WO2018064058A1 - Dro1 related genes influence lateral root orientation and growth in arabidopsis and prunus species - Google Patents

Abstract

Root orientation, or angle, is an important component of root architecture and depth of the root system. We have determined that DRO1 and DRO1-related genes are present across diverse plant phyla and fall within the IGT gene family. DRO1, present in both Arabidopsis and peach, displayed root specific expression patterns. AtDRO1 is predominantly expressed in both the root vasculature and root tips in a distinct developmental pattern. Mutation of AtDRO1 led to more horizontal lateral root angles; over-expression of AtDRO1 under a constitutive promoter reduced lateral root angles and resulted in shoot phenotypes including upward leaf curling, shortened siliques, and narrow lateral branch angles. Over-expression of PpeDRO1 in plum (Prunus domestica) led to deeper rooting phenotypes. These data establish that DRO1-related genes serve a role in altering root architecture, providing a method for drought avoidance.

Description

DR01 Related Genes Influence Lateral Root Orientation and Growth

in Arabidopsis and Prunus Species

CROSS-REFERENCE TO PRIOR FILED APPLICATIONS

[0001] This application claims priority to U.S. Patent Application 15/703,434 filed Sept. 13, 2017, which claims benefit of U.S. Patent Application 62/403,033 filed on September 30, 2016, the contents of which are incorporated herein by reference in its entirety.

SEQUENCE LISTING

[0002] The Sequence Listing submitted via EFS-Web as ASCII compliant text file format (.txt) and filed on September 26, 2017, named "SequenceListing_ST25", (created on August 28, 2017, 56 KB), is incorporated herein by reference. This Sequence Listing serves as paper copy of the Sequence Listing required by 37 C.F.R. § 1 .821 (c) and the Sequence Listing in computer- readable form (CRF) required by 37 C.F.R. § 1 .821 (e). A statement under 37 C.F.R. § 1 .821 (f) is not necessary.

BACKGROUND OF THE INVENTION

Field of the Invention

[0003] This invention relates to a gene PpeDROI identified from peach and the role of

DEEPER ROOTING genes in controlling root orientation and overall depth of the root system of two economically important Prunus tree species and to new methods of manipulating root system length by overexpression of PpeDROI.

Description of the Relevant Art

[0004] Plant productivity can be greatly influenced by root architectural traits, which makes them an important target of agricultural improvement (Lopez-Arredondo et al. 2015.

F 1000 Research 4:651 ; Kong et al. 2014. Trends Biotech. 32:597-598). Roots are essential for uptake of water and nutrients, as well as stability within the soil. Changes to root architectural traits can alter access to different layers within the heterogeneous soil column, resulting in changes to nutrient and water availability or interaction with biotic factors. This is because resources such as water and nitrogen are found in deeper soil layers, while other nutrients such as phosphorous are more abundant in shallower strata (Lynch, J. P. 201 1 . Plant Physiol.

156:1041 -1049; Lynch, J. P. 2013. Ann. Bot. 1 12:347-357). Thus, alterations in root system architecture can improve access to limiting resources.

[0005] Root system architecture refers to the spatial distribution of roots within the soil. Root system architecture changes are mediated by multiple processes, including growth rates and lengths of individual roots, the rate and extent of root branching, and the orientation, or angle, of those branches. The types of roots that contribute to root system architecture can differ between plant species. Dicots typically have taproot systems that consist of an embryonic primary root and a branching network of secondary lateral roots (LR). Monocots generally have a more complex fibrous root system. The fibrous systems also have an embryonic primary root and secondary lateral roots, but their contribution is smaller (McSteen, P. 2010. Cold Spring Harb. Perspect. Biol. 2:1 -18; Smith and De Smet. 2012. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 367:1441 -1452). Instead, the majority of monocot root mass and volume comes from seed- borne seminal roots and/or shoot-borne crown roots (McSteen, supra; Smith and De Smet, supra; Hochholdinger and Zimmerman. 2008. Curr. Opin. Plant Biol. 1 1 :70-74). Many genetic and environmental factors influence root architectural traits. Work in Arabidopsis thaliana, maize, and rice has uncovered a great deal of information as to root structure, the genetic components regulating root system architecture, and the close relationship between root system architecture and the soil environment (Malekkpoor Mansoorkhani et al. 2014. Biotechnol. Genet. Eng. flei/.30:95-1 12; Wachsman et al. 2015. New Phytol. 208:26-38; Smith and De Smet, supra; Uga et al. 2015. Breed Sci. 65:1 1 1 -1 19; Giehl et al. 2014. J. Exp. Bot. 65:769-778).

[0006] Past and current root system architecture research focusing on primary and lateral root growth and branching has revealed key roles for numerous genes and gene networks, multiple hormones including auxin, cytokinins, giberellins, brassinosteroids, abscisic acid (ABA), and ethylene, and soil nutrients including nitrogen and phosphorous (Satbhai et al. 2015. J. Exp. Bot. 66:1099-1 1 12; De Smet, I. 2012. New Phytol. 193:867-873; Vermeer and Geldner. 2015. FWOOPrime Rep. 7:32; Wachsman et al., supra). In contrast, relatively little is known about the factors that regulate root growth orientation, or angle. In Arabidopsis, a role for the hormone auxin was identified in influencing lateral root growth angle (Rosquete et al. 2013. Curr. Biol. 23: 817-822). In monocots, many quantitative trait loci have been identified for deep rooting and root angle (Uga et al., supra), however few genes have been identified as regulators of these traits. Through a quantitative trait loci analysis in rice, Uga et al. identified DEEPER ROOTING 1 (DR01 ) as a regulator of root system architecture depth by modulating crown root angles (Uga et al. 2013a. Nat. Genet. 45:1097-1 102). A rice variety containing a truncated copy of DR01 exhibited shallow rooting, while another variety with a full-length copy had a deeper and narrower root system architecture. Transgenic introduction of an additional single or double copy of full length DR01 resulted in incremental increases in root system depth. Importantly, the deeper rooting in rice conferred by DR01 allowed drought avoidance, and thus increased grain yield and seed filling under drought conditions. This finding highlights the advantage for plant roots that can reach lower levels of the soil column under water-limited conditions. The ability to rapidly exploit lower soil layers is a beneficial trait in maize, as well, to optimize water capture (Lynch 2013, supra). Similarly, a recent study of tree species during a drought in Italy found deep rooting as a key trait associated with survival (Nardini et al. 2016. Plant Cell Environ. 39:618-627).

SUMMARY OF THE INVENTION

[0007] We have identified and isolated PpeDROI cDNA (SEQ ID NO:1 ) as the causative nucleic acid molecule for the deep rooting phenotype in Arabidopsis and plum and confirmed that overexpression of PpeDROI cDNA and increased production of PpeDROI result in the creation of altered root architectures such as narrow root angles in genetically altered

Arabidopsis and deep rooting in genetically altered Prunus trees (and both narrow root angles and deep rooting in transgenic Prunus) compared to the root architecture (angles and depth) in wild-type Arabidopsis and Prunus trees.

