Theoretical and Applied Genetics

, 123:1173 | Cite as

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

  • Song Yan
  • Guihua Zou
  • Sujuan Li
  • Hua Wang
  • Heqin Liu
  • Guowei Zhai
  • Peng Guo
  • Hongmiao Song
  • Changjie Yan
  • Yuezhi Tao
Original Paper

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.

Supplementary material

122_2011_1657_MOESM1_ESM.doc (648 kb)
Supplementary material 1 (DOC 647 kb)

References

  1. 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 116:881–890PubMedCrossRefGoogle Scholar
  2. 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 26:11–16Google Scholar
  3. Benfey PN, Mitchell-Olds T (2008) From genotype to phenotype: Systems biology meets natural variation. Science 320:495–497PubMedCrossRefGoogle Scholar
  4. 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 13:297–306PubMedGoogle Scholar
  5. 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 112:1164–1171PubMedCrossRefGoogle Scholar
  6. 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 118:465–472PubMedCrossRefGoogle Scholar
  7. He X, Zhang J (2006) Toward a molecular understanding of pleiotropy. Genetics 173:1885–1891PubMedCrossRefGoogle Scholar
  8. 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 6:271–282PubMedCrossRefGoogle Scholar
  9. 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 3:105–113CrossRefGoogle Scholar
  10. 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 18:26–28Google Scholar
  11. 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 22:255–260Google Scholar
  12. 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 168:2187–2195PubMedCrossRefGoogle Scholar
  13. Lin LH, Wu WR (2003) Mapping of QTL underlying grain shape and grain weight in rice. Mol Plant Breed 1:337–342Google Scholar
  14. 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 28:1–7Google Scholar
  15. 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 107:19579–19584PubMedCrossRefGoogle Scholar
  16. 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 279:53857–53866PubMedCrossRefGoogle Scholar
  17. 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 137:325–332CrossRefGoogle Scholar
  18. Redona ED, Mackill DJ (1998) Quantitative trait locus analysis for rice panicle and grain characteristics. Theor Appl Genet 96:957–963CrossRefGoogle Scholar
  19. Rogers SO, Bendch AJ (1988) Extraction of DNA from plant tissues. Plant Mol Biol Man 6:1–10Google Scholar
  20. 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 226:99–108PubMedCrossRefGoogle Scholar
  21. 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 40:1023–1028PubMedCrossRefGoogle Scholar
  22. 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 39:623–630PubMedCrossRefGoogle Scholar
  23. 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 182:1323–1334PubMedCrossRefGoogle Scholar
  24. 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 101:823–829CrossRefGoogle Scholar
  25. 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 107:479–493PubMedCrossRefGoogle Scholar
  26. 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 112:570–580PubMedCrossRefGoogle Scholar
  27. 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 112:1258–1270PubMedCrossRefGoogle Scholar
  28. 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 179:2239–2252PubMedCrossRefGoogle Scholar
  29. 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 40:1370–1374PubMedCrossRefGoogle Scholar
  30. 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 122:905–913PubMedCrossRefGoogle Scholar
  31. 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 18:1199–1209PubMedCrossRefGoogle Scholar
  32. Williams GC (1957) Pleiotropy, natural selection, and the evolution of senescence. Evolution 11:398–411CrossRefGoogle Scholar
  33. 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 113:885–894PubMedCrossRefGoogle Scholar
  34. 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 43:840–845Google Scholar
  35. 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 16:6–10Google Scholar
  36. Yamagishi M, Takeuchi Y, Kono I, Yano M (2002) QTL analysis for panicle characteristics in temperate japonica rice. Euphytica 128:219–224CrossRefGoogle Scholar
  37. 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 30:711–716Google Scholar
  38. 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 115:1093–1100PubMedCrossRefGoogle Scholar
  39. 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 169:215–226CrossRefGoogle Scholar
  40. 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 112:1052–1062PubMedCrossRefGoogle Scholar
  41. 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 282:20002–20014PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Song Yan
    • 1
    • 2
  • Guihua Zou
    • 1
  • Sujuan Li
    • 1
  • Hua Wang
    • 1
  • Heqin Liu
    • 1
  • Guowei Zhai
    • 1
  • Peng Guo
    • 1
  • Hongmiao Song
    • 1
  • Changjie Yan
    • 3
  • Yuezhi Tao
    • 1
  1. 1.State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Crop and Nuclear Technology UtilizationZhejiang Academy of Agricultural SciencesHangzhouPeople’s Republic of China
  2. 2.Rice Research InstituteJiangxi Academy of Agricultural SciencesNanchangPeople’s Republic of China
  3. 3.The Key Laboratory of Plant Functional Genomics, Ministry of Education of China; Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityJiangsuPeople’s Republic of China

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