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QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects

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Abstract

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.

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Acknowledgements

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).

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Authors and Affiliations

  1. National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, 210095, Nanjing, China

    X. Y. Wan, J. M. Wan, L. Jiang, J. F. Weng & H. L. Wang

  2. Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China

    X. Y. Wan, J. M. Wan, J. K. Wang, H. Q. Zhai, C. L. Lei, J. L. Wang, X. Zhang, Z. J. Cheng & X. P. Guo

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  1. X. Y. Wan
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  3. L. Jiang
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  4. J. K. Wang
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Correspondence to J. M. Wan.

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Communicated by T. Sasaki

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Wan, X.Y., Wan, J.M., Jiang, L. et al. QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects. Theor Appl Genet 112, 1258–1270 (2006). https://doi.org/10.1007/s00122-006-0227-0

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  • DOI: https://doi.org/10.1007/s00122-006-0227-0

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