[0008] In accordance with this discovery, it is an object of the invention to provide a method to routinely control root architecture in Prunus trees by overexpression of PpeDROI cDNA (SEQ ID NO: 1 ) or a DNA sequence encoding PpeDROI (SEQ ID NO: 2) in genetically altered Prunus trees or germplasm to obtain novel root architectures such as deep rooting in genetically altered Prunus trees while still retaining normal flower and fruit development. It is another object of the invention to provide an isolated or recombinant polypeptide (SEQ ID NO: 2) encoded by PpeDROI cDNA (SEQ ID NO: 1 ).

[0009] It is an object of this invention to have an expression vector that contains a heterologous promoter operably linked to a polynucleotide that encodes PpeDROI which has the amino acid sequence of SEQ ID NO: 2. It is a further object of this invention that the polynucleotide has the DNA sequence of SEQ ID NO: 1 . It is another object of this invention to have a genetically altered cell containing this expression vector. It is yet another object of this invention that the genetically altered cell is a genetically altered Prunus plant cells and genetically altered Prunus plants generated from this genetically altered Prunus plant cell produces PpeDROI in increased amounts than wild-type Prunus plants, and that the increased amount of PpeDROI causes the genetically altered Prunus plant to have a root architecture of narrower lateral root branch angles and longer root systems compared to the lateral root branch angles and depth of root systems in the root architecture of wild-type Prunus plants. It is a further object of this invention that the genetically altered Prunus cell and the genetically altered Prunus plant can be Prunus persica (peach), Prunus domestica (plum), Prunus avium (cherry), Prunus salicina (Japanese plum) and/or Prunus armeniaca (apricot).

[0010] It is a further object of the invention to have methods of controlling root architectures in plants by generating a genetically altered plant having the expression vector described above. It is a further object that the genetically altered plant can be P. persica, P. domestica, P. avium, P. salicina, and/or P. armeniaca.

[0011] It is another object of the invention to have a method of producing a genetically altered Prunus plant having the altered characteristics of deep rooting (narrower lateral root branch angles and longer root system compared to lateral root branch angles and root system depth of a wild-type Prunus plant) by (i) transforming at least one wild-type Prunus cell with an expression vector that contains a heterologous promoter operably linked to a polynucleotide that encode PpeDROI , such that PpeDROI has at least the amino acid sequence of SEQ ID NO: 2 to produce at least one transformed Prunus cell, (ii) selecting at least one transformed Prunus cell that produces an increased amount of PpeDROI compared to the amount of PpeDROI produced by a wild-type Prunus cell to produce a transgenic Prunus cell that produces an increased amount of PpeDROI , and (iii) inducing the transgenic Prunus cell that produces increased amount of PpeDROI to grown into a genetically altered Prunus plant that produces increased amount of PpeDROI compared to the amount of PpeDROI produced by a wild-type Prunus plant, such that the increased amount of PpeDROI causes the genetically altered Prunus plant to have the altered root architecture of narrower lateral root branch angles and longer root system compared to the lateral root branch angles and root system depth of a wild- type Prunus plant. It is another object of this invention that the polynucleotide encoding

PpeDROI has a DNA sequence of at least SEQ ID NO: 1 . It is a further object of this invention to have a genetically altered Prunus plant produced by this method, as well as seed, stem, leaf, flower, pollen, fruit, cells, and progeny, so long as these genetically altered plant parts and progeny contain the heterologous promoter operably linked to the polynucleotide that encodes PpeDROI and can produce PpeDROI in increased amounts compared to the amount produced by wild-type Prunus plant or part or progeny.

[0012] It is an object of this invention to have a genetically altered Prunus cell containing an expression vector that contains a heterologous promoter operably linked to a polynucleotide that encodes PpeDROI which has the amino acid sequence of at least SEQ ID NO: 2. It is another object of this invention that the genetically altered Prunus cell can be induced to grow into a genetically altered Prunus plant which produces increased amount of PpeDROI compared to amount of PpeDROI produced by a wild-type Prunus plant, and that increased amount of PpeDROI causes the genetically altered Prunus plant to have an altered root architecture, namely narrower lateral root branch angles and longer root system, compared to the lateral root branch angles and root system depth of a wild-type Prunus plant. It is another object of this invention that the polynucleotide encoding PpeDROI has a sequence of at least SEQ ID NO: 1 . Another object of this invention is a germplasm containing the genetically altered Prunus cell or its progeny. [0013] Another object of the invention is a genetically altered Prunus plant having an altered root architecture of narrower lateral root branch angles and longer root system compared to the lateral root branch angles and root system depth of a wild-type Prunus plant. This genetically altered Prunus plant contains a heterologous promoter operably linked to a polynucleotide encoding PpeDROI which has the sequence of SEQ ID NO: 2, and the genetically altered Prunus plant produces increased amount of PpeDROI compared to the amount of PpeDROI produced by a wild-type Prunus plant, and the said increased amount of PpeDROI causes the genetically altered Prunus plant to have the altered root architecture of narrower lateral root branch angles and longer root system compared to the lateral root branch angles and root system depth of a wild-type Prunus plant. It is further object of this invention that polynucleotide (which is operably linked to the heterologous promoter) in the genetically altered Prunus plant has a DNA sequence of at least SEQ ID NO: 1 . It is further object of this invention to have genetically altered Prunus plant parts such as, but not limited to, seeds, stems, leaves, flowers, pollen, fruits, cells, and germplasm, as well as progeny of the genetically altered Prunus plant, so long as these genetically altered plant parts and progeny contain the heterologous promoter operably linked to the polynucleotide that encodes PpeDROI .

[0014] Other objects and advantages of this invention will become readily apparent from the ensuing description.

BRIEF DESCRIPTION OF THE DRAWINGS

[0015] The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the U.S. Patent and Trademark Office upon request and payment of the necessary fee.

[0016] FIG. 1 depicts the phylogenetic tree of IGT genes across plant phyla. The phylogenetic tree was constructed using the UMPGA algorithm using CLC Workbench software. The alignment used to construct the tree was built using a combination of MUSCLE and manual refinement. TAC, DRO, and LAZY clades are indicated on the right. Species common names and sequence IDs are listed. Blue, dicots; magenta, monocots; orange, lycophytes; green, bryophytes.

[0017] FIGs. 2A, 2B and 2C show that AtDROI control lateral root orientation in Arabidopsis: atdro l mutants exhibit wide branch angles and tip angles, as seen qualitatively (FIG. 2A) and quantitatively (FIG. 2B), as well as shorter primary roots (FIG. 2C). Asterisks indicate Student t- test values of p <.05, unless otherwise noted.

[0018] FIG. 3A and FIG. 3B depict atdrol mutant responds normally to gravity stimulus. After a 90 degree gravistimulus at 5 days post germination, images were taken of WT and atdro l seedlings. Primary root tip angle in relation to the root-shoot junction was measured at each time point for atdrol mutant (FIG. 3A, inset). FIG. 3A shows graphs of the changes in tip angles over time for wild-type and atdro l mutant. FIG. 3B shows representative images for wild-type and atdro l mutant at the indicated time points.

