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Association mapping for seed size and shape traits in soybean cultivars

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Abstract

Seed size and shape traits are closely related to seed yield and appearance quality in soybean (Glycine max L.). Previous studies were mainly derived from bi-parental segregating populations and relatively little is known about the results in soybean cultivars. In this study, 257 soybean cultivars obtained by stratified random sampling from six geographic ecotypes in China were used to carry out association mapping for these traits using information from 135 simple sequence repeat markers and an epistatic association mapping approach implemented using an empirical Bayes algorithm. In this analysis, seed size was measured by seed length (SL), width (SW) and thickness (ST), and seed shