Abstract
Grain size is a main component of rice appearance quality. In this study, we performed the SSR mapping of quantitative trait loci (QTLs) controlling grain size (grain length and breadth) and shape (length/breadth ratio) using an F2 population of a cross between two Iranian cultivars, Domsephid and Gerdeh, comprising of 192 individuals. A linkage map with 88 markers was constructed, which covered 1367.9 cM of the rice genome with an average distance of 18 cM between markers. Interval mapping procedure was used to identify the QTLs controlling three grain traits, and QTLs detected were further confirmed using composite interval mapping. A total of 11 intervals carrying 18 QTLs for three traits were identifed, that included five QTLs for grain length, seven QTLs for grain breadth, and six QTLs for grain shape. A major QTL for grain length was detected on chromosome 3, that explained 19.3% of the phenotypic variation. Two major QTLs for grain breadth were mapped on chromosomes 3 and 8, which explained 34.1% and 20% of the phenotypic variation, respectively. Another two major QTLs were identified for grain shape on chromosomes 3 and 8, which accounted for 27.1% and 20.5% of the phenotypic variance, respectively. The two QTLs that were mapped for grain shape coincided with the major QTLs detected for grain length and grain breadth. Intrestingly, gs2 QTL specific to grain shape was detected on chromosome 2 that explained 15% of the phenotypic variation.
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References
Basten, C.J., B.S. Weir & Z.B. Zeng, 2001. QTL Cartographer: A reference manual and tutorial for QTL mapping, North Carolina State University, USA.
Brondani, C., P.H.N. Rangel, R.P.V. Brondani & M.E. Ferreira, 2002. QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theor Appl Genet 104: 1192–1203.
Causse, M.A., T.M. Fulton, Y.G. Cho, S.N. Ahn, J. Chunwongse, K. Wu, J. Xiao, A. Yu, P.C. Ronald, S.E. Harrington, G. Second, S.R. McCouch & S.D. Tanksley, 1994. Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138: 1251–1274.
Chen, X., S. Temnykh, Y. Xu, Y.G. Cho & S.R. McCouch, 1997. Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95: 553–567.
Dellaporta, S.C., F. Wood & J.B. Hicks, 1983. A plant DNA minipreparation: Version II. Plant Mol Biol Rep 1(4): 19–21.
Dong, Y. & Y. Zheng, 2002. Quantitative trait loci controlling steamed-rice shape in a recombinant inbred population. IRRN 27(1): 19–20.
He, P., S.G. Li, Q. Qian, Y.Q. Ma, J.Z. Li, W.M. Wang, Y. Chen & L.H. Zhu, 1999. Genetic analysis of rice grain quality. Theor Appl Genet 98: 502–508.
Hittalmani, S., H.E. Shashidhar, P.G. Bagali, N. Huang, J.S. Sidhu, V. P. Singh & G.S. Khush, 2002. Molecular mapping of quantitative trait loci for plant growth, yield and yield related traits across three diverse locations in a doubled haploid rice population. Euphytica 125: 207–214.
Huang, N., A. Parco, T. Mew, G. Magpantay, S.R. McCouch, E. Guiderdoni, J.C. Xu, P. Subudhi, E.R. Angeles & G.S. Khush, 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.
Juliano, B.O., 1985. Rice chemistry and technology. 2nd Edition, American Association of Cereal Chemists, Inc, St. Paul, MN, USA.
Kosambi, D.D., 1944. The estimation of map distances from recombination values. Ann Eugen 12: 172–175.
Lander, E.S., P. Green, J. Abrhamson, A. Barlow, M.J. Daly, S.E. Lincoln & L. Newburg, 1987. Mapmaker: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174–181.
Lander, E.S. & D. Botstein, 1989. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185–199.
Lin, H.X., H.R. Qian, J.Y. Zhuang, J. Lu, S.K. Min, Z.M. Xiong, N. Huang & K.L. Zheng, 1996. RFLP mapping of QTLs for yield and related characters in rice (Oryza sativa L.). Theor Appl Genet 92: 920–927.