[0019] FIG. 4A depicts qPCR data comparing AtDROI expression in dissected roots and shoots and shows that AtDROI expression is largely root specific. FIGs. 4B, 4C, 4D, 4E, 4F, and 4G depict pAtDROI ::GUS staining in primary root and lateral root (LR) and shoot organs across 2 week old seedlings. FIG. 4H, the cartoon on the left, indicates the regions of the root where different staining patterns were found; 2-3 examples of each region are represented.

[0020] FIG. 5A and FIG. 5B depict representative full-root images of roots from two

pAtDROI ::GUS seedling lines. FIG. 5A shows Arabidopsis pAtDROI ::GUS transgenic line 2; FIG. 5B shows Arabidopsis pAtDROI ::GUS transgenic line 7. Asterisks indicate stage of staining pattern, referring to FIGs. 4B - 4G. Black, oldest lateral roots; green, middle lateral roots; red, young lateral roots; blue, newly emerged lateral roots.

[0021] FIG. 6A presents qPCR data testing two T2 AtDROI overexpression (OE) lines (Lines 3 and 8) for AtDROI overexpression. FIGs. 6B, 6C and 6D show that AtDROI overexpression results in narrower lateral root angles. Lines 3 and 8 were selected for subsequent experiments. Images (FIG. 6B) and graphs (FIG. 6C) show the significant decrease in lateral root branch angles of Lines 3 and 8 with respect to gravity and compared to wild-type Arabidopsis. FIG. 6D shows that primary root length was shorter in Line 8, but not Line 3. Asterisks indicate Student t- test values of p <.05, unless otherwise noted.

[0022] FIGs. 7A, 7B, 7C, and 7D show that AtDROI OE Line 1 is a silenced line exhibiting a similar phenotype to atdrol mutants. FIG. 7A shows qPCR data demonstrating that AtDROI OE Line 1 has higher relative express DR01 expression compared to wild-type Arabidopsis. FIG. 7B shows qPCR data measuring native 3' UTR expression and indicating native gene silencing. FIG. 7C and FIG. 7D show that Line 1 exhibits wide lateral root branch angles, both

quantitatively (FIG. 7C) and qualitatively (FIG. 7D).

[0023] FIGs. 8A, 8B, 8C, and 8D show differences in Arabidopsis shoot architecture depending on AtDROI expression. FIG. 8A shows wild-type Arabidopsis (WT) shoot architecture. FIG. 8B show AtDROI OE plants with altered shoot architecture by exhibited narrower shoot branch angles, upward cauline leaf curling, shorter and "shrink-wrapped" siliques, and upward rosette leaf curling compared to WT. FIG. 8C shows that this altered shoot and leaf phenotypes were not seen in Arabidopsis plants overexpressing AtDROI lacking the C-terminal EAR-like motif (AtDROI AEAR OE). FIG. 8D shows that shoot branch angles were statistically narrower in Arabidopsis AtDROI OE plants Lines 3 and 8 compared to WT. P-values from a Student t-test are indicated on the graph.

[0024] FIGs. 9A, 9B, and 9C depicts IGT family protein alignment showing conserved domains. Alignment of rice, Arabidopsis and peach TAC1 , LAZY1 and DR01 related genes highlights the 5 conserved domains shared among IGT family members. The fifth domain contains an EAR motif (LxLxL) in LAZY1 genes, and a similar motif in DR01 and DR01 -related genes.

[0025] FIG. 10A and FIG. 10B show that C-terminal EAR-like motif is required for AtDROI OE lines to have altered root architect phenotypes. No statistical quantitative difference (FIG. 10A) or qualitative difference (FIG. 10B) was found in lateral root branch angle in Arabidopsis lines overexpressing AtDROI AEAR, compared with WT. A Student's t-test was used to evaluate significance. [0026] FIG. 1 1 A shows relative expression of PpeDROI in the indicated plum tissue from plum plant lines overexpressing PpeDROI using qPCR. Highest PpeDROI expression occurred in roots. FIG. 1 1 B shows that leaf curling was seen in young transformed plum plants

overexpressing PpeDROI , similar to the upward leaf-curling phenotype in Arabidopsis AtDROI OE plants. FIG. 1 1 C and FIG. 1 1 E show that transformed plums overexpressing PpeDROI in tissue culture grow roots normally on rooting medium. FIG. 1 1 D and FIG. 1 1 F show that transformed PpeDROI OE plums grow long roots on shoot multiplication medium containing cytokinin (BA), which is not seen in wild-type, control plum plants.

[0027] FIG. 12 depicts overexpression of PpeDROI in individual genetically altered plum lines. qPCR data confirm overexpression across multiple genetically altered plum lines transformed with a PpeDROI OE construct.

[0028] FIGs. 13A, 13B, 13C and 13D depict genetically altered plums overexpressing

PpeDROI (PpeDROI OE plums) exhibit altered phenotypes from wild-type plum. FIG. 13A shows that for a fixed shoot height, PpeDROI OE plums had significantly longer roots than controls (wild-type plums). FIG. 13B shows that PpeDROI OE plums exhibited greater shoot dry weight, and greater root dry weight as a population, compared to controls. FIG. 13C shows that the number of roots growing through the lower mesh grid in pots was significantly higher in PpeDROI OE plum plants when considered as a population compared to control plum plants. FIG. 13D shows a pictorial comparison between control plum and PpeDROI OE plum Line 2. Asterisks indicate Student t-test values of p <.05.

DETAILED DESCRIPTION OF THE INVENTION

[0029] Currently, most fruit and nut trees are grown as scions grafted to rootstocks. Rootstock varieties are generally chosen for resistance to soil pathogens and their ability to dwarf the scion. Root architectures are only selected as a general trait, as there is substantial variation. Root orientation, or angle, is an important component of the overall architecture and depth of the root system, however little is known about the genetic control of this trait. Numerous studies have been conducted in plants to understand the genetics underlying root structure. Recent reports in rice identified a role for DEEPER ROOTING 1(DR01) in controlling the orientation of the root system, leading to positive changes in grain yields under drought conditions.

[0030] We previously proposed that DR01 was a member of the IGT gene family (named for a conserved amino acid motif), which plays a major role in controlling lateral organ orientation (Hollender and Dardick. 2015. New Phytol. 206:541 -556). Other IGT family members include TILLER ANGLE CONTROL 1 (TAC1 ) and LAZY1 which have been shown in both monocot, including rice and maize, and dicot species, including Arabidopsis and Prunus persica (peach), to control the orientation of various lateral shoot organs, including tillers, pedicels, petioles, and branches (Roychoudhry and Kepinski. 2015. Curr. Opin. Plant Biol. 23:124-131 ). Loss of TAC1 results in narrower angles in branch, tiller, leaf and flower angles compared to wild-type controls in both monocots and dicots (Yu et al. 2007. Plant J. 52:891 -898; Ku et al. 201 1 . PLoS One 6:1 - 7; Dardick et al. 2013. Plant J. 75:618-630). In contrast, loss of LAZY1 leads to wider branch angles of these lateral organs compared to controls (Yoshihara et al. 2013. Plant J. 74:267-279; Li et al. 2007. Cell Res. 17:402-410; Dong et al. 2013. Plant PhysiolA 63:1306-1322; Yoshihara and Lino. 2007. Plant Cell Physiol. 48:678-688). While the functions of these IGT genes appear to function in the same processes, the genes show a very low level of sequence similarity having only 4 or 5 conserved short protein motifs. Due to the lack of sequence conservation, the authors of the DR01 manuscript (Uga et al., supra) did not identify the gene as an IGT family member or that counterparts exist in dicot species. This lack of sequence identity across the IGT family makes their identification in plant genomes sometimes difficult. Conservation of TAC1 and LAZY1 function across angiosperms led us to hypothesize that DR01 has a similar function in monocots and dicots, despite having different root types and little sequence similarity.

