Skip to main content
SpringerLink
Log in

Seed size is determined by the combinations of the genes controlling different seed characteristics in rice

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Rice seed size is an important agronomic trait in determining the yield potential, and four seed size related genes (GS3, GW2, qSW5/GW5 and GIF1) have been cloned in rice so far. However, the relationship among these four genes is still unclear, which will impede the process of gene pyramiding breeding program to some extent. To shade light on the relationship of above four genes, gene expression analysis was performed with GS3-RNAi, GW2-RNAi lines and CSSL of qSW5 at the transcriptional level. The results clearly showed that qSW5 and GW2 positively regulate the expression of GS3. Meanwhile, qSW5 can be down-regulated by repression of GW2 transcription. Additionally, GIF1 expression was found to be positively regulated by qSW5 but negatively by GW2 and GS3. Moreover, the allelic effects of qSW5 and GS3 were detailedly characterized based on a natural population consisting of 180 rice cultivars. It was indicated that mutual interactions exist between the two genes, in which, qSW5 affecting seed length is masked by GS3 alleles, and GS3 affecting seed width is masked by qSW5 alleles. These findings provide more insights into the molecular mechanisms underlying seed size development in rice and are likely to be useful for improving rice grain yield.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Ando T, Yamamoto T, Shimizu T, Ma XF, Shomura A, Takeuchi Y, Lin SY, Yano M (2008) Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice. Theor Appl Genet 116:881–890

    Article  PubMed  Google Scholar 

  • Bai X, Luo L, Yan W, Kovi MR, Zhan W, Xing Y (2010) Genetic dissection of rice grain shape using a recombinant inbred line population derived from two contrasting parents and fine mapping a pleiotropic quantitative trait locus qGL7. BMC Genet 26:11–16

    Google Scholar 

  • Benfey PN, Mitchell-Olds T (2008) From genotype to phenotype: Systems biology meets natural variation. Science 320:495–497

    Article  PubMed  CAS  Google Scholar 

  • Colombatti A, Bonaldo P, Doliana R (1993) Type A modules: interacting domains found in several non–fibrillar collagens and in other extracellular matrix proteins. Matrix 13:297–306

    PubMed  CAS  Google Scholar 

  • Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171

    Article  PubMed  CAS  Google Scholar 

  • Fan C, Yu S, Wang C, Xing Y (2009) A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker. Theor Appl Genet 118:465–472

    Article  PubMed  CAS  Google Scholar 

  • He X, Zhang J (2006) Toward a molecular understanding of pleiotropy. Genetics 173:1885–1891

    Article  PubMed  CAS  Google Scholar 

  • Hiei Y, Ohta S, Komari T, Kumashiro T (1994) Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium tumeficience and sequence analysis of the boundaries of the T-DNA. Plant J 6:271–282

    Article  PubMed  CAS  Google Scholar 

  • Huang N, Parco A, Mew T, Magpantay G, McCouch S, Guiderdoni E, Xu J, Subudhi P, Angeles ER, Khush GS (1997) RFLP mapping of isozymes, RAPD and QTLs for grain shape, brown planthopper resistance in a doubled haploid rice population. Mol Breed 3:105–113

    Article  CAS  Google Scholar 

  • Kubo T, Takano-Kai N, Yoshimura A (2001) RFLP mapping of genes for long kernel and awn on chromosome 3 in rice. Rice Genet Newsl 18:26–28

    CAS  Google Scholar 

  • Lei DY, Xie FM, Xu JL, Chen LY (2008) QTL mapping and epistasis analysis for grain shape and chalkiness degree of rice. Chinese J Rice Sci 22:255–260

    Google Scholar 

  • Li JM, Thomson M, McCouch SR (2004) Fine mapping of a grain weight quantitative trait locus in the pericentromeric region of rice chromosome 3. Genetics 168:2187–2195

    Article  PubMed  CAS  Google Scholar 

  • Lin LH, Wu WR (2003) Mapping of QTL underlying grain shape and grain weight in rice. Mol Plant Breed 1:337–342

