WO2015143972A1 - 水稻穗部性状调控基因pt2及其应用 - Google Patents

水稻穗部性状调控基因pt2及其应用 Download PDF

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WO2015143972A1
WO2015143972A1 PCT/CN2015/073574 CN2015073574W WO2015143972A1 WO 2015143972 A1 WO2015143972 A1 WO 2015143972A1 CN 2015073574 W CN2015073574 W CN 2015073574W WO 2015143972 A1 WO2015143972 A1 WO 2015143972A1
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gene
rice
grain
panicle
seq
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French (fr)
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邓华凤
张武汉
孙平勇
舒服
何强
邢俊杰
王杰
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湖南杂交水稻研究中心
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/415—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from plants
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H5/00—Angiosperms, i.e. flowering plants, characterised by their plant parts; Angiosperms characterised otherwise than by their botanic taxonomy
    • A01H5/10—Seeds
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H6/00—Angiosperms, i.e. flowering plants, characterised by their botanic taxonomy
    • A01H6/46—Gramineae or Poaceae, e.g. ryegrass, rice, wheat or maize
    • A01H6/4636—Oryza sp. [rice]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A40/00—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production
    • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
    • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants

Definitions

  • the invention belongs to the field of plant genetic engineering, and particularly relates to a panicle trait regulating gene PT2 of rice, and relates to the application of the gene in plant breeding such as rice and corn.
  • Rice is one of the most important food crops in the world. More than half of the world's population is rice-based. The yield and quality of rice are related to food security in the world.
  • the ear traits of rice include ear length, number of primary branches, number of secondary branches, grain shape, number per grain, etc., which have important effects on rice yield and quality.
  • the grain shape includes grain length, grain width and grain thickness. It not only directly affects the important component of rice yield, 1000-grain weight, but also the appearance quality, commodity quality and processing of rice. Quality has an important impact. Therefore, the genetic mechanism and molecular mechanism of rice grain shape have important theoretical and practical significance for rice high yield and high quality breeding. So far, according to the data published by the international database Gramene, 508 QTLs controlling rice grain traits have been located and distributed on 12 chromosomes of rice. At present, several major genes controlling the shape of the grain have been cloned by means of map cloning, such as GS3, GW2, GW5, TGW6, GS5, GW8, etc.
  • ear traits such as ear length, number of first branch, number of secondary branches, number of grains per panicle, and granulation, are similar to the research progress of grain shape, and generally locate more relevant QTLs or genes. Some genes have been cloned.
  • the gene regulatory network of rice panicle traits is complex: there are major regulatory genes, there are also a large number of micro-effect QTLs; there are pluripotency genes, There are also genes that affect only a single or a few traits. At the same time, there are complex interactions between genes. Therefore, it is urgent to clone more new genes related to panicle traits, and gradually understand the gene regulatory network based on the understanding of the function of individual genes, so as to provide genetic resources and theoretical basis for the cultivation of new varieties.
  • the object of the present invention is to provide a novel panicle trait regulatory gene and its application for rice and other plants.
  • the present invention first provides a rice panicle trait regulation gene PT2, the nucleotide sequence of which comprises the nucleotide sequence shown in positions 2102 to 3286 of SEQ ID NO. 1, or the sequence A nucleotide sequence that replaces, deletes or adds one or more nucleotides and encodes an amino acid sequence that is identical or similar and has the same function.
  • nucleotide sequence of the promoter regulating the major gene PT2 is shown by the nucleotide corresponding to the 1-2014 position in SEQ ID NO.
  • rice panicle trait control gene PT2 has a nucleotide sequence as shown in SEQ ID NO.
  • the present invention also provides a protein encoded by the rice panicle trait control gene PT2 having the amino acid sequence of SEQ ID NO.
  • the present invention also provides the allele pt2-J of the rice panicle trait regulatory gene PT2, the nucleotide sequence of which comprises the nucleotide sequence shown in positions 2098 to 3237 of SEQ ID NO. 3; A sequence is a nucleotide sequence that replaces, deletes or adds one or more nucleotides and encodes an amino acid sequence that is identical or similar and has the same function.
  • nucleotide sequence of the pt2-J promoter is shown by the nucleotide corresponding to the 1-2010 position in SEQ ID NO.
  • the rice panicle trait regulatory gene pt2-J has a nucleotide sequence as shown in SEQ ID NO.
  • the present invention also provides the protein encoded by the rice panicle trait control gene pt2-J, which has the amino acid sequence shown in SEQ ID NO.
  • the present invention also provides the allele pt2-I of the rice panicle trait control gene PT2, the nucleotide sequence of which comprises the nucleotide sequence shown in positions 2088 to 3272 of SEQ ID NO. 5; A sequence is a nucleotide sequence that replaces, deletes or adds one or more nucleotides and encodes an amino acid sequence that is identical or similar and has the same function.
  • nucleotide sequence of the pt2-I promoter is represented by the nucleotide corresponding to the 1-1991 position in SEQ ID NO.
  • rice panicle trait control gene pt2-I has a nucleotide sequence as shown in SEQ ID NO.