[0031] Here we used phylogenetic analysis to evaluate DR01 -like genes across the plant kingdom and found that they form a distinct clade of the IGT gene family. Using genetic and molecular tools, we evaluated the presence, expression, and functionality of DR01 -like genes in dicots, demonstrating that DR01 -related genes in Arabidopsis, peach, and Prunus domestica (plum) influence root system architecture via changes in primary root length and lateral root angle and define the spatial expression in Arabidopsis. However, our data suggests that the role of DR01 in gravity sensing in the primary root tip may not be conserved from rice to

Arabidopsis. DR01, present in both Arabidopsis and peach, displayed root-specific expression patterns. Promoter-reporter constructs revealed that AtDROI is predominantly expressed in both the root vasculature and root tips in a distinct developmental pattern. The lack of staining in the youngest lateral roots suggests that AtDROI does not affect growth orientation until roots have grown ~200-250μηι. This appears to correlate with the stage at which the lateral roots cease strict horizontal growth and can begin to explore the soil and respond to gravity

(Rosquete et al., supra). The loss of staining in the oldest lateral root tips suggests that they are released from AtDROI control after a certain period of growth. The strong root tip staining is consistent with a role in directing growth orientation, however the normal gravitropic response in atdro l primary roots suggests that, unlike rice, AtDROI may not be directly connected to gravity in Arabidopsis primary roots, but may function transiently to orient lateral roots to gravity.

Alternatively, these genes may be involved in modulating responses to smaller changes in gravity, and a 90 degree rotation assay is above a set response threshold. Mutation of DR01 led to more horizontal lateral root angles.

[0032] While loss of AtDROI led to dramatic changes in lateral root angles, overexpression had a relatively minor effect despite the high level of overexpression. This may be due to physical constraints of the root cells. For example, cells on the lower side of the emerging lateral root may not be able to compress or decrease in size enough to allow for a much more downward angle. In contrast, because lateral roots emerge and grow at a downward angle already in wild type plants, there is more space to explore above the root than below. Despite the relatively minor decrease in lateral root angle in plants with overexpressed DR01 , these small changes could lead to a large cumulative angle change over the life of the plant, particularly in perennial species.

[0033] In addition, we demonstrate that ectopic AtDROI expression gives architectural phenotypes in shoot organs as well as roots. Overexpression of AtDROI under a constitutive promoter reduced lateral root angles and resulted in shoot phenotypes including upward leaf curling, shortened siliques, and narrow lateral branch angles. A conserved C-terminal EAR-like motif found in IGT genes was required for these ectopic phenotypes. Overexpression of PpeDROI in plum (Prunus domestica) led to deeper rooting phenotypes. Collectively, these data indicate a potential application for DR01 related genes to alter root architecture for drought avoidance and improved resource utilization.

[0034] Experiments in plums suggest that DR01 will be a useful tool in controlling rooting capacity and depth in crops. In addition, the ability of PpeDROI OE plums to root on shoot- multiplication media may prove useful in developing tools for the vegetative propagation of fruit trees. Deep rooting fruit/nut trees created by DR01 overexpression would be useful as rootstocks or as ungrafted scions for high density fruit/nut production, as well as the potential to mitigate the effects of drought. Drought avoidance strategies may be very advantageous for designing rootstocks to be grown in moisture-poor soils. Such trees would produce roots that explore deeper into the soil subsurface allowing them to tap into additional water and nutrients. Having narrower root structures would also allow the trees to be planted more closely together, as their roots would not directly compete for the same resources. Deeper roots may also provide trees with enhanced stability particularly in loose or wet soils. The implications of using DR01 to generate designer crops and rootstocks could have a great impact on agriculture as the population increases and the climate changes.

[0035] "Transformation" refers to the transfer of a nucleic acid fragment into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as "transgenic" organisms. Examples of methods of plant transformation include Agrobacterium- mediated transformation (De Blaere et al. 1987. Meth. Enzymol. 143:277) and particle-accelerated or "gene gun" transformation technology (Klein et al. 1987. Nature (London) 327:70-73; U.S. Pat. No. 4,945,050, incorporated herein by reference). Additional transformation methods are disclosed below. Thus, isolated polynucleotides of the present invention can be incorporated into recombinant constructs, typically DNA constructs, capable of introduction into and replication in a host cell. Such a construct can be a vector that includes a replication system and sequences that are capable of transcription and translation of a polypeptide-encoding sequence in a given host cell. A number of vectors suitable for stable transfection of plant cells or for the establishment of transgenic plants have been described in, e.g., Pouwels et al. 1985. Supp. 1987. Cloning Vectors: A Laboratory Manual; Weissbach and Weissbach. 1989. Methods for Plant Molecular Biology, Academic Press, New York; and Flevin et al. 1990. Plant Molecular Biology Manual, Kluwer Academic Publishers, Boston. Typically, plant expression vectors include, for example, one or more cloned plant genes under the transcriptional control of 5' and 3' regulatory sequences and a dominant selectable marker. Such plant expression vectors also can contain a promoter regulatory region (e.g., a regulatory region controlling inducible or constitutive, environmentally- or developmentally-regulated, or cell- or tissue-specific expression), a transcription initiation start site, a ribosome binding site, an RNA processing signal, a transcription termination site, and/or a polyadenylation signal.

[0036] As used herein, the terms "nucleic acid molecule", "nucleic acid sequence",

"polynucleotide", "polynucleotide sequence", "nucleic acid fragment", "isolated nucleic acid fragment" are used interchangeably herein. These terms encompass nucleotide sequences and the like.

[0037] The term "isolated" polynucleotide refers to a polynucleotide that is substantially free from other nucleic acid sequences, such as other chromosomal and extrachromosomal DNA and RNA, that normally accompany or interact with it as found in its naturally occurring environment. However, isolated polynucleotides may contain polynucleotide sequences which may have originally existed as extrachromosomal DNA but exist as a nucleotide insertion within the isolated polynucleotide. Isolated polynucleotides may be purified from a host cell in which they naturally occur. Conventional nucleic acid purification methods known to skilled artisans may be used to obtain isolated polynucleotides. The term also embraces recombinant polynucleotides and chemically synthesized polynucleotides.

[0038] As used herein, "recombinant" refers to a nucleic acid molecule which has been obtained by manipulation of genetic material using restriction enzymes, ligases, and similar genetic engineering techniques as described by, for example, Sambrook et al. 1989. Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY or DNA Cloning: A Practical Approach, Vol. I and II (Ed. D. N. Glover), IRL Press, Oxford, 1985.

