sterility,

Late flowering, Phosphate use efficiency, Shade, Biomass, Chronic heat, Aluminum, Sodium chloride, Disease resistance

Arabidopsis LEAF ABA,HEAT,LI Biomass, drought, heat thaliana - GHT,DROUG

WS HT

Arabidopsis FLOWER, SILIQUE, STEM NITROGEN Nitrogen use efficiency, yield thaliana - WS

Oryza sativa SPIKELET,LEAF,ROOT,PANICLE,MAIN Nitrogen use efficiency, drought,

CULM,TILLER biomass, yield

PD3092 10 Arabidopsis VEGETATIVE NITROGEN Nitrogen use efficiency, biomass, thaliana - yield

WS

[00276] Derivatives of PD3796, PD3800, PD3579, PD2695, YP2959, PD3256,

PD3548, PD3408, PD3492, PD3092, PD3428, PD3395, PD3583, PD3607, PD3716, PD3623, PD3684, PD3689, PD3407, PD3490, PD3701, PD3777, PD3343, PD3201, PD2946, PD2998, PD3389, PD3324, PD3304, PD3695, P02916, PD3505, PD3423, PD3558, PD3536, PD3485, PD3333, PD3422, PD3540, PD3421, PD3684, PD3492, PD3801, or PD3579 are generated by introducing mutations into the nucleotide sequence set forth in SEQ ID NO: l-SEQ ID NO:44 as disclosed in U.S. Pat. No. 6,747,189, incorporated herein by reference. A plurality of mutagenized DNA segments derived from PD3796, PD3800, PD3579, PD2695, YP2959, PD3256, PD3548, PD3408, PD3492, PD3092, PD3428, PD3395, PD3583, PD3607, PD3716, PD3623, PD3684, PD3689, PD3407, PD3490, PD3701, PD3777, PD3343, PD3201, PD2946, PD2998, PD3389, PD3324, PD3304, PD3695, P02916, PD3505, PD3423, PD3558, PD3536, PD3485, PD3333, PD3422, PD3540, PD3421, PD3684, PD3492, PD3801, or PD3579, including derivatives with nucleotides deletions and modifications are generated and inserted into a plant transformation vector operably linked to a GFP marker gene. Each of the plant transformation vectors are prepared essentially as described above, except that the full length promoter is replaced by a mutagenized derivative. Plants (e.g., rice, switchgrass, or Arabidopsis) are transformed with each of the plant transformation vectors and analyzed for expression of the GFP marker to identify those mutagenized derivatives having promoter activity.

[00277] Fragments of PD3796, PD3800, PD3579, PD2695, YP2959, PD3256,

PD3548, PD3408, PD3492, PD3092, PD3428, PD3395, PD3583, PD3607, PD3716, PD3623, PD3684, PD3689, PD3407, PD3490, PD3701, PD3777, PD3343, PD3201, PD2946, PD2998, PD3389, PD3324, PD3304, PD3695, P02916, PD3505, PD3423, PD3558, PD3536, PD3485, PD3333, PD3422, PD3540, PD3421, PD3684, PD3492, PD3801, or PD3579 are isolated by designing primers to clone fragments of the promoters set forth in SEQ ID NO: l-44. A plurality of cloned fragments of PD3796, PD3800, PD3579, PD2695, YP2959, PD3256, PD3548, PD3408, PD3492, PD3092, PD3428, PD3395, PD3583, PD3607, PD3716, PD3623, PD3684, PD3689, PD3407, PD3490, PD3701, PD3777, PD3343, PD3201, PD2946, PD2998, PD3389, PD3324, PD3304, PD3695, P02916, PD3505, PD3423, PD3558, PD3536, PD3485, PD3333, PD3422, PD3540, PD3421, PD3684, PD3492, PD3801, or PD3579 ranging in size from 50 nucleotide up to the full length sequence set forth in SEQ ID NO: 1-44 are obtained using PCR. For example, a fragment of PD3796 of about 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1475 or 1490 nucleotides in length from various parts of PD3796 (SEQ ID NO: l) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3796 can include one or more of a TATABOX4, GAREAT, and CARGCW8GAT motif

[00278] A fragment of PD3800 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1475 or 1490 nucleotides in length from various parts of PD3800 (SEQ ID NO:2) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3800 can include one or more of a CARGNCAT and one or more of a CARGCW8GAT motif.

[00279] A fragment of PD3560 of about 50, 100, 150, 200, 250, 275, 300, 350,

375, or 390 nucleotides in length from various parts of PD3560 (SEQ ID NO:3) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3560 can include one or more of an AREl, SBOXATRBCS, TE2F2NTPCNA, GADOWNAT, ACGTABREMOTIFA20SEM, and TATABOX motif.

[00280] A fragment of PD3561 of about 50, 100, 150, 200, 250, 275, 300, 350,

375, 390, 400, or 410 nucleotides in length from various parts of PD3561 (SEQ ID NO:4) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3561 can include one or more of a

ROOTMOTIFTAPOX1, RYREPE AT VFLEB4 , and TATABOX motif.

[00281] A fragment of YP2959 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 990, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, or 1750 nucleotides in length from various parts of YP2959 (SEQ ID NO:5) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of YP2959 can include one or more of an ATHB1ATCONSENSUS, GAREAT, P1BS, GARE20SREP 1 , ABRE, and TATC-box motif.

[00282] A fragment of PD3256 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 484, 500, 550, 575, or 590 nucleotides in length from various parts of PD3256 (SEQ ID NO: 6) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3256 can include one or more of a Phosphate- starvation induced binding site and a GAREAT motif.

[00283] A fragment of PD3548 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, or 475 nucleotides in length from various parts of PD3548 (SEQ ID NO:7) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3548 can include one or more of a P1BS and GAREAT motif.

[00284] A fragment of PD3408 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 990, 1000, 1050, 1100, 1150, 1200, 1250, or 1275 nucleotides in length from various parts of PD3408 (SEQ ID NO:8) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3408 can include one or more of a TATABOX4, TCA-element, and cytokinin-inducible\element motif.

[00285] A fragment of PD3492 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 990, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, or 1375 nucleotides in length from various parts of PD3492 (SEQ ID NO: 9) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3492 can include one or more of a TATABOX4 and an ATHB6COREAT motif.

[00286] A fragment of PD3092 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, or 675 nucleotides in length from various parts of PD3092 (SEQ ID NO: 10) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3092 can include one or more of an

TCAlMotif, TATABOX motif, and ATCT motif.

[00287] A fragment of PD3428 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 990, 1000, 1050, 1100, 1150, or 1175 nucleotides in length from various parts of PD3428 (SEQ ID NO: l 1) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3428 can include one or more of a GATABOX and

CARGCW8GAT motif.

[00288] A fragment of PD3395 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, or 925 nucleotides in length from various parts of PD3395 (SEQ ID NO: 12) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3395 can include one or more of a TATABOX4, UP2ATMSD, and ELI-box3 motif.

[00289] A fragment of PD3583 of about 50, 100, 150, 200, 250, 300, 350, 400, or 425 nucleotides in length from various parts of PD3583 (SEQ ID NO: 13) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3583 can include one or more of a TATA BOX,

CTRMCAMV35S, ACE, and CACGTGMOTIF motif.

[00290] A fragment of PD3607 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, or 675 nucleotides in length from various parts of PD3607 (SEQ ID NO: 14) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3607 can include one or more of an

ACGTABREMOTIFAOSOSEM, ABREL ATERD 1 , and ABRE motif.

[00291] A fragment of PD3716 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, or 990 nucleotides in length from various parts of PD3716 (SEQ ID NO: 15) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3716 can include one or more of a TATABOX4, UP2ATMSD, TC richVepeats, and

GAGAGMGSA1 motif.

[00292] A fragment of PD3623 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, or 825 nucleotides in length from various parts of PD3623 (SEQ ID NO: 16) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3623 can include one or more of a PRECONSCRHSP70A, TATABOX, ABRE, and HSE motif.

[00293] A fragment of PD3684 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, or 750 nucleotides in length from various parts of PD3684 (SEQ ID NO: 17) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3684 can include one or more of a GT1MOTIFPSRBCS, TATABOX, and RYREPEATVFLEB4 motif.