  • the present invention also provides the protein encoded by the rice panicle trait control gene pt2-I having the amino acid sequence of SEQ ID NO.
  • the present invention also provides a vector comprising the rice panicle trait regulatory gene PT2 or pt2-J or pt2-I.
  • the invention also provides the application of the rice panicle trait regulation gene PT2 or pt2-J or pt2-I in the breeding of rice and other new plant varieties.
  • the invention also provides the application of the rice panicle trait regulation gene PT2 or pt2-J or pt2-I in regulating panicle traits of rice and other plants.
  • the invention also provides the application of the rice panicle trait regulation gene PT2 or pt2-J or pt2-I in preparing transgenic rice and other plants.
  • the novel gene PT2 cloned in rice of the present invention has a large positive effect on ear length and 1000-grain weight, and the total storage capacity is extremely significantly increased, which can provide new genetic resources for rice high-yield breeding.
  • the new gene PT2 has a large positive effect on the grain length, and through the polymerization with the narrow-grain gene, a new high-grade long-grain high-quality rice variety can be selected.
  • novel gene PT2 in the present invention significantly reduces grain shattering and reduces losses during mechanized harvesting of rice.
  • the heterozygous genotype (PT2pt2) can maintain a high level of kernel number and 1000-grain weight, and greatly increase the storage capacity. Therefore, the heterozygous genotype (PT2pt2) can Significantly increase the storage capacity of hybrid rice, and significantly reduce grain shattering, and provide technical support for high-yield breeding of hybrid rice.
  • the PT2 gene of the present invention has homologous genes in many plants such as corn and sorghum, and the PT2 gene can be used not only for rice but also for breeding new varieties of other plants.
  • Figure 1 is a schematic diagram showing the expression levels of the PT2 gene in different tissues of rice during the whole growth period.
  • the materials used were 2 near isogenic lines material R642-1 (genotype pt2pt2, pt2 from R1126) and R642-2 (genotype PT2PT2, PT2 from CDL).
  • Figure 2 is a complementary verification of the PT2 candidate gene of the present invention.
  • OX and RNAi represent overexpression and RNA interference, respectively; (+) and (-) represent T1 transgenic positive and negative plants, respectively.
  • Figure 3 is a schematic diagram showing the structure of the cloned PT2 gene of the present invention and its natural variation analysis.
  • the black box represents the exon
  • the thin line represents the intron
  • the "ATG” and “TGA” are the translation initiation codon and the stop codon, respectively
  • the thick line before the ATG represents the 2000bp promoter
  • large grain and
  • SNPs and InDel variants between the granules are located in the promoter and coding region of the PT2 gene (SNP substitutions are represented by the corresponding bases, InDel deletions are represented by corresponding dots), and the coding region has 3 amino acid variations.
  • LOC_Os02g47280 is a candidate gene, and the gene was preliminarily named as GS2 (Grain shape 2) (Zhang et al., 2013), but did not complete the subsequent gene cloning work. Subsequent analysis showed that the large-grain gene GS2 from 'CDL' not only significantly increased the grain length, grain width and 1000-grain weight, but also significantly increased the panicle length and significantly reduced the shattering property (Table 1).
  • the inventors of the panicle trait regulatory gene Renamed to PT2 (Panicle Traits 2).
  • Real-Time PCR expression analysis showed that the PT2PT2 genotype had a higher expression level in the critical stage of the development of panicle traits, and the recessive allele genotype pt2pt2 expression was lower (Fig. 1). It is speculated that the difference in the expression level of LOC_Os02g47280 gene leads to differences in function and phenotype.
  • the expression of LOC_Os02g47280 gene in RNA interference decreased, and the panicle length, grain length and grain width decreased significantly. So far, the inventors completed the cloning of the PT2 gene.
  • the PT2 gene of the present invention is preferably derived from rice, but other plant genes highly homologous to the rice PT2 gene are also within the scope of the present invention.
  • GS2 Gram Shape 2
  • LOC_Os02g47280 is the candidate gene GS2 ( Zhang et al., 2013).
  • the gene can increase rice grain length by 3mm, grain width by 0.4mm, and 1000-grain weight by more than 18g (the increase may vary in different genetic backgrounds).
  • PT2 Pieris Traits 2
  • the PT2 gene can simultaneously regulate the panicle length and 1000-grain weight of rice, which has an important impact on yield and quality.
  • R642-1 and R642-2 are derived from the recombinant inbred line population (F 8 ) of R1126/CDL. There are only differences in the LOC_Os02g47280 gene, and the genetic background is basically the same, which is a near isogenic line.
  • R642-1 is a medium-grain material (pt2pt2, pt2 is derived from the parent R1126), and R642-2 is a large-grain material (PT2PT2, PT2 is derived from the parental CDL).
  • BTS breaking tensile strength indicates the tensile strength of the grain, and the measured material is 40 days after the heading period.
  • LOC_Os02g47280 gene was expressed in various organs during the whole growth period, but it was expressed in young ears. This is the key period for the growth and development of young ears, and the table that mainly affects the ear traits of rice. The type is consistent. In most tissue materials, the expression of R642-2 (PT2PT2) was significantly higher than that of the medium material R642-1 (pt2pt2) (Fig. 1). The difference in expression of LOC_Os02g47280 gene was predicted to result in gene function and phenotype. The difference.