[0039] A "construct" or "chimeric gene construct" refers to a nucleic acid sequence encoding a protein, here the DR01 protein, operably linked to a promoter and/or other regulatory sequences.

[0040] As used herein, the term "express" or "expression" is defined to mean transcription alone. The regulatory elements are operably linked to the coding sequence of the DR01 gene such that the regulatory element is capable of controlling expression of the DR01 genes.

"Altered levels" or "altered expression" refers to the production of gene product(s) in transgenic organisms (or genetically altered organisms) in amounts or proportions that differ from that of normal or non-transformed organisms.

[0041] As used herein, the terms "encoding", "coding", or "encoded" when used in the context of a specified nucleic acid mean that the nucleic acid comprises the requisite information to guide translation of the nucleotide sequence into a specified protein. The information by which a protein is encoded is specified by the use of codons. A nucleic acid encoding a protein may comprise non-translated sequences {e.g., introns) within translated regions of the nucleic acid or may lack such intervening non-translated sequences {e.g., as in cDNA).

[0042] The term "operably linked" refers to the association of two or more nucleic acid fragments on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence {i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.

[0043] "Regulatory sequences" refer to nucleotide sequences located upstream (5' non-coding sequences), within, or downstream (3' non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, and polyadenylation recognition sequences.

[0044] "Promoter" refers to a nucleotide sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3' to a promoter sequence. The promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. Accordingly, an "enhancer" is a nucleotide sequence that can stimulate promoter activity and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue-specificity of a promoter.

Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic nucleotide segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. The tissue-specificity of a promoter, for example, is exemplified by the promoter sequence (described above) which specifically induces gene expression in root tips. Promoters that cause a nucleic acid fragment to be expressed in most cell types at most times are commonly referred to as "constitutive promoters". New promoters of various types useful in plant cells are constantly being

discovered; numerous examples may be found in the compilation by Okamuro and Goldberg. 1989. Biochemistry of Plants 15:1 -82. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, nucleic acid fragments of different lengths may have identical promoter activity. A "heterologous promoter" is a promoter that is operably linked to a polynucleotide to which the promoter is not normally operably linked. That is, if the polynucleotide is usually operably linked to an inducible promoter, then, when the polynucleotide is linked to a constitutive promoter, that constitutive promoter is "heterologous" to that polynucleotide. The polynucleotide could be usually operably linked to a particular inducible promoter; but when it is operably linked to a different inducible promoter, that different inducible promoter is "heterologous" to that polynucleotide.

[0045] "RNA transcript" refers to the product resulting from RNA polymerase-catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is referred to as the primary transcript or it may be an RNA sequence derived from posttranscriptional processing of the primary transcript and is referred to as the mature RNA. "Messenger RNA (mRNA)" refers to the RNA that is without introns and that can be translated into polypeptides by the cell. "cDNA" refers to a DNA that is complementary to and derived from an mRNA template. The cDNA can be single-stranded or converted to double stranded form using, for example, the Klenow fragment of DNA polymerase I. "Sense" RNA refers to an RNA transcript that includes the mRNA and so can be translated into a polypeptide by the cell. "Antisense", when used in the context of a particular nucleotide sequence, refers to the complementary strand of the reference transcription product. "Antisense RNA" refers to an RNA transcript that is complementary to all or part of a target primary transcript or mRNA and that blocks the expression of a target gene. The complementarity of an antisense RNA may be with any part of the specific nucleotide sequence, i.e., at the 5' non-coding sequence, 3' non- coding sequence, introns, or the coding sequence. "Functional RNA" refers to sense RNA, antisense RNA, ribozyme RNA, or other RNA that may not be translated but yet has an effect on cellular processes.

[0046] A "protein" or "polypeptide" is a chain of amino acids arranged in a specific order determined by the coding sequence in a polynucleotide encoding the polypeptide. Each protein or polypeptide has a unique function.

[0047] It is to be understood that as used herein the term "transgenic" includes any cell, cell line, callus, tissue, plant part, or plant the genotype of which has been altered by the presence of a heterologous nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic. The term

"transgenic" as used herein does not encompass the alteration of the genome (chromosomal or extra-chromosomal) by conventional plant breeding methods or by naturally occurring events such as random cross-fertilization, non-recombinant viral infection, non-recombinant bacterial transformation, non-recombinant transposition, or spontaneous mutation. "Genetically altered" is a synonym of transgenic.

[0048] As used herein, the term "plant" includes reference to whole plants, plant organs {e.g., leaves, stems, roots, etc.), seeds, plant cells, and progeny of same. Parts of transgenic plants are to be understood within the scope of the invention to comprise, for example, plant cells, protoplasts, tissues, callus, embryos as well as flowers, stems, fruits, leaves, roots originating in transgenic plants or their progeny previously transformed with a DNA molecule of the invention and therefore consisting at least in part of transgenic cells, are also an object of the present invention.

[0049] As used herein, the term "plant cell" includes, without limitation, seeds suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, and microspores. The class of plants that can be used in the methods of the invention is generally as broad as the class of higher plants amenable to transformation techniques, including both monocotyledonous and dicotyledonous plants.

[0050] The successful transformation of Prunus with PpeDROI is a major step in manipulating root system length by overexpression of PpeDROI , thus ensuring the development of improved varieties of Prunus.

[0051] The creation of deep rooting Prunus trees DR01 overexpression would be useful as rootstocks or as ungrafted scions for high density fruit production and also provides drought avoidance strategies may be very advantageous for designing rootstocks to be grown in moisture-poor soils.

[0052] Having now generally described this invention, the same will be better understood by reference to certain specific examples, which are included herein only to further illustrate the invention and are not intended to limit the scope of the invention as defined by the claims.

EXAMPLE 1 Phylogeny

[0053] Phylogenetic analyses revealed that the Arabidopsis genome harbors three potential DR01 -like genes: AtDROI (At1 g72490), /AfDfl02 (At1 g191 15) and AtDR03 (At1 g 17400). Based on protein sequence similarity, we placed rice DR01 and its Arabidopsis homolog (At1 g72490) within the IGT gene family, named for a conserved motif (FIG. 1 , Uga et al. 2013b. Nat. Genet. 45:1097-1 102; Hollender and Dardick, supra). This gene family shows relatively low levels of sequence conservation, but is marked by five short motifs as well as a conserved intron-exon structure (Dardick et al., supra). Members of the IGT family can be found throughout moss, lycophyte, monocot, and dicot species (FIG. 1 , Hollender and Dardick, supra). Our phylogenetic analysis revealed the presence of multiple Dfl07-related genes in both monocots and dicots. To further define the evolutionary relationships of IGT family members, we performed BLAST and conserved motif searches to identify DRO -like genes in Arabidopsis, maize, rice, tomato, peach, brachypodium, selaginella, physcomitrella and sphagnum.

Maxiumum likelihood analyses revealed that DR01 formed a distinct IGT gene clade that was more closely related to LAZY1 than TAC1 (FIG. 1 ). In addition, the DR01 clade contained two sub-clades; one consisting of monocot DR01 genes and another that contained unknown monocot and dicot DRO -like genes. Arabidopsis, peach, and tomato DR01 -like genes were more closely related to the uncharacterized family of DROi -like genes than to rice DR01 .