[00294] A fragment of PD3689 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 990, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, or 1675 nucleotides in length from various parts of PD3689 (SEQ ID NO: 18) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3689 can include one or more of an UPRMOTIFIIAT, PRECONSCRHSP70A, and GCC\Box motif.

[00295] A fragment of PD3407 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, or 475 nucleotides in length from various parts of PD3407 (SEQ ID NO: 19) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3407 can include one or more of a TATABOX4,

ATHB2ATCONSENSUS, and SORLREP2AT motif.

[00296] A fragment of PD3490 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, or 775 nucleotides in length from various parts of PD3490 (SEQ ID NO:20) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3490 can include one or more of a PRECONSCRHSP70A, UPRMOTIFIIAT, ABRE, and MBS motif.

[00297] A fragment of PD3701 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 1000, 1050 or 1075 nucleotides in length from various parts of PD3701 (SEQ ID NO:21) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3701 can include one or more of a MYB PLANT motif.

[00298] A fragment of PD3777 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1475 or 1490 nucleotides in length from various parts of PD3777 (SEQ ID NO:22) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3777 can include one or more of a PRECONSCRHSP70A, ACIIPVPAL2, and CAAT-box motif.

[00299] A fragment of PD3343 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, or 850 nucleotides in length from various parts of PD3343 (SEQ ID NO:23) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3343 can include one or more of a TATABOX4 and ABREATCONSENSUS motif.

[00300] A fragment of PD3201 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, or 990 nucleotides in length from various parts of PD3201 (SEQ ID NO:24) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3201 can include one or more of a TATABOX4, TATC-box, P1BS, and

OSE2ROOTNODULE motif.

[00301] A fragment of PD2946 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 990, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, or 1775 nucleotides in length from various parts of PD2946 (SEQ ID NO:25) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD2946 can include one or more of a TATABOX2,

ABREATCONSENSUS, IBOX, ABREL ATERD 1 , and MBS motif

[00302] A fragment of PD2998 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, or 850 nucleotides in length from various parts of PD2998 (SEQ ID NO:26) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD2998 can include one or more of a MYB1AT, TATABOX, and MBS motif.

[00303] A fragment of PD3389 of about 50, 100, 150, 200, 250, 300, 350, or

375 nucleotides in length from various parts of PD3389 (SEQ ID NO:27) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3389 can include one or more of a TATABOX5, CARGCW8GAT, E2FCONSENSUS, LEAFYATAG, and ROOTMOTIFTAPOX1 motif.

[00304] A fragment of PD3324 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, or 475 nucleotides in length from various parts of PD3324 (SEQ ID NO:28) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3324 can include one or more of an ABRELATERDl motif.

[00305] A fragment of PD3304 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 990, 1000, 1050, 1100, 1150, or 1175 nucleotides in length from various parts of PD3304 (SEQ ID NO:29) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3304 can include one or more of an ABRELATERDl motif.

[00306] A fragment of PD3695 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, or 750 nucleotides in length from various parts of PD3695 (SEQ ID NO: 30) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3695 can include one or more of a TATABOX motif. [00307] A fragment of P02916 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 990, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, 2100, 2150, 2200, 2250, 2300, 2350, 2400, 2450, 2500, 2550, 2600, 2650, 2700, 2750, 2800, 2850, 2900, 2950, or 3000 nucleotides in length from various parts of P02916 (SEQ ID NO:31) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of P02916 can include one or more of an UP2ATMSD and TATABOX motif. For example, a fragment of P02916 can have the nucleotide sequence set forth in SEQ ID NO:32.

[00308] A fragment of PD3423 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, or 925 nucleotides in length from various parts of PD3423 (SEQ ID NO:33) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3423 can include one or more of a TATAbox4, RGATAOS, 3-AFl\binding\site light responsive element, or P-box gibberellin-responsive element motif.

[00309] A fragment of PD3558 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, or 475 nucleotides in length from various parts of PD3558 (SEQ ID NO:34) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene.

[00310] A fragment of PD3536 of about 50, 100, 150, 200, 250, 300, or 325 nucleotides in length from various parts of PD3536 (SEQ ID NO:35) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene.

