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Theoretical and Applied Genetics

, Volume 112, Issue 6, pp 1164–1171 | Cite as

GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein

  • Chuchuan Fan
  • Yongzhong Xing
  • Hailiang Mao
  • Tingting Lu
  • Bin Han
  • Caiguo Xu
  • Xianghua Li
  • Qifa Zhang
Original Paper

Abstract

The GS3 locus located in the pericentromeric region of rice chromosome 3 has been frequently identified as a major QTL for both grain weight (a yield trait) and grain length (a quality trait) in the literature. Near isogenic lines of GS3 were developed by successive crossing and backcrossing Minghui 63 (large grain) with Chuan 7 (small grain), using Minghui 63 as the recurrent parent. Analysis of a random subpopulation of 201 individuals from the BC3F2 progeny confirmed that the GS3 locus explained 80–90% of the variation for grain weight and length in this population. In addition, this locus was resolved as a minor QTL for grain width and thickness. Using 1,384 individuals with recessive phenotype (large grain) from a total of 5,740 BC3F2 plants and 11 molecular markers based on sequence information, GS3 was mapped to a DNA fragment approximately 7.9 kb in length. A full-length cDNA corresponding to the target region was identified, which provided complete sequence information for the GS3 candidate. This gene consists of five exons and encodes 232 amino acids with a putative PEBP-like domain, a transmembrane region, a putative TNFR/NGFR family cysteine-rich domain and a VWFC module. Comparative sequencing analysis identified a nonsense mutation, shared among all the large-grain varieties tested in comparison with the small grain varieties, in the second exon of the putative GS3 gene. This mutation causes a 178-aa truncation in the C-terminus of the predicted protein, suggesting that GS3 may function as a negative regulator for grain size. Cloning of such a gene provided the opportunity for fully characterizing the regulatory mechanism and related processes during grain development.

Keywords

Cleave Amplify Polymorphic Sequence Cleave Amplify Polymorphic Sequence Marker BC3F2 Plant Rice Breeding Program Recessive Phenotype 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

This work was supported in part by grants from the National Program on the Development of Basic Research, the National Special Key Project of Functional Genomics and Biochips, and the National Natural Science Foundation of China.

References

  1. Abreu JG, Coffinier C, Larraín J, Oelgeschläger M, Robertis EMD (2002) Chordin-like CR domains and the regulation of evolutionarily conserved extracellular signaling systems. Gene (Amst) 287:39–47Google Scholar
  2. Aluko G, Martinez C, Tohme J, Castano C, Bergman C, Oard HJ (2004) QTL mapping of grain quality traits from the interspecific cross Oryza sativa × O. glaberrima. Theor Appl Genet 109:630–639CrossRefPubMedGoogle Scholar
  3. Brondani C, Rangel PHN, Brondani RPV, Ferreira ME (2002) QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theor Appl Genet 104:1192–1203CrossRefPubMedGoogle Scholar
  4. Evans LT (1972) Storage capacity as a limitation on grain yield. In: Banos Los (ed) Rice breeding. International Rice Research Institute, Manila, pp 499–511Google Scholar
  5. Fan CC, Yu XQ, Xing YZ, Xu CG, Luo LJ, Zhang Q (2005) The main effects, epistatic effects and environmental interactions of QTLs on cooking and eating quality of rice in a doubled haploid line population. Theor Appl Genet 110:1445–14452CrossRefPubMedGoogle Scholar
  6. Hua JP, Xing YZ, Xu CG, Sun XL, Yu SB, Zhang Q (2002) Genetic dissection of an elite rice hybrid revealed that heterozygotes are not always advantageous for performance. Genetics 162:1885–1895PubMedGoogle Scholar
  7. Huang N, Parco A, Mew T, Magpantay G, McCouch S, Guiderdoni E, Xu JC, 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
  8. Juliano BO, Villareal CP (1993) Grain quality evaluation of world rices. International Rice Research Institute, ManilaGoogle Scholar
  9. 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
  10. Li JX, Yu SB, Xu CG, Tan YF, Gao YJ, Li XH, Zhang Q (2000) Analyzing quantitative trait loci for yield using a vegetatively replicated F2 population from a cross between the parents of an elite rice hybrid. Theor Appl Genet 101:248–254CrossRefGoogle Scholar
  11. Li J, Thomson M, McCouch SR (2004a) Fine mapping of a grain-weight quantitative trait locus in the pericentromeric region of rice chromosome 3. Genetics 168:2187–2195CrossRefGoogle Scholar
  12. Li J, Xiao J, Grandillo S, Jiang L, Wan Y, Deng Q, Yuan L, McCouch SR (2004b) QTL detection for rice grain quality traits using an interspecific backcross population derived from cultivated Asian (O. sativa L.) and African (O. glaberrima S.) rice. Genome 47:697–704CrossRefGoogle Scholar
  13. Lincoln S, Daly M, Lander E (1992) Constructing genetics maps with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report, Whitehead Institute, CambridgeGoogle Scholar
  14. Liu JP, Eck JV, Cong B, Tanksley SD (2002) A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc Natl Acad Sci USA 99:13302–13306CrossRefPubMedGoogle Scholar
  15. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2,240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207CrossRefPubMedGoogle 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 279:53857–53866CrossRefPubMedGoogle Scholar
  17. Redoña ED, Mackill (1998) Quantitative trait locus analysis for rice panicle and grain characteristics. Theor Appl Genet 96:957–963CrossRefGoogle Scholar
  18. 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
  19. Temnykh S, Park WD, Ayres N, Cartihour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712CrossRefGoogle Scholar
  20. Temnykh S, Declerck G, Luashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452CrossRefPubMedGoogle Scholar
  21. Thomson M, Tai T, McClung A, Xai XH, Hinga M, Lobos K, Xu Y, Martinez P, McCouch S (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 107:479–493CrossRefPubMedGoogle Scholar
  22. Unnevehr LJ, Duff B, Juliano BO (1992) Consumer demand for rice grain quality. International Rice Research Institute, Manila, and International Development Research Center, OttawaGoogle Scholar
  23. Xiao JH, Li JM, Grandillo S, Ahn SN, Yuan LP, Tanksley SD, McCouch SR (1998) Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics 150:899–909PubMedGoogle Scholar
  24. 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 43:721–726Google Scholar
  25. Xing YZ, Tan YF, Hua JP, Sun XL, Xu CG, Zhang Q (2002) Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theor Appl Genet 105:248–257CrossRefPubMedGoogle Scholar
  26. Xu JY, Xue QZ, Luo LJ, Li ZK (2002) Genetic dissection of grain weight and its related traits in rice (Oryza sativa L.). Chin J Rice Sci 16:6–10 (in Chinese with an English abstract)Google Scholar
  27. Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, Li XH, Zhang Q, Saghai Maroof MA (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 94:9226–9231CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Chuchuan Fan
    • 1
  • Yongzhong Xing
    • 1
  • Hailiang Mao
    • 1
  • Tingting Lu
    • 2
  • Bin Han
    • 2
  • Caiguo Xu
    • 1
  • Xianghua Li
    • 1
  • Qifa Zhang
    • 1
  1. 1.National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
  2. 2.National Center for Gene Research, Shangai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina

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