Consistent with previous reports, TAC1 genes were not found in primitive plant species (Dardick et al., supra). Primitive plant IGT genes formed outgroups from the LAZY and DRO clades, suggesting these clades split off from an ancient ancestor.

[0054] While the closest Arabidopsis protein to OsDROI is At1 g72490 (which we named AtDROI here), AtDROI was found to be more closely related to a separate clade of

uncharacterized monocot DR01 -related genes, including three rice genes (FIG. 1 ). The dicot Dfl07-related genes group together into a single clade, however, some Dfl07-related family members may have independently arisen through duplication. For example, in addition to DR01, Arabidopsis contained two other DflO-related genes while peach contained only one other. These genes formed independent out-groups from AtDROI and PpeDROh

[0055] Alignments and trees were constructed using CLC genomics workbench (CLC bio). Sequences were obtained from the most recent versions of sequenced genomes available on the Phytozome web tool. Amino acid alignment was generated using MUSCLE and then manually refined. A minimum likelihood tree was constructed using the UPGMA algorithm.

EXAMPLE 2 Arabidopsis Mutants [0056] To determine if AtDROI plays a role in root growth orientation, we evaluated the phenotypic effects of putative AtDROI loss-of-function mutations. The Columbia (Col-0) ecotype was used as the wild-type (WT) line in all experiments. The T-DNA insertional line atdro l mutant (SALK 201221 C) and seed were obtained from Arabidopsis Biological Resource Center (ABRC, Ohio State University, Columbus, OH). For phenotyping, seed from homozygous lines were grown on large, vertically oriented plates. Seeds were surface sterilized and sown on plates containing 0.5xMS and 0.8% bactoagar. To observe root growth, seeds were sown on square plates and grown vertically. Both standard size (100 x 15 mm) and large (245 x 25 mm) growth plates were used. Once sown, seedlings were stratified at 4°C in the dark for 2 days, then placed in growth chambers at 20 °C, 16L: 8D, and ~100μηιοΙ m-2 sec-1 . Plates were imaged weekly for 2-4 weeks using a Canon EOS Rebel T3 camera, and lateral root branch and tip angles were manually calculated from these images using ImageJ. For gravity experiments, plates were rotated 90 degrees on the 5^th day after germination, then imaged every 10 minutes. Primary root tip angles were measures with respect to the root-shoot junction. For shoot branch angles, seedlings were grown for 2 weeks on plates, then transplanted into 4-inch pots containing Metromix 360 soil, (Sun-Gro Horticulture) and grown until bolting (~6-7inches in height). Bolts were then photographed and pressed. Angles were manually calculated by measuring the tangent of each lateral branch point.

[0057] Lateral root branch angles, tip angles, and primary root lengths were measured in 14 dpg plants. The atdrol mutants exhibited wide lateral root growth angles with respect to gravity (FIG. 2A). Branch and tip angles were significantly increased, by an average of 18 and 25 degrees, respectively, and primary root length was 1 1 mm shorter on average compared to WT plants (FIGs. 2B and 2C). The wide lateral root angle phenotype led to wider root systems overall.

[0058] In rice, primary root tips of plants containing the truncated version of OsDROI were reported to display a delayed response to gravity stimulation (Uga et al. 2013b, supra). To assess whether atdro l mutants display similar gravitropic defects, we performed gravity response assays. Mutants and wild-type control plants were grown on vertically oriented plates for 5 days, and then rotated 90 degrees. As the root grew downward toward the gravity vector, we recorded the angle of the primary root tip with respect to the root-shoot junction and gravity (FIG. 3A, inset). Neither the rate nor the degree of tip reorientation was significantly different from wild-type, however atdrol mutants showed a non-significant difference toward the end of the experiment (FIG. 3B).

EXAMPLE 3 Arabidopsis Transgenic Lines

[0059] Arabidopsis pAtDRO ::GUS transgenic lines were constructed by cloning a 2kb fragment of the AtDROI promoter sequence, including the 5' UTR, upstream of the GUS (beta- glucuronidase) coding sequence in the pBM 01 vectors, using Sail and Smal restriction sites. AtDROI overexpression lines were made by amplifying the coding sequence of AtDROI (At1 g72490) from Arabidopsis cDNA, and cloning downstream of the 35S promoter in our in- house pBIN-AFRS overexpression vector, using Sail and BamHI restriction sites (SEQ ID NO: 3). pBIN-AFRS was created by replacing the T-DNA region of pBIN-ARS with an artificially synthesized T-DNA that removes unwanted plasmid sequences and includes several multiple cloning sites (unpublished). Similarly, AEAR constructs were made by amplifying the AtDROI coding sequence, using a reverse primer that removed the final 15bp (the EAR-like motif) from the C-terminal end of the protein. The resulting fragment was also cloned into the 35S pBIN- AFRS vector using Sail and BamHI restriction sites. Constructs were transformed into Col-0 plants using the floral dip method, and transformants were subsequently selected on 0.5xMS plates containing kanamycin.

[0060] Seedlings were grown on 0.5x MS plates and collected at 14 days past germination (dpg) for analysis. Localization of pAtDROI gene activity in cells and tissues of the transformed seedlings was demonstrated by histological staining. The staining is very sensitive. Beta- glucuronidase (GUS) converts 5-bromo-4-chloro-3-indolyl glucuronide (X-Gluc) to a blue product. Seedlings were immersed in cold 90% acetone for 20 minutes, washed in GUS reaction buffer without X-gluc, and then immersed in GUS reaction buffer containing X-gluc. Samples were then vacuum-infiltrated for 20 minutes on ice, and subsequently placed at 37°C in the dark for 4 hours. Seedlings were dehydrated through an ethanol series, and fixed in FAA fixative (50% Ethanol, 5% Formaldehyde, 10% Acetic acid, rest water). Light microscopy was performed using a Zeiss Axiozoom microscope.

[0061] In 14 dpg seedlings, pAtDROI ::GUS staining was strongest in primary and lateral root tips, as well as root vasculature nearest the tips, with faint expression visible in the shoot vasculature of the strongest lines (FIGs. 4B-4G, FIGs. 5A and 5B ). In some lines, a gradient of expression could be observed along the longitudinal axis of the youngest part of the primary root (FIGs. 5A and 5B). In the oldest part of the root system, nearest the root-shoot junction, lateral roots exhibited a gradient of staining along their longitudinal axes (FIGs. 4C and 4D). Within each plant, staining was excluded from the root tips of a subset of these oldest lateral roots (FIG. 4C). In younger lateral roots, staining was restricted to the root tips (FIG. 4E). This tip-specific expression only became apparent when lateral roots reached -200-250 μηι in length, as newly emerged lateral roots lacked staining all together (FIGs. 4F and 4G). In roots with staining along the primary root access, expression was restricted from the region surrounding a new, developing lateral root. This overall pattern was consistent with a potential role for DR01 in root growth and root tip in situ data shown in rice (Uga et al., supra).