  • LOC_Os02g47280 gene consists of 394 amino acids, including two conserved domains, WRC and QLQ. The domains are involved in DNA binding and protein interactions, respectively (Kim et al., 2003, plant J. 36: 94-104).
  • the protein structure consisting of 394 amino acids encoded by LOC_Os02g47280 gene was searched by BLASTp and found to encode a growth regulator protein belonging to the GRF protein family.
  • the LOC_Os02g47280 gene (including the coding region and promoter region) of 26 materials including R642-1 (middle kernel) and R642-2 (large particle) was sequenced. Using 12 pairs of PCR products that partially overlap each other (Table 2), high-fidelity TransStart FastPfu Fly DNA Polymerase (purchased from TransGen) was used for PCR amplification from the genomes of these varieties, and then PCR products were sent to platinum. The company is sequencing. The sequences were spliced using Sequencher 4.5 software (Gene Codes Corporation, USA). The DNA sequences of the two alleles are set forth in SEQ ID NO: 1 (CDL) and SEQ ID NO: 3 (R1126).
  • the coding region and promoter region of the 26 material LOC_Os02g47280 gene were compared and analyzed (Fig. 3).
  • the promoter region of 10 materials was found to be identical to the large material R642-2 and CDL. Most of these 10 materials have longer grain lengths, but there are types with very short grain lengths (such as II-32A, Bing 1A) (Table 3).
  • the rice type (pt2-I) one is the indica type (pt2-J)
  • the large material R642-2 and CDL are basically the same as the indica type, but there is also a unique variation in the coding region that is different from the indica and japonica. This variation was not found in the remaining 24 materials (Table 4).
  • the unique region of R642-2 and CDL is the regulatory site of miRNA396 for LOC_Os02g47280 gene, indicating that this mutation may make miRNA396
  • the regulation of the LOC_Os02g47280 gene is attenuated, resulting in an increase in the expression of the LOC_Os02g47280 gene, which in turn changes the panicle traits of rice. Therefore, promoter variants and unique variants of the coding region (or either) result in a significant increase in R642-2 and CDL (PT2PT2) ear length, grain length, grain width and grain shattering compared to R642-1 (pt2pt2). The reason for the significant decrease.
  • Primer 1390DL-1 (Table 5) was designed to amplify 4073 bp of the target genomic DNA from the large parental CDL, and the pCUbi1390 vector was digested with BamH I, and the target fragment was cloned with the clontech infusion kit. Linearized vector The fusion was performed, the competent cells were transformed, the positive monoclonal plasmid was sequenced, and the correct plasmid without mutation was transformed into Agrobacterium competent state, and Agrobacterium-mediated genetic transformation was carried out to the donor material R642-1 (medium material). Construction and transformation of microRNA interference vector: The following primers were designed with pNW55 vector as template to obtain 290 bp microRNA fragment:
  • the microRNA fragment was ligated into the PstI and SpeI cleavage sites, and the target fragment was digested with the vector pCUbi1390. Then, the ligation reaction was carried out, the competent cells were transformed, and the positive monoclonal sequence was selected, and the correctly cloned plasmid was obtained by Agrobacterium-mediated rice.
  • the genetic transformation system was introduced into rice large-grain material R642-2. After induction, subculture, infection and co-culture, the hyacinth-resistant callus, differentiation, rooting and seedling transplanting were screened to obtain transgenic rice. Plant. Agrobacterium-mediated rice genetic transformation was commissioned by Wuhan Boyuan Biotechnology Co., Ltd.
  • the invention obtains 15 independent transgenic overexpressed T0 rice plants, including 8 positive single plants and 7 negative individual plants; 18 plants interfering with T0 generation rice plants, including 10 positive single plants and 8 negative individual plants.
  • the grain shape of the T1 generation rice positive single plant is close to the large grain material R642-2, negative single
  • the strain was similar to the grain material R642-1 (Fig. 2).
  • the above results confirmed that the LOC_Os02g47280 gene from 'CDL' is PT2QTL; the RNA interference T1 generation rice positive single grain shape is close to the middle grain material R642-1, and the negative single grain shape is consistent with the large particle material R642-2.
  • the ear length, grain length and grain width of Pi-2S/R642-2 are comparable to those of the control Y Liangyou 1 , and the primary branch, the second branch, the 1000-grain weight, and the reservoir capacity are all larger than the control, and the differences are Extremely significant level (see Table 6).
  • the number of grains per panicle of R642-2 was significantly less than that of R1126, but the combination of Y58S/R642-2 and Pi-2S/R642-2 was equivalent to the control in the number of grains per panicle.
  • the storage capacity was significantly higher than that of the control Y. Excellent No. 1, indicating that it has good combining ability.
  • the storage capacity of Y58S/R642-2 and Pi-2S/R642-2 was 15.82t/hm 2 and 15.87t/hm 2 respectively under the condition of moderately high fertility level, while the control Y Liangyou 1 was 11.54t/hm2.