Lincoln, S.E., M.J. Daly & E.S. Lander, 1993a. Constructing genetic linkage maps with Mapmaker/EXP version 3.0: A tutorial and reference manual, 2nd Edition. Whitehead Institute for Biometrical Research, Cambridge, MA, USA, pp. 920–927.
Lincoln, S.E., M.J. Daly & E.S. Lander, 1993b. Mapping genes controling quantitative traits using Mapmaker/QTL version 1.1: A tutorial and reference manual, 2nd Edition. Whitehead Institute for Biometrical Research, Cambridge, MA, USA.
McCouch, S.R., L. Teytelman, Y. Xu, K. Lobos, K. Clare & M. Walton, 2002. Development of 2243 new SSR markers for rice by the International Rice Microsatellite Initiative. In: Proceedings of the first International Rice Congress, China.
Paterson, A.H., S. Damon, J.D. Hewitt, D. Zamir, H.D. Rabinowitch, S.E. Lincoln, E.S. lander & S.D. Tanksley, 1991. Mendelian factors underlying quantitative traits in tomato: Comparison across species, generations and environments. Genetics 127: 181–197.
Redona, E.D. & D.J. Mackill, 1998. Quantitative trait locus analysis for rice panicle and grain characteristics. Theor Appl Genet 96: 957–963.
Singh, N.B. & H.G. Singh, 1985. Heterosis and combining ability for kernel size in rice. Indian J Genet 45: 181–185.
Tan, Y.F., J.X. Li, S.B. Yu, Y.Z. Xing, C.G. Xu & Q. Zhang, 1999. The three important traits for cooking and eating quality of rice grains are controlled by a single locus. Theor Appl Genet 99: 942–648.
Tan, Y.F., Y.Z. Xing, J.X. Li, S.B. Yu, C.G. Xu & Q. Zhang, 2000. Genetic bases of appearance quality of rice grains in Shanyou 63, and elite rice hybrid. Theor Appl Genet 101: 823–829.
Temnykh, S., W.D. Park, N. Ayres, S. Cartinhour, N. Hauck, L. Lipovich, Y.G. Cho, T. Ishii & S.R. McCouch, 2000. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L ). Theor Appl Genet 100: 697–712.
Tsunematsu, H., A. Yoshimura, M. Yano & N. Iwata, 1996. Quantitative trait locus analysis using recombinant inbred lines and restriction fragment length polymorphism markers in rice. In: G.S. Khush (Ed.), Rice genetic III. Proceeding of the Third Inter-national Rice Genetics Symposium, 16–20 October 1995, IRRI, Manila, Philippines.
Wu, P., G. Zhang & N. Huang, 1996. Identification of QTLs controlling quantitative characters in rice using RFLP markers. Euphytica 89: 349–354.
Xiao, J., J. Li, L. Yuan & S.D. Tanksley, 1996. Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross. Theor Appl Genet 92: 230–244.
Yano, M. & T. Sasaki, 1997. Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35: 145–153.
Yu, S.B., J.X. Li, C.G. Xu, Y.F. Tan, X.H. Li & Q. Zhang, 2002. Identification of quantitative trait loci and epistatic interactions for plant height and heading date in rice. Theor Appl Genet 104: 619–625.
Zeng, Z.B., 1993. Theoretical basis of separation of multiple linked gene effects on mapping quantitative trait loci. Proc Natl Acad Sci USA 90: 10972–10976.
Zeng, Z.B., 1994. Precision mapping of quantitative trait loci. Genetics 136: 1457–1468.
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Rabiei, B., Valizadeh, M., Ghareyazie, B. et al. Identification of QTLs for rice grain size and shape of Iranian cultivars using SSR markers. Euphytica 137, 325–332 (2004). https://doi.org/10.1023/B:EUPH.0000040452.76276.76
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DOI: https://doi.org/10.1023/B:EUPH.0000040452.76276.76