[0062] Next, we tested if overexpression of AtDROI is sufficient to decrease lateral root angles and increase primary root length. We generated and tested expression levels in whole seedlings of transgenic T2 overexpression (OE) lines transformed with 35S::AtDR01 and selected representative homozygous OE lines from two lines (Line 3 and Line 4). See FIG. 6A for qPCR data. qPCR data was also obtained from other AtDROI OE lines (data not shown). AtDROI OE lines displayed a significant decrease in the average angle of lateral root branching, by 5 degrees in OE Line 3 and 9 degrees in OE Line 8 (FIGs. 6B and 6C), thus giving narrower lateral root branch angles. Primary root lengths in OE Line 3 were not significantly different from the wild-type; however, they were significantly shorter in OE Line 8 (FIG. 6D).

[0063] A single OE line (Line 1 ) exhibited horizontal roots, similar to the atdrol T-DNA mutant line, and compared to wild-type (FIG. 7D). While the transgene was confirmed to be

overexpressed via qRT-PCR compared to wild-type (FIG. 7A), we hypothesized that gene silencing was occurring. To test this, we evaluated native AtDROI gene expression using primers targeting the 3' UTR that was not present in the OE transgene construct. Consistent with this hypothesis, OE Line 1 showed substantially reduced native AtDROI expression compared with the wild-type (FIG. 7B). See also FIG. 7C for quantitative data on lower root branch angles compared to wild-type. These results are consistent with the phenotype observed in atdrol T-DNA line.

[0064] Shoots of AtDROI OE plants exhibited pronounced phenotypes. Both the rosette and cauline leaves displayed a distinct upward curling at the leaf margins (FIG. 8B) compared to wild-type Arabidopsis plants (WT) (FIG. 8A). With cauline leaves, this often led to the leaf curling completely around the lateral shoot above it. This may be due to differential cell expansion or division on upper and lower leaf surface. Siliques of AtDROI OE plants were also typically shorter than in WT, and the outlines of the seeds were more defined (FIGs. 8A and 8B). In addition, shoot branch angles were narrower by -12 or -10 degrees in Arabidopsis AtDROI OE Lines 3 and 8 (respectively) compared to WT (FIG. 8D).

[0065] In rice, Uga et al. found that the shallow rooting IR64 varieties contain a C-terminal truncated DR01 allele. Within the C-terminal truncated sequence are two conserved motifs - a KWVKTDS (SEQ ID NO: 4) motif of unknown function, and an IVLEI (SEQ ID NO: 5) motif that is very similar to the EAR motif present in LAZY1 (FIGs. 9A-9C). To test whether this EAR-like motif is required for AtDROI function, we deleted the last 5 residues (IVLEI) from AtDROI (AtDROI AEAR) and overexpressed this truncated version in Arabidopsis. When grown on vertically oriented plates, we observed that, for AtDROI AEAR Lines 6 and 7, the roots showed neither significant change in lateral root angle compared with wild-type Arabidopsis (WT) (FIGs. 10A and 10B) nor any shoot phenotype (FIG. 8C). This suggests that the EAR-like motif is required for AtDROI overexpression plants to have the desired altered root phenotypes.

EXAMPLE 4 Plum Transformation

[0066] The functionality of PpeDROI was tested by generating overexpression lines in plum. Peach transformation remains highly intractable, therefore the closely related and readily transformed plum is often used for in planta assays (Petri et al. 2012. Methods Mol. Biol. 847:191 -199). PpeDROI overexpression (OE) constructs were made by amplifying the coding sequence of PpeDROI (Ppa021925) from peach cDNA, and cloning downstream of the 35S promoter in our in-house pBIN-AFRS overexpression vector, using Sail and BamHI restriction sites. The OE construct was subsequently transformed into Agrobacterium tumefaciens.

European plums {Prunus domestica L.) were transformed with the PpeDROI OE strain and a control (pSUC2::GUS) strain using a previously established protocol (Petri et al., supra). Briefly, cold {4°C) stored seeds of the 'Stanley' plum variety were used for transformation. Seeds were surface sterilized with 15% commercial bleach for 15 min and washed three times with sterile water. Hypocotyls were excised from the zygotic embryos under sterile conditions using a stereomicroscope, and then sliced into 2-3 segments. After slices were immersed in an

Agrobacterium suspension for 20 min, the transformed hypocotyl segments were cultured for 3 days in co-cultivation medium. Hypocotyl segments were then plated on antibiotic (80mg/l kanamycin) selection medium to regenerate transgenic shoots. Recovered kanamycin resistant transgenic shoots were multiplied in multiplication medium before being transferred to rooting medium. Finally, plants were transferred to soil and acclimatized in a growth chamber for several weeks before being moved to greenhouse conditions.

[0067] PpeDROI overexpression in plum results in root growth and leaf curling phenotypes. Consistent with Arabidopsis, expression of PpeDROI was highest in peach roots, about 7-14 fold higher than in leaf, node and internode samples (FIG. 1 1 A). Shoot meristems also showed expression, about half as much as the root samples (FIG. 1 1 A). Shoots of select lines regenerated under antibiotic selection in tissue culture displayed a similar upward leaf-curling phenotype to Arabidopsis AtDROI OE plants (compare FIG. 1 1 B and FIG. 8B). Unlike

Arabidopsis, the curling phenotype disappeared within 2-3 weeks after the plants were transplanted to soil. During the plum regeneration process, abnormal rooting phenotypes were also observed. The process of plum transformation involves generating plant shoots from callus, then transferring regenerated shoots first to shoot multiplication medium (FIGs. 1 1 C and 1 1 E), followed by transfer to rooting medium (FIGs. 1 1 D and 1 1 F), which stimulates root production. Shoot multiplication media contains the cytokinin BA that normally inhibits root growth. Before the transfer to rooting medium, wild-type plum regenerated shoots do not typically form roots

(FIGs. 1 1 C and 1 1 E). Unlike control plum plants (wild-type), regenerated transgenic plum shoots overexpressing PpeDROI frequently formed thin roots while growing on shoot multiplication medium (FIGs. 1 1 D and 1 1 F).

EXAMPLE 5 Plum Root Assays

[0068] Transformed plums (genetically altered plums) that had been recovered from tissue culture and placed in soil (Metromix 360) in 3-inch pots and then placed in a growth chamber for 2-3 weeks were tested to determine whether PpeDROI overexpression has an effect on rooting depth. Once root systems were established in these pots, PpeDROI expression levels in multiple lines of recovered seedlings were confirmed. (FIG. 12) using qPCR. Then, seedlings were transplanted to 9 inch pots containing two tiers of wire mesh. Mesh grids were placed at a soil depth of 2 and 5 inches below the surface. The wire mesh grids capture the number of roots growing to each depth. Seedlings were allowed to grow in the mesh-containing pots until shoot heights reached approximately 8-12cm. Plants were then carefully removed from soil, and the number of roots and diameter of root system growing through each mesh grid were recorded. Root and shoot lengths were recorded, and plants were subsequently dissected and dried in a drying oven overnight to measure root and shoot dry weight. For tissue culture rooting assays, shoots were generated on multiplication medium over 3-4 weeks, then transplanted to jars containing either the same shoot multiplication medium or rooting medium and allowed to grow for another 3-4 weeks.