  • the results of the actual measurement showed that Y58S/R642-2 (10.07t/hm 2 , 85.2%) had an increase of 23.8% compared with the control Y Liangyou 1 (8.13t/hm 2 , 88.9%).
  • Pi-2S /R642-2 (9.29t/hm 2 , the seed setting rate of 78.3%) increased yield by 14.2% compared with the control Y Liangyou 1 .
  • Short grain length has always been one of the indicators of China's glutinous rice than international brand-name rice.
  • the breeding of long-grain hybrid rice is difficult because the grain length of the hybrid is generally close to the average of the length of the sterile line and the restorer. If one of the parents has a short grain length, the grain length of the commercial rice will not be very long. . It is generally accepted that the long grain high quality rice has a grain length of about 12 mm.
  • the present inventors have now selected a new long-grain material having a grain length of 15 mm or more. Of course, too long a grain length will also bring about the disadvantages of a low milled rice rate.
  • the above-mentioned special long-grain new material is used as the recovery system, and the general rice sterile line (rice grain length 8 to 9 mm) is matched to form a high-grade, high-yield and high-quality rice new variety with a grain length of about 12 mm.
  • the rice panicle trait control gene PT2 disclosed in the present invention has a large positive effect on ear length and 1000-grain weight, and the total storage capacity is extremely significantly increased, which can provide new genetic resources for rice high-yield breeding.
  • PT2 has a large positive effect on the grain length, and through the polymerization with the narrow grain gene, it can choose to breed high-grade long-grain high-quality rice varieties.
  • PT2 can significantly reduce grain shattering and reduce losses during mechanized harvesting.
  • the heterozygous genotype (PT2pt2) kept the grain number per spike and 1000-grain weight at a high level, greatly increasing the storage capacity, and providing technical support for high-yield breeding of hybrid rice.
  • the PT2 gene of the present invention has homologous genes in many plants such as corn and sorghum, and the PT2 gene can be used not only for rice but also for breeding new varieties of other plants.

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Abstract

提供了水稻穗部性状调控基因PT2及其应用。该PT2基因的核苷酸序列如SEQ ID NO.1所示，其能调控水稻穗部性状包括粒形、千粒重、穗长和籽粒落粒性。还提供了PT2基因的等位基因pt2-J和pt2-I，其核苷酸序列如SEQ ID NO.3和SEQ ID NO.5所示。该PT2基因及其等位基因可用于植物新品种的选育，同时可降低水稻籽粒落粒性以减少机械化收获过程中的损失，也可用于玉米、高粱等其它植物新品种的培育。