[00311] A fragment of PD3485 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, or 975 nucleotides in length from various parts of PD3485 (SEQ ID NO:36) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene.

[00312] A fragment of PD3333 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 825, or 840 nucleotides in length from various parts of PD3423 (SEQ ID NO:37) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3423 can include one or more of a TATAbox motif.

[00313] A fragment of PD3422 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, or 925 nucleotides in length from various parts of PD3422 (SEQ ID NO:38) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3422 can include one or more of a TATAbox and CAAT-box motif.

[00314] A fragment of PD3540 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, or 475 nucleotides in length from various parts of PD3540 (SEQ ID NO:39) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene.

[00315] A fragment of PD3421 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, or 825 nucleotides in length from various parts of PD3421 (SEQ ID NO:40) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3421 can include one or more of a TATAbox and enhancer motif.

[00316] A fragment of PD3684 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 725, or 750 nucleotides in length from various parts of PD3684 (SEQ ID NO:41) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene.

[00317] A fragment of PD3492 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, or 1375 nucleotides in length from various parts of PD3492 (SEQ ID NO:42) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene.

[00318] A fragment of PD3801 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, or 650 nucleotides in length from various parts of PD3801 (SEQ ID NO:43) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene.

[00319] A fragment of PD3812 of about 50, 100, 150, 200, 250, 300, 350, 400,

450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 975, 990, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, or 1475 nucleotides in length from various parts of PD3812 (SEQ ID NO:44) are obtained and inserted into a plant transformation vector operably linked to a GFP marker gene. Such fragments of PD3812 can include one or more of a UPRMOTIFIIAT, CACGCAATGMGH3, and SP8BFIBSP8AIB motif.

[00320] Each of the plant transformation vectors are prepared essentially as described above except that the full length sequence is replaced by a fragment containing one or more of the motifs described herein. Arabidopsis plants are transformed with each of the plant transformation vectors and analyzed for expression of the GFP marker to identify those fragments having promoter activity.

[00321] The invention being thus described, it will be apparent to one of ordinary skill in the art that various modifications of the materials and methods for practicing the document can be made. Such modifications are to be considered within the scope of the document as defined by the following claims.

[00322] Each of the references from the patent and periodical literature cited herein is hereby expressly incorporated in its entirety by such citation.

Claims

WHAT IS CLAIMED IS:

1. An isolated nucleic acid comprising a regulatory region having 90 percent or greater sequence identity to any one of the nucleotide sequences set forth in SEQ ID NOs. 1-11 or 13-44, or a fragment of SEQ ID NOs: 1-11 or 13-44, wherein said regulatory region directs transcription of an operably linked heterologous polynucleotide.

2. The nucleic acid of claim 1, wherein said sequence identity is 95 percent or greater.

3. The nucleic acid of claim 1, wherein said sequence identity is 98 percent or greater.

4. The isolated nucleic acid of claim 1, wherein said nucleic acid contains one or more motifs selected from the group consisting of an ABRE motif, ABREATCONSENSUS motif, ABRELATERD 1 motif, ACE motif, ACGTABREMOTIFAOSOSEM motif, ACIIPVPAL2 motif, 3-AFl\binding\site light responsive element motif, ATCT motif motif, ATHB2ATCONSENSUS motif, ATHB6COREAT motif, CAAT-box motif, CACGTGMOTIF motif, CACGCAATGMGH3 motif, CARGCW8GAT motif,

CARGNCAT motif, CTRMC AMV35 S motif, E2FCONSENSUS motif, ELI-box3 motif, enhancer motif, GAGAGMGSA1 motif, GARE20SREP1 motif, GAREAT motif, GATABOX motif, GCC\Box motif, GTIMOTIFPSRBCS motif, HSE motif, IBOX motif, LEAFYATAG motif, MBS motif, MYBPLANT motif, MYB1AT motif,

OSE2ROOTNODULE motif, P1BS motif, P-box gibberellin-responsive element motif, Phosphate-starvation induced binding site motif, PRECONSCRHSP70A motif,

RGATAOS motif, ROOTMOTIFTAPOX1 motif, RYREPEATVFLEB4 motif,

SORLREP2AT motif, SP8BFIBSP8AIB motif, TATABOX motif, TATABOX2 motif, TATABOX4 motif, TATABOX5 motif, TATAbox motif, TATC-box motif, TCAlMotif motif, TCA-Element motif, TC richVepeats motif, UP1ATMSD motif, UP2ATMSD motif, and UPRMOTIFIIAT motif.

