Abstract
In the present study a population consisting of 247 F2 individuals from the cross between Basmati 370, a superior quality basmati variety and ASD16, a non-basmati high-yielding variety was analyzed for their segregation pattern of grain length (GL), grain breadth (GB), cooked grain length (CGL), cooked grain breadth (CGB), and gelatinization temperature (GT). Except GT, all other traits showed normal distribution indicating the polygenic control over the traits. The correlation analysis between traits indicated that GT had positive significant association with GL (0.125), and CGL (0.243). To identify main effect QTL (MQTL) for the above grain quality traits, both the parents were surveyed with 86 primer pairs of simple sequence repeats (SSR). The parental survey revealed 63.95% polymorphism between parents. In order to detect the MQTL associated with grain quality traits, a strategy of combining the DNA pooling from selected segregants and genotyping was adopted. The number of individuals forming the bulk influenced the identification of putative marker(s) for each of the traits. The association of putative markers identified based on DNA pooling from selected segregants was established by Single Marker Analysis (SMA). The results of SMA revealed that SSR markers, RM225 on chromosome #6 and RM247 on chromosome #12 showed significant association with GB and CGB respectively. It is established that molecular marker analysis involving DNA pooling of phenotypic extremes and selective genotyping helps to detect MQTL for complex traits involving early segregating generations. The molecular marker analysis involving the DNA pooling of phenotypic extremes could be a useful strategy to detect the genetic loci with major effects of other complex grain quality traits in rice.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Azez, M.A. & M. Shafi, 1966. Quality of rice, Dept of Agrl Bulletin West Pakistan, 50p.
Beachell, H.M. & J.W. Stansel, 1963. Selecting rice for specific cooking characteristics in a breeding program. Int Rice Comm Newslett (Special issue), 25–40.
Bollich, C.N., 1957. Inheritance of several economic quantitative characters in rice. Dissertation Abstr 17: 1638.
Chakravarthi, A.K., 1948. Genetical study of the botanical characters of rice (Oryza sativa L). Bull Botan Soc Bengal 2: 55–57.
Chang, T.M., 1974. Studies on the inheritance of grain shape of rice. J Taiwan Agrl Res Inst 23: 9–15.
Chang, T.T. & B. Somrith, 1979. Genetic studies on the grain quality of rice. In: Proceedings of the workshop on chemical aspects of rice grain quality, International Rice Research Institute, Los Banos, Philippines. pp.49–58.
Chao, L.F., 1928. Linkage studies in rice. Genetics 13: 133–169.
Cordeiro, G.M., M.J. Christopher, R.J. Henry & R.F. Reinke, 2002. Identification of microsatellite markers for fragrance in rice by analysis of the rice genome sequence. Mol Breed 9: 245–250.
Falconer, R., 1993. Introduction to Quantitative Genetics, Ronad, New York.
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.
Huang, N., A. Parco, T. Mew, G. Magapantay, S.R. McCouch, E. Guiderdoni, J. 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 2: 105–113.
Jennings, P.R., W.R. Coffman & H.E. Kauffman, 1979. Grain quality. In: Rice Improvement, IRRI, Philippines, pp.101–120.
Jones, J.W., C.R. Adair & H.M. Beachell, 1935. Inheritance of earliness and length of kernel in rice. J Am Soc Agron 27: 910–921.
Kang, H.J., Y.G. Cho, Y.T. Lee, Y.D. Kim, M.Y. Eun & J.U. Shim, 1998. QTL mapping of genes related with grain chemical properties based on molecular map of rice. Korean J Crop Sci 43: 199–204.
Lander, E.S. & D. Botstein, 1989. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185–199.
Lin, M.H., 1978. Genetic study of the relationship between the lowland rice varieties and the traditional upland rice varieties. MS Thesis, University of Philippines, Los Banos, 94p.
Little, R.R., G.D. Hilder & E.H. Dawson, 1958. Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem 35: 111.
Martin, G.B., J.G.K. Williams & S.D. Tanksley, 1991. Rapid identification of markers linked to Pseudomonas resistance gene in tomato by using random primers and near-isogenic lines. Proc Natl Acad Sci 88: 2336–2340.
Mc Couch, S.R., G. Kochert, Z.H. Yu, Z.Y. Wang, G.S. Khush, W.R. Coffman & S.D. Tanksley, 1988. Molecular mapping of rice chromosomes. Theor Appl Genet 76: 815–829.
Mitra, G.N., 1962. Inheritance of grain size in rice. Curr Sci India 31: 105–106.
Morinaga, T., E. Fukushima & S. Hara, 1943. Inheritance of length of rice grain. Agr Hort Tokyo 18: 519–522.
Nakatat, S., & B.R. Jackson, 1973. Inheritance of some physical grain quality characteristics in a cross between a Thai and Taiwanese rice. Thai J Agrl Sci 6: 223–235.
Paterson, A.H., E.S. Lander, J.D. Hewitt, S. Peterson, S.E. Lincoln & S.D. Tanksley, 1988. Resolution of quantitative traits into Mendelian factors using a complete linkage map of restriction fragment length polymorphisms. Nature 335: 721–726.
Panaud, O., X. Chen & S.R. McCouch, 1996. Development of microsatellite markers and characterization of simple sequence length polymorphisms (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252: 597–607.
Ramaiah, K., S. Jobithraz & S.D. Mudaliar, 1931. Inheritance of characters in rice. Part IV, Mem Dept Agr India Botany Ser 18: 229–259.
Ramiah, K. & N. Parthasarathy, 1933. Inheritance of grain length in rice (Oryza sativa.L). Indian J Agr Sci 3: 808–819.
Redona, D. & D.L. Mackill, 1998. Quantitative trait locus analysis for rice panicle and grain characteristics. Theor Appl Genet 96: 957–963.
Somrith, B., 1974. Genetic analysis of traits related to grain yield and quality in two crosses of rice (Oryza sativa L.) Ph.D. Thesis, Indian Agricultural Research Institute, New Delhi, India 138p.
Stuber, C.W., M.D. Edwards & Wendel, 1987. Molecular marker facilitated investigation of quantitative trait loci in Maize II. Factors influencing yield and its component traits. Crop Sci 27: 639–648.
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 in an elite rice hybrid, Shanyou 63. Theor Appl Genet 99: 642–648.
Tanksley, S.D. & S.R. McCouch, 1997. Seed bank and molecular maps, unlocking genetic potential from the wild. Science 227: 1063–1066.
Tanksley, S.D., H. Medina-Filho & C.M. Rick, 1982. Use of naturally occurring enzyme variation to detect and map gene controlling quantitative trait in an interspecific backcross of tomato. Heredity 49: 11–25.
Temnykh, S., W.D. Park, N. Ayres, S. Cartinhous, N. Hauck, L. Lipovich, Y.G. Cho, Ishii & S.R. McCouch, 2000. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100: 697–712.
Yano, M. & T. Sasaki, 1997. Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35: 145–153.
Zhang, Q., B.Z. Shen, X.K. Dai, M.H. Mei, M.A. Saghai Maroof & Z.B. Li, 1994. Using bulked extremes and recessive class to map genes for photoperiod-sensitive genetic male sterility in rice. Proc Natl Acad Sci 91: 8675–8679.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Govindaraj, P., Arumugachamy, S. & Maheswaran, M. Bulked segregant analysis to detect main effect QTL associated with grain quality parameters in Basmati 370/ASD 16 cross in rice Oryza sativa L) using SSR markers. Euphytica 144, 61–68 (2005). https://doi.org/10.1007/s10681-005-4316-y
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/s10681-005-4316-y