Description

水稻穗部性状调控基因PT2及其应用 技术领域
本发明属于植物基因工程领域，具体涉及一种水稻穗部性状调控基因PT2，同时还涉及该基因在水稻、玉米等植物育种中的应用。
背景技术
水稻是世界上最重要的粮食作物之一，全球一半以上的人口以大米为主食，稻谷的产量及品质关系到世界的粮食安全。水稻穗部性状包括穗长、一次枝梗数、二次枝梗数、粒形、每穗粒数等，对水稻的产量和品质有重要影响。
以水稻穗部性状——粒形为例，粒形包括粒长、粒宽、粒厚，它不仅直接影响水稻产量的重要构成因子——千粒重，同时也对稻米的外观品质、商品品质和加工品质有重要影响。因此，水稻粒形的遗传机制和分子机理研究对水稻高产及优质育种有着重要的理论和实践意义。迄今为止，根据国际数据库Gramene公布的数据，已有508个控制水稻粒形性状的QTL被定位，分布在水稻的12条染色体上。目前已有若干控制粒形的主效基因通过图位克隆的方法被克隆出来，如GS3、GW2、GW5、TGW6、GS5、GW8等(Fan et al.，2006，Theor.Appl.Genet.112:1164-1171；Song et al.，2007，Nature Genetics39:623-630；Weng et al.,2008,Cell Research,18(12):1199-1209；Ishimaru et al.2013，Nature Genetics,45(6):707-711；Li et al.,2011,Nature Genetics,43(12):1266-1269；Wang et al.,2012,Nature Genetics,44(8):950-954)。其它穗部性状的研究进展，如穗长、一次枝梗数、二次枝梗数、每穗粒数、落粒性，与粒形的研究进展相类似，一般定位了较多相关QTL或基因，同时有部分基因被克隆出来。
根据目前的研究结果来看，水稻穗部性状的基因调控网络比较复杂：其中有主效调控基因，也存在大量的微效QTL；有多效基因， 也有只影响单一或少数性状的基因。同时，基因之间存在复杂的互作关系。因此，迫切需要克隆更多与穗部性状相关的新基因，在了解单个基因功能的基础上逐渐明晰其基因调控网络，从而为新品种培育提供基因资源和理论依据。
发明内容
本发明的目的是为水稻及其它植物提供一种新的穗部性状调控基因及其应用。
为了实现本发明目的，本发明首先提供一种水稻穗部性状调控基因PT2，其核苷酸序列含有如SEQ ID NO.1的第2102～3286位所示的核苷酸序列；或该序列经替换、缺失或增加一个或多个核苷酸，且编码相同或相似，且具有相同功能的氨基酸序列的核苷酸序列。
其中，调控主效基因PT2的启动子的核苷酸序列如序列表SEQ ID NO.1中1-2014位对应的核苷酸所示。
进一步地，所述水稻穗部性状调控基因PT2，其核苷酸序列如SEQ ID NO.1所示。
本发明还提供了所述水稻穗部性状调控基因PT2编码的蛋白，其具有SEQ ID NO.2所示的氨基酸序列。
本发明还提供了所述水稻穗部性状调控基因PT2的等位基因pt2-J，其核苷酸序列含有如SEQ ID NO.3的第2098～3237位所示的核苷酸序列；或该序列经替换、缺失或增加一个或多个核苷酸，且编码相同或相似，且具有相同功能的氨基酸序列的核苷酸序列。
其中，pt2-J启动子的核苷酸序列如序列表SEQ ID NO.3中1-2010位对应的核苷酸所示。
进一步地，所述水稻穗部性状调控基因pt2-J，其核苷酸序列如SEQ ID NO.3所示。
本发明还提供了所述水稻穗部性状调控基因pt2-J编码的蛋白，其具有SEQ ID NO.4所示的氨基酸序列。
本发明还提供了所述水稻穗部性状调控基因PT2的等位基因pt2-I，其核苷酸序列含有如SEQ ID NO.5的第2088～3272位所示的核苷酸序列；或该序列经替换、缺失或增加一个或多个核苷酸，且编码相同或相似，且具有相同功能的氨基酸序列的核苷酸序列。
其中，pt2-I启动子的核苷酸序列如序列表SEQ ID NO.5中1-1991位对应的核苷酸所示。
进一步地，所述水稻穗部性状调控基因pt2-I，其核苷酸序列如SEQ ID NO.5所示。
本发明还提供了所述水稻穗部性状调控基因pt2-I编码的蛋白，其具有SEQ ID NO.6所示的氨基酸序列。
本发明还提供了含有所述水稻穗部性状调控基因PT2或pt2-J或pt2-I的载体。
本发明还提供了所述水稻穗部性状调控基因PT2或pt2-J或pt2-I在水稻及其它植物新品种选育中的应用。
本发明还提供了所述水稻穗部性状调控基因PT2或pt2-J或pt2-I在调节水稻及其它植物穗部性状中的应用。
本发明还提供了所述水稻穗部性状调控基因PT2或pt2-J或pt2-I在制备转基因水稻及其它植物中的应用。
本发明的有益效果在于：
(1)本发明在水稻中克隆的新基因PT2对穗长和千粒重具有较大正效应，总库容量极显著增加，可为水稻高产育种提供新的基因资源。新基因PT2对粒长具有较大正效应，通过与窄粒基因的聚合，可选育出高档长粒优质稻新品种。
(2)本发明中新基因PT2显著降低籽粒落粒性，可减少水稻机械化收获过程中的损失。
(3)相似遗传背景条件下，杂合基因型(PT2pt2)可使穗粒数和千粒重保持较高水平，大幅增加库容量。因此，杂合基因型(PT2pt2)可 大幅提高杂交水稻的库容量，并显著降低籽粒落粒性，为杂交水稻高产育种提供技术支持。
(4)本发明中的PT2基因在玉米、高粱等众多植物中具有同源基因，PT2基因不仅可用于水稻，也可用于其它植物的新品种培育。
附图说明