5. The isolated nucleic acid of claim 1, wherein said regulatory region consists of any one of the nucleotide sequences set forth in SEQ ID NOs. 1 - 11 or 13 - 44.

6. A vector construct comprising :

(a) a first nucleic acid according to claim 1 ; and

(b) a second nucleic acid to be transcribed, wherein said first and second nucleic acids are heterologous to each other and are operably linked.

7. The vector construct according to claim 6, wherein said first nucleic acid consists of a nucleic acid sequence set forth in any one of SEQ ID NOs: 1 - 11 or 13 - 44.

8. The vector according to claim 6 or claim 7, wherein said second nucleic acid comprises a nucleic acid sequence encoding a polypeptide.

9. The vector according to claim 8, wherein said second nucleic acid is operably linked to said first nucleic acid in sense orientation.

10. The vector according to claim 9, wherein said second nucleic acid is transcribed into an R A molecule that expresses the polypeptide encoded by said second nucleic acid.

11. The vector according to claim 6 or claim 7, wherein said second nucleic acid is operably linked to said first nucleic acid in antisense orientation.

12. The vector according to claim 11, wherein said second nucleic acid is transcribed into an antisense RNA molecule.

13. The vector according to claim 6 or claim 7, wherein said second nucleic acid is transcribed into an interfering RNA against an endogenous gene.

14. A plant or plant cell transformed with:

(a) the nucleic acid according to claim 1 that is operably linked to a heterologous polynucleotide, or

(b) the vector construct according to claim 6.

15. The plant or plant cell of claim 14, wherein said first nucleic acid consists of a nucleotide sequence set forth in any one of SEQ ID NOs: 1 - 11 or 13 - 44.

16. A plant or plant cell transformed with the vector construct according to any one of claims 6 - 13.

17. A method of directing transcription by combining, in an environment suitable for transcription:

(a) a first nucleic acid according to claim 1 ; and

(b) a second nucleic acid to be transcribed;

wherein said first and second nucleic acids are heterologous to each other and operably linked.

18. The method of claim 17, wherein said first nucleic acid molecule consists of a sequence according to any one of SEQ ID NOs: 1 - 11 or 13 - 44.

19. The method of claim 17 or 18, wherein said operably linked first and second nucleic acids are inserted into a plant cell and said plant cell is regenerated into a plant.

20. A transgenic plant comprising the vector according to claim 6.

21. A transgenic plant according to claim 20, wherein said second nucleic acid encodes a polypeptide of agronomic interest.

22. A seed of the plant according to claim 20 or 21.

23. A method of expressing an exogenous coding region in a plant comprising:

(a) transforming a plant cell with the vector of claim 8;

(b) regenerating a stably transformed plant from the transformed plant cell of step (a); and

(c) selecting plants containing a transformed plant cell,

wherein expression of the vector results in production of a polypeptide encoded by said second nucleic acid.

24. A method of altering the expression of a gene in a plant comprising:

(a) transforming a plant cell with a nucleic acid according to claim 1 that is operably linked to a heterologous polynucleotide, and

(b) regenerating stably transformed plants from said transformed plant cell.

25. A plant prepared according to the method of claim 23 or 24.

26. Seed from the plant according to claim 25.

27. A method of producing a transgenic plant, said method comprising:

(a) introducing into a plant cell:

(i) an isolated polynucleotide comprising a nucleic acid according to claim 1 that is operably linked to a heterologous polynucleotide, or

(ii) the vector according to claim 6; and

(b) growing a plant from said plant cell.

28. The method of claim 27, wherein said heterologous polynucleotide comprises a nucleic acid sequence encoding a polypeptide.

29. The method of claim 27, wherein said heterologous polynucleotide is operably linked to said regulatory region in the antisense orientation.

30. The method of claim 27, wherein said heterologous polynucleotide is transcribed into an interfering R A.