QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects
- 1.3k Downloads
Grain length in rice plays an important role in determining rice appearance, milling, cooking and eating quality. In this study, the genetic basis of grain length was dissected into six main-effect quantitative trait loci (QTLs) and twelve pairs of epistatic QTLs. The stability of these QTLs was evaluated in four environments using an F7 recombinant inbred line (RIL) population derived from the cross between a Japonica variety, Asominori, and an Indica variety, IR24. Moreover, chromosome segment substitution lines (CSSLs) harboring each of the six main-effect QTLs were used to evaluate gene action of QTLs across eight environments. A major QTL denoted as qGL-3a, was found to express stably not only in the isogenic background of Asominori but also in the recombinant background of Asominori and IR24 under multiple environments. The IR24 allele at qGL-3a has a positive effect on grain length. Based on the test of advanced backcross progenies, qGL-3a was dissected as a single Mendelian factor, i.e., long rice grain was controlled by a recessive gene gl-3. High-resolution genetic and physical maps were further constructed for fine mapping gl-3 by using 11 simple sequence repeat (SSR) markers designed using sequence information from seven BAC/PAC clones and a BC4F2 population consisting of 2,068 individuals. Consequently, the gl-3 gene was narrowed down to a candidate genomic region of 87.5 kb long defined by SSR markers RMw357 and RMw353 on chromosome 3, which provides a basis for map-based cloning of this gene and for marker-aided QTL pyramiding in rice quality breeding.
We greatly appreciate Professor A. Yoshimura, Kyushu University, Japan, for kindly providing us with the RIL and CSSL populations and genotype data. This research was supported by grants from the National High Technology Research and Development Program of China (Nos. 2003AA222131 and 2003AA207020), and the National Natural Science Foundation of China (No. 30270811).
- Harlan J (1992) Crops & Man. American Society of Agronomy/Crop Science Society of American, MadisonGoogle Scholar
- Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 Population. Genetics 148:479–494PubMedGoogle Scholar
- Kubo T, Nakamura K, Yoshimura A (1999) Development of a series of Indica chromosome segment substitution lines in Japonica background of rice. Rice Genet Newsl 16:104–106Google Scholar
- Li ZK (2001) QTL mapping in rice: a few critical considerations. In: Rice genetics IV. Science Publishers, New Delhi, pp 153–171Google Scholar
- Li ZK, Yu SB, Lafitte HR, Huang L, Courtois B, Hittalmani S, Vijayakumar CHM, Liu GF, Wang GC, Shashidhar HE, Zhuang JY, Zheng KL, Singh VP, Sidhu JS, Srivantaneeyakul S, Khush GS (2003) QTL × environment interactions in rice. I. Heading date and plant height. Theor Appl Genet 108:141–153CrossRefPubMedGoogle Scholar
- Luo YK, Zhu ZW, Chen N, Duan BW, Zhang LP (2004) Grain types and related quality characteristics of rice in China. Chinese J Rice Sci 18(2):135–139Google Scholar
- Sanguinetti CJ, Dias NE, Simpson AJG (1994) Rapid silver staining and recover of PCR products separated on polyacrylamide gels. Biotechniques 17:915–919Google Scholar
- Tsunematsu H, Yoshimura A, Harushima Y, Nagamura Y, Kurata N, Yano M, Sasaki T, Iwata N (1996) RFLP framework map using recombinant inbred lines in rice. Breed Sci 46:279–284Google Scholar
- Wan XY, Weng JF, Zhai HQ, Wan JM (2004b) Fine mapping of pgwc-8 gene affecting percentage of grains with chalkiness in rice (Oryza sativa. L), Rice. Genet Newsl 21, (in press)Google Scholar
- Yamamoto R, Horisue N, Ikeda R (1995) Rice Breeding Manual. Miscellaneous Publication of the National Agriculture Research Centre in Japan. No. 30, OctoberGoogle Scholar
- Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna Lisa, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd-1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant cell 12:2473–2483CrossRefPubMedGoogle Scholar