图1为本发明PT2基因在水稻全生育期不同组织中表达水平示意图。使用材料是2个近等基因系材料R642-1(基因型为pt2pt2,pt2来自R1126)和R642-2(基因型为PT2PT2,PT2来自CDL)。
图2为本发明PT2候选基因的互补验证。A.超表达植株粒型图，标尺:10mm；B.超表达植株穗型图，标尺:10cm；C.干涉植株粒型图，标尺:10mm；D.干涉植株穗型图，标尺:10cm。OX和RNAi分别表示超表达和RNA干涉；(+)和(-)分别表示T1代转基因阳性和阴性植株。
图3为本发明克隆的PT2基因的结构示意图和其自然变异分析。其中：黑色的方框代表外显子，细线代表内含子，“ATG”和“TGA”分别是翻译起始密码子和终止密码子，ATG前的粗线代表2000bp的启动子，大粒和中粒间的38个SNP和InDel变异位于PT2基因的启动子和编码区(SNP替换均用相应的碱基代表，InDel缺失均用相应的圆点代表)，编码区有3个氨基酸变异，内含子有11个SNP变异和3个InDel变异。
图4为本发明超表达和RNA干涉植株穗部性状的比较。所有的数据用平均值±SD表示(n＝6株)，T测验用于计算P值。OX和RNAi分别表示超表达和RNA干涉；(+)和(-)分别表示T1代转基因阳性和阴性植株；BTS(breaking tensile strength)表示籽粒抗拉强度。
具体实施方式
以下实施例用于说明本发明，但不用来限制本发明的范围。
2013年，本申请发明人成功将1个控制粒长、粒宽和千粒重的主效基因首次精细定位到水稻第2染色体上的33.2kb区间，推测LOC_Os02g47280就是候选基因，并将该基因初步命名为GS2(Grain shape 2)(Zhang et al.,2013)，但当时没有完成后续基因克隆工作。后续考察分析表明，来自‘CDL’的大粒基因GS2不仅可显著增加粒长、粒宽和千粒重，而且显著增加穗长，显著降低落粒性(表1)，发明人将该穗部性状调控基因重新命名为PT2(Panicle Traits 2)。Real-Time PCR表达分析表明：在决定穗部性状发育的关键期——幼穗期，PT2PT2基因型具有较高的表达量，其隐性等位基因型pt2pt2表达量较低(图1)，推测LOC_Os02g47280基因表达量的不同导致了功能及表型的差异。通过转基因验证试验证实，过表达单株中LOC_Os02g47280基因表达量增加，穗长、粒长、粒宽显著增加；RNA干涉单株中LOC_Os02g47280基因表达量降低，穗长、粒长、粒宽显著降低。至此，本发明人完成了对PT2基因的克隆。
本发明的PT2基因优选自水稻，但是与水稻PT2基因高度同源的其它植物基因也在本发明保护的范围之内。
实施例1 基因的精细定位、表型分析与命名
发明人经过深入的研究，成功将1个控制粒长、粒宽和千粒重的新主效基因GS2(Grain Shape 2)精细定位到水稻第2染色体上的33.2kb区间，推测LOC_Os02g47280就是候选基因GS2(Zhang et al.,2013)。该基因可使水稻粒长增加3mm、粒宽增加0.4mm、千粒重增加18g以上(不同遗传背景下增幅可能有差异)。后续研究表明，该基因不仅可显著增加粒长、粒宽和千粒重，而且显著增加穗长，显著降低籽粒落粒性，发明人将其重新命名为PT2(Panicle Traits 2)。PT2基因可同时调控水稻的穗长和千粒重，从而对产量和品质产生重要影响。
表1 LOC_Os02g47280基因的近等基因系材料穗部性状考种结果
Figure PCTCN2015073574-appb-000001
注：R642-1和R642-2来自R1126/CDL的重组自交系群体(F8)，仅在LOC_Os02g47280基因上存在差异，遗传背景基本一致，为近等基因系。R642-1为中粒材料(pt2pt2，pt2来自亲本R1126)，R642-2为大粒材料(PT2PT2，PT2来自亲本CDL)。BTS(breaking tensile strength)表示籽粒抗拉强度，测量材料为齐穗期后40天。
实施例2 LOC_Os02g47280基因的Real-Time PCR表达分析
Real-Time PCR表达分析发现，LOC_Os02g47280基因全生育期在各个器官中表达，但在幼穗中表达量较高，此时正是幼穗生长发育的关键时期，与其主要影响水稻穗部性状的表型相一致。在大多数的组织材料中，大粒材料R642-2(PT2PT2)的表达量显著高于中粒材料R642-1(pt2pt2)(图1)，预测LOC_Os02g47280基因表达量的不同导致了基因功能及表型的差异。
实施例3 LOC_Os02g47280功能预测
根据Interproscan(http://www.ebi.ac.uk/Interproscan/)对蛋白质结构进行预测，LOC_Os02g47280基因编码的蛋白质由394个氨基酸组成，包含WRC和QLQ两个保守的结构域，这两个结构域分别与DNA的结合和蛋白质间的互作有关(Kim et al.，2003，plant J.36:94-104)。利用BLASTp对LOC_Os02g47280基因编码的由394个氨基酸组成的蛋白质结构进行搜索，发现该基因编码一生长调控因子蛋白，属于GRF蛋白家族。以前的研究表明该蛋白家族参与水稻茎的生长调控和种子的发育、拟南芥子叶和叶的生长(Knaap et al.，2000，plant physiol.122:695-704；Kim et al.，2003，plant J.36:94-104；Ye et al.，2004，plant J.38:348-357)。
实施例4 比较测序确定PT2等位基因间的自然变异
1、序列测定