[0069] Individual seedlings reached this shoot height at different times, however this was not a genotype-specific effect. For the fixed shoot height window, the roots of genetically altered PpeDROI OE plums were found to be significantly longer than roots of wild-type plum (control) (FIGs. 13A and 13D). Both root dry weight (as a population) and shoot dry weight of genetically altered PpeDROI OE plums were greater than controls (FIG. 13B). In addition, genetically altered PpeDROI OE plums lines had more roots (when considered as a population) growing through the lower mesh grids than the number of roots growing through the lower mess grids of control plums (FIG. 13C). Asterisks indicate Student t-test values of p <.05.

EXAMPLE 6 AtDROI and PpeDROI Expression [0070] Expression profiles of AtDROI and AtDROI were assessed via qualitative real-time PCR (qPCR) analysis on Arabidopsis seedlings. Arabidopsis seedlings were grown on vertical plates for 14 days, and then hand dissected to separate the shoot and the root. Each biological replicate consisted of a plate of 12 seedlings. Three biological replicates were used. Arabidopsis RNA was extracted using a Directzol RNA Extraction Kit (Zymogenetics).

[0071] The expression profiles of PpeDROI was assessed on plum tissue. Plum tissue containing the PpeDROI OE construct was collected from apical meristems of 2-month old plants growing in soil. Peach roots were collected for use as a standard. Peach tissue was collected and flash frozen, lyophilized for ~1 week and ground. 20-30mg of tissue was used in the RNeasy Plant Mini Kit (Qiagen), then treated with the Ambion Turbo DNA-free kit (Ambion).

[0072] QPCR was performed as previously described by Dardick et al. (2013. Plant J. 75:618- 630). Briefly, each reaction was run in triplicate using 50 ng of RNA in a 12 μΙ reaction volume, using the Superscript III Platinum SYBR Green qRT-PCR Kit (Invitrogen). The reactions were performed on a 7900 DNA sequence detector (Applied Biosystems). Quantification for

Arabidopsis samples was performed using a relative curve derived from a serially diluted standard RNA run in parallel. Quantification for peach and plum samples was performed using the delta Ct method, and normalized to actin.

[0073] AtDROI expression was evaluated in dissected roots and shoots, and AtDROI expression was shown to be largely root specific (FIG. 4A). qPCR data comparing PpeDROI expression in different peach organs indicates highest expression in roots (FIG. 1 1 A).

[0074] All publications and patents mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent was specifically and individually indicated to be incorporated by reference.

[0075] The foregoing description and certain representative embodiments and details of the invention have been presented for purposes of illustration and description of the invention. It is not intended to be exhaustive or to limit the invention to the precise forms disclosed. It will be apparent to practitioners skilled in this art that modifications and variations may be made therein without departing from the scope of the invention.

Claims

Claims We claim:

Claim 1 . An expression vector comprising a heterologous promoter operably linked to a polynucleotide encoding PpeDROI , wherein said PpeDROI comprises an amino acid sequence of SEQ ID NO: 2.

Claim 2. The expression vector of Claim 1 , wherein said polynucleotide comprises SEQ ID NO: 1 .

Claim 3. A transgenic cell comprising the expression vector of Claim 1 .

Claim 4. The transgenic cell of Claim 3, wherein said transgenic cell is a transgenic Prunus cell.

Claim 5. The transgenic Prunus cell of Claim 4, wherein said transgenic Prunus cell is a transgenic cell from the group consisting of transgenic Prunus persica, transgenic Prunus domestica, transgenic Prunus avium, transgenic Prunus salicina and transgenic Prunus armeniaca.

Claim 6. A method of producing a genetically altered Prunus plant having an altered root architecture of narrower lateral root branch angles and longer root system compared to lateral root branch angles and root system depth of a wild-type Prunus plant, said method comprising:

(a) transforming at least one wild-type Prunus cell with an expression vector comprising a heterologous promoter operably linked to a polynucleotide encoding PpeDROI , wherein said PpeDROI comprises an amino acid sequence of SEQ ID NO: 2 to produce at least one transformed Prunus cell; and

(b) selecting at least one transformed Prunus cell that produces an increased amount of said PpeDROI compared to amount of PpeDROI produced by said wild-type Prunus cell to produce a transgenic Prunus cell that produces an increased amount of said PpeDROI ; (c) inducing said transgenic Prunus cell that produces said increased amount of said PpeDROI to grown into a genetically altered Prunus plant that produces said increased amount of said PpeDROI compared to said amount of PpeDROI produced by said wild- type Prunus plant, wherein said increased amount of PpeDROI causes said genetically altered Prunus plant to have said altered root architecture of narrower lateral root branch angles and longer root system compared to said lateral root branch angles and root system depth of a wild-type Prunus plant.

Claim 7. The method of Claim 6, wherein said polynucleotide comprises SEQ ID NO: 1 .

Claim 8. A genetically altered Prunus plant produced by the method of Claim 6 or the progeny thereof, wherein said genetically altered Prunus plant and said progeny produce increased amount of PpeDROI compared to amount of PpeDROI produced by a wild-type Prunus plant, and wherein said increased amount of PpeDROI causes said genetically altered Prunus plant and said progeny thereof to have said altered root architecture of narrower lateral root branch angles and longer root system compared to said lateral root branch angles and root system depth of a wild-type Prunus plant.

Claim 9. A genetically altered Prunus seed of the transgenic plant of Claim 8, wherein said genetically altered Prunus seed comprises an expression vector comprising a heterologous promoter operably linked to a polynucleotide encoding PpeDROI , wherein said PpeDROI comprises an amino acid sequence of SEQ ID NO: 2.

Claim 10. A genetically altered Prunus cell comprising an expression vector comprising a heterologous promoter operably linked to a polynucleotide encoding PpeDROI , wherein said PpeDROI comprises SEQ ID NO: 2, wherein a genetically altered Prunus plant generated from said genetically altered Prunus cell produces increased amount of PpeDROI compared to amount of PpeDROI produced by a wild-type Prunus plant, and wherein said increased amount of PpeDROI causes said genetically altered Prunus plant to have altered root architecture of narrower lateral root branch angles and longer root system compared to said lateral root branch angles and root system depth of a wild-type Prunus plant.

Claim 1 1 . The genetically altered Prunus cell of Claim 10, wherein said polynucleotide comprises SEQ ID NO: 1 .

Claim 12. A germplasm of said genetically altered Prunus cell of Claim 10.

Claim 13. A genetically altered Prunus plant having an altered root architecture of narrower lateral root branch angles and longer root system compared to lateral root branch angles and root system depth of a wild-type Prunus plant, said genetically altered Prunus plant comprising a heterologous promoter operably linked to a polynucleotide encoding PpeDROI , wherein said PpeDROI comprises SEQ ID NO: 2, wherein said genetically altered Prunus plant produces increased amount of PpeDROI compared to amount of PpeDROI produced by a wild-type Prunus plant, and wherein said increased amount of PpeDROI causes said genetically altered Prunus plant to have said altered root architecture of narrower lateral root branch angles and longer root system compared to said lateral root branch angles and root system depth of a wild- type Prunus plant.

Claim 14. The genetically altered Prunus plant of Claim 13, wherein said polynucleotide comprises SEQ ID NO: 1 .