    CAS  Google Scholar 

  • Lin HX, Min SK, Xiong ZM, Qian HR, ZhuangJY LuJ, Huang N, Zheng KL (1995) RFLP mapping of QTLs for grain shape traits in indica rice (Oryza sativa L. subsp. indica). Scientia Agric Sin 28:1–7

    Google Scholar 

  • Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA 107:19579–19584

    Article  PubMed  CAS  Google Scholar 

  • O’Leary JM, Hamilton JM, Deane CM, Valeyev NV, Sandell LJ, Downing AK (2004) Solution structure and dynamics of a prototypical chordin-like cysteine-rich repeat (von Willebrand Factor type C module) from collagen IIA. J Biol Chem 279:53857–53866

    Article  PubMed  Google Scholar 

  • Rabiei B, Valizadeh M, Ghareyazie B, Moghaddam M, Ali AJ (2004) Identification of QTLs for rice grain size and shape of Iranian cultivars using SSR markers. Euphytica 137:325–332

    Article  CAS  Google Scholar 

  • Redona ED, Mackill DJ (1998) Quantitative trait locus analysis for rice panicle and grain characteristics. Theor Appl Genet 96:957–963

    Article  CAS  Google Scholar 

  • Rogers SO, Bendch AJ (1988) Extraction of DNA from plant tissues. Plant Mol Biol Man 6:1–10

    Google Scholar 

  • Shi ZY, Wang J, Wan XS, Shen GZ, Wang XQ, Zhang JL (2007) Over-expression of rice OsAGO7 gene induces upward curling of the leaf blade that enhanced erect–leaf habit. Planta 226:99–108

    Article  PubMed  CAS  Google Scholar 

  • Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023–1028

    Article  PubMed  CAS  Google Scholar 

  • Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING—type E3 ubiquitin ligase. Nat Genet 39:623–630

    Article  PubMed  CAS  Google Scholar 

  • Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamante C, Yoshimura A, Doi K, McCouch S (2009) Evolutionary history of GS3, a gene conferring grain size in rice. Genetics 182:1323–1334

    Article  PubMed  CAS  Google Scholar 

  • Tan YF, Xing YZ, Li JX, Yu SB, Xu CG, Zhang Q (2000) Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid. Theor Appl Genet 101:823–829

    Article  CAS  Google Scholar 

  • Thomson MJ, Tai TH, McClung AM, Lai XH, Hinga ME, Lobos KB, Xu Y, Martinez CP, McCouch SR (2003) Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479–493

    Article  PubMed  CAS  Google Scholar 

  • Tian F, Li DJ, Fu Q, Zhu ZF, Fu YC, Wang XK, Sun CQ (2005) Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor Appl Genet 112:570–580

    Article  PubMed  Google Scholar 

  • Wan XY, Wan JM, Jiang L, Wang JK, Zhai HQ, Weng JF, Wang HL, Lei CL, Wang JL, Zhang X, Cheng ZJ, Guo XP (2006) QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects. Theor Appl Genet 112:1258–1270

    Article  PubMed  CAS  Google Scholar 

  • Wan XY, Weng JF, Zhai HQ, Wang JK, Lei CL, Liu XL, Guo T, Jiang L, Su N, Wan JM (2008) Quantitative trait loci (QTL) analysis for rice grain width and fine mapping of an identified QTL allele gw-5 in a recombination hotspot region on the chromosome 5. Genetics 179:2239–2252

    Article  PubMed  CAS  Google Scholar 

  • Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q, Zhang L, He W, Lu B, Lin H, Ma H, Zhang G, He Z (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40:1370–1374

    Article  PubMed  CAS  Google Scholar 

  • Wang C, Chen S, Yu S (2011) Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice. Theor Appl Genet 122:905–913

    Article  PubMed  Google Scholar 

  • Weng JF, Gu SH, Wan XY, Gao H, Guo T, Su N, Lei CL, Zhang X, Cheng ZJ, Guo XP, Wang JL, Jiang L, Zhai HQ, Wan JM (2008) Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res 18:1199–1209

    Article  PubMed  CAS  Google Scholar 

  • Williams GC (1957) Pleiotropy, natural selection, and the evolution of senescence. Evolution 11:398–411