对包括R642-1(中粒)和R642-2(大粒)在内不同粒形的26个材料的LOC_Os02g47280基因(包括编码区和启动子区)测序。利用12对PCR产物相互部分重叠的引物(表2)，采用高保真度的TransStart FastPfu Fly DNA Polymerase(购自TransGen公司)从这些品种的基因组中进行PCR扩增，然后将PCR产物送铂尚生物公司测序。使用Sequencher 4.5软件(美国Gene Codes Corporation)拼接序列。两个等位基因的DNA序列如SEQ ID NO：1(CDL)和SEQ ID NO：3(R1126)所示。
表2 用于本发明比较测序的引物
Figure PCTCN2015073574-appb-000002
2、发生自然变异的序列比较
对26个材料LOC_Os02g47280基因的编码区和启动子区进行了比较分析(图3)。发现有10个材料的启动子区与大粒材料R642-2和CDL完全一致。这10个材料大部分粒长较长，但存在粒长很短的类型(如Ⅱ-32A、炳1A)(表3)。编码区的变异主要存在两种类型，一种为籼 稻类型(pt2-I)，一种为粳稻类型(pt2-J)，大粒材料R642-2和CDL基本上与籼稻类型一致，但在编码区还有一个与籼、粳均不相同的特有变异，此变异在其余24个材料中均未发现(表4)。利用公共分子生物学数据资源(http://ricevarmap.ncpgr.cn/django/region/)，分析了一千多份材料，结果与之相类似：存在籼稻、粳稻两种类型的变异，没发现与大粒材料R642-2和CDL特有变异一致的材料。前人研究结果表明，miRNA396对LOC_Os02g47280基因起负调控作用(翟俊淼等，2013)，大粒材料R642-2和CDL的特有变异区域正是miRNA396对LOC_Os02g47280基因的调控位点，说明该变异有可能使miRNA396对LOC_Os02g47280基因的调控减弱，导致LOC_Os02g47280基因的表达量增加，进而使水稻的穗部性状发生改变。因此，启动子差异和编码区的特有变异(或两者之一)是导致R642-2和CDL(PT2PT2)较R642-1(pt2pt2)穗长、粒长、粒宽显著增加及籽粒落粒性显著降低的原因。
Figure PCTCN2015073574-appb-000003
Figure PCTCN2015073574-appb-000004
Figure PCTCN2015073574-appb-000005
Figure PCTCN2015073574-appb-000006
表4 26个测序材料的编码区差异与粒长
Figure PCTCN2015073574-appb-000007
实施例5 LOC_Os02g47280基因的转基因互补试验
超表达载体构建及转化：根据目的基因序列设计引物1390DL-1(表5)从大粒亲本CDL扩增到目的基因组DNA 4073bp，用BamH I单酶切pCUbi1390载体，利用clontech infusion试剂盒将目的片段与线性化的载体进 行融合，转化感受态细胞，挑阳性单克隆质粒测序，无突变的正确质粒转化农杆菌感受态，进行农杆菌介导的遗传转化到供体材料R642-1(中粒材料)。MicroRNA干扰载体构建及转化：以pNW55载体为模板设计下列引物扩增获得290bp MicroRNA片段：
I miR-s agTAAAACGTTGACATCTCCCTTcaggagattcagtttga；
II miR-a tgAAGGGAGATGTCAACGTTTTActgctgctgctacagcc；
III miR*s ctAAGGGTGATCTCAACGTTTTAttcctgctgctaggctg；
IV miR*a aaTAAAACGTTGAGATCACCCTTagagaggcaaaagtgaa。
将MicroRNA片段添加PstI和SpeI酶切位点，双酶切目的片段和载体pCUbi1390，然后进行连接反应，转化感受态细胞，挑阳性单克隆测序，将得到正确克隆的质粒通过农杆菌介导的水稻遗传转化体系导入到水稻大粒材料R642-2中，经过诱导、继代、侵染、共培养，筛选具有潮霉素抗性的愈伤，分化、生根、练苗移栽，得到转基因的水稻小植株。农杆菌介导的水稻遗传转化委托武汉伯远生物科技有限公司完成。
表5 用于本发明表达分析和克隆的引物
Figure PCTCN2015073574-appb-000008
本发明共获得独立转基因过表达T0代水稻植株15株，包括8株阳性单株和7株阴性单株；干扰T0代水稻植株18株，包括10株阳性单株和8株阴性单株。过表达T1代水稻阳性单株的粒形接近大粒材料R642-2，阴性单 株与中粒材料R642-1粒形相似(图2)。上述结果证明了来自‘CDL’的LOC_Os02g47280基因就是PT2QTL；RNA干扰T1代水稻阳性单株粒形接近中粒材料R642-1，阴性单株粒形与大粒材料R642-2一致。干扰植株的粒形接近中粒材料R642-1的结果进一步说明，LOC_Os02g47280基因的表达量变化是导致穗部性状发生变化的主要原因：表达量增加，粒长、粒宽、千粒重、穗长增加，籽粒落粒性显著降低；表达量减少，粒长、粒宽、千粒重、穗长减少，籽粒变得容易落粒(图4)。同时也表明可通过控制LOC_Os02g47280基因的表达量来调控水稻的穗部性状。至此，本发明人完成了对穗部性状调控基因PT2的克隆工作。
实施例6 利用PT2基因培育高产新品种
2012年11月到2013年3月，利用携带PT2基因的恢复系R642-2所配组合Y58S/R642-2、Pi-2S/R642-2在海南种植，每穗粒数、有效穗数与对照Y两优1号相当；Y58S/R642-2的穗长、粒长、粒宽、千粒重、库容量均大于对照Y两优1号(长江中下游地区中稻主栽品种)，且差异都达显著或极显著水平；Pi-2S/R642-2的穗长、粒长、粒宽与对照Y两优1号相当，一次枝梗、二次枝梗、千粒重、库容量均大于对照，且差异都达极显著水平(见表6)。R642-2每穗粒数极显著少于R1126，但其所配组合Y58S/R642-2、Pi-2S/R642-2在每穗粒数上与对照相当，库容量极显著高于对照Y两优1号，说明其具有较好的配合力。Y58S/R642-2、Pi-2S/R642-2在中等偏高肥力水平条件下库容量分别高达15.82t/hm2和15.87t/hm2，而对照Y两优1号为11.54t/hm2。实收测产结果显示，Y58S/R642-2(10.07t/hm2，结实率85.2％)较对照Y两优1号(8.13t/hm2，结实率88.9％)增产23.8％，Pi-2S/R642-2(9.29t/hm2，结实率78.3％)较对照Y两优1号增产14.2％。
表6 R642-2所配组合长沙种植的产量性状
Figure PCTCN2015073574-appb-000009
实施例7 利用PT2基因创制特长粒新材料
粒长较短一直是中国籼米不及国际名牌大米的指标之一。长粒杂交稻的选育难度较大，因为杂种的粒长一般接近于不育系和恢复系粒长的平均值，如果双亲之一粒长较短，商品大米的粒长就不会很长。一般公认的长粒优质稻稻谷粒长在12mm左右。利用携带PT2基因的材料和长粒优质稻杂交，目前本发明人已选育出粒长达15mm以上的特长粒新材料。当然，粒长过长也会带来整精米率低的弊端。但以上述特长粒新材料作恢复系，与一般水稻不育系(稻谷粒长8～9mm)配组，即可培育出粒长在12mm左右的高档高产优质稻新品种。
虽然，上文中已经用一般性说明及具体实施方案对本发明作了详尽的描述，但在本发明基础上，可以对之作一些修改或改进，这对本领域技术人员而言是显而易见的。因此，在不偏离本发明精神的基础上所做的这些修改或改进，均属于本发明要求保护的范围。
工业实用性
本发明公开的水稻穗部性状调控基因PT2对穗长和千粒重具有较大正效应，总库容量极显著增加，可为水稻高产育种提供新的基因资源。PT2对粒长具有较大正效应，通过与窄粒基因的聚合，可选育出高档长粒优质稻新品种。PT2可显著降低籽粒落粒性，可减少机械化收获过程中的损失。相似遗传背景条件下，杂合基因型(PT2pt2)使穗粒数和千粒重保持较高水平，大幅增加库容量，可为杂交水稻高产育种提供技术支持。本发明中的PT2基因在玉米、高粱等众多植物中具有同源基因，PT2基因不仅可用于水稻，也可用于其它植物的新品种培育。
Figure PCTCN2015073574-appb-000010
Figure PCTCN2015073574-appb-000011
Figure PCTCN2015073574-appb-000012
Figure PCTCN2015073574-appb-000013
Figure PCTCN2015073574-appb-000014
Figure PCTCN2015073574-appb-000015
Figure PCTCN2015073574-appb-000016
Figure PCTCN2015073574-appb-000017
Figure PCTCN2015073574-appb-000018
Figure PCTCN2015073574-appb-000019
Figure PCTCN2015073574-appb-000020
Figure PCTCN2015073574-appb-000021

Claims (9)

  1. 水稻穗部性状调控基因PT2，其特征在于，其核苷酸序列如SEQ ID NO.1所示。
  2. 权利要求1所述的水稻穗部性状调控基因PT2的等位基因pt2-J，其特征在于，其核苷酸序列如SEQ ID NO.3所示。
  3. 权利要求1所述的水稻穗部性状调控基因PT2的等位基因pt2-I，其特征在于，其核苷酸序列如SEQ ID NO.5所示。
  4. 含有权利要求1所述水稻穗部性状调控基因PT2的载体。
  5. 含有权利要求2所述水稻穗部性状调控基因PT2等位基因pt2-J的载体。
  6. 含有权利要求3所述水稻穗部性状调控基因PT2等位基因pt2-I的载体。
  7. 权利要求1所述的水稻穗部性状调控基因PT2在水稻、玉米等植物新品种选育中的应用。
  8. 权利要求1所述的水稻穗部性状调控基因PT2在调节水稻、玉米等植物新品种穗部性状中的应用。
  9. 权利要求1所述的水稻穗部性状调控基因PT2在制备转基因水稻、玉米等植物新品种中的应用。
PCT/CN2015/073574 2014-03-26 2015-03-03 水稻穗部性状调控基因pt2及其应用 WO2015143972A1 (zh)

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CN112375130B (zh) * 2020-11-27 2021-12-24 华中农业大学 玉米穗长基因和分子标记及其应用
CN114686460A (zh) * 2020-12-30 2022-07-01 中国科学院分子植物科学卓越创新中心 调控禾谷类植物粒宽的基因及其应用
CN113817755A (zh) * 2021-09-18 2021-12-21 中国水稻研究所 水稻长粒基因log1及其应用
CN113817754A (zh) * 2021-09-18 2021-12-21 中国水稻研究所 水稻短粒基因shg1及其应用
CN113817755B (zh) * 2021-09-18 2023-03-31 中国水稻研究所 水稻长粒基因log1及其应用
CN113817754B (zh) * 2021-09-18 2023-03-31 中国水稻研究所 水稻短粒基因shg1及其应用

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