    Article  Google Scholar 

  • Xie XB, Song MH, Jin FX, Ahn SN, Suh JP, Hwang HG, McCouch SR (2006) Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between Oryza sativa and Oryza rufipogon. Theor Appl Genet 113:885–894

    Article  PubMed  CAS  Google Scholar 

  • Xing YZ, Tan YF, Xu CG, Hua JP, Sun XL (2001) Mapping quantitative trait loci for grain appearance traits of rice using a recombinant inbred line population. Acta Bot Sin 43:840–845

    CAS  Google Scholar 

  • Xu JL, Xue QZ, Luo LJ, Li ZK (2002) Genetic dissection of grain weight and its related traits in rice (Oryza sativa L.). Chinese J Rice Sci 16:6–10

    Google Scholar 

  • Yamagishi M, Takeuchi Y, Kono I, Yano M (2002) QTL analysis for panicle characteristics in temperate japonica rice. Euphytica 128:219–224

    Article  CAS  Google Scholar 

  • Yan CJ, Liang GH, Chen F, Li X, Yi CD, Tian S, Lu JF, Gu MH (2003) Mapping quantitative trait loci associated with rice grain shape based on an Indica/Japonica backcross population. Acta Genetica Sin 30:711–716

    CAS  Google Scholar 

  • Yan CJ, Zhou JH, Yan S, Chen F, Yeboah M, Tang SZ, Liang GH, Gu MH (2007) Identification and characterization of a major QTL responsible for erect panicle trait in japonica rice (Oryza sativa L.). Theor Appl Genet 115:1093–1100

    Article  PubMed  CAS  Google Scholar 

  • Yan CJ, Yan S, Yang YC, Zeng XH, Fang YW, Zeng SY, Tian CY, Sun YW, Tang SZ, Gu MH (2009) Development of gene-tagged markers for quantitative trait loci underlying rice yield components. Euphytica 169:215–226

    Article  CAS  Google Scholar 

  • Yoon DB, Kang KH, Kim HJ, Ju HG, Kwon SJ, Suh JP, Jeong QY, Ahn SN (2006) Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza grandiglumis and the O. sativa japonica cultivar Hwaseongbyeo. Theor Appl Genet 112:1052–1062

    Article  PubMed  CAS  Google Scholar 

  • Zhang JL, Huang Y, Qiu LY, Nickel J, Sebald W (2007) von Willebrand factor type C domain-containing proteins regulate bone morphogenetic protein signaling through different recognition mechanisms. J Biol Chem 282:20002–20014

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This study was financially supported by the Ministry of Science and Technology of China ( Grant No. 2006AA10A102) and the Ministry of Agriculture of China (Grant No. 2009ZX08001-008B), the National Natural Science Foundation of China (Grant No. 31071385), and the Key Subject Construction Program of Zhejiang for Modern Agricultural Biotechnology and Crop Disease Control.

Author information

Authors and Affiliations

  1. State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou, 310021, People’s Republic of China

    Song Yan, Guihua Zou, Sujuan Li, Hua Wang, Heqin Liu, Guowei Zhai, Peng Guo, Hongmiao Song & Yuezhi Tao

  2. Rice Research Institute, Jiangxi Academy of Agricultural Sciences, 602 Nanlian Road, Nanchang, 330200, People’s Republic of China

    Song Yan

  3. The Key Laboratory of Plant Functional Genomics, Ministry of Education of China; Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, 12 East Wenhui Road, Jiangsu, 225009, People’s Republic of China

    Changjie Yan

Authors
  1. Song Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Guihua Zou
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sujuan Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hua Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Heqin Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Guowei Zhai
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Peng Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hongmiao Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Changjie Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yuezhi Tao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yuezhi Tao.

Additional information

Communicated by A. Paterson.

S. Yan and G. Zou contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 647 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yan, S., Zou, G., Li, S. et al. Seed size is determined by the combinations of the genes controlling different seed characteristics in rice. Theor Appl Genet 123, 1173–1181 (2011). https://doi.org/10.1007/s00122-011-1657-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-011-1657-x

Keywords

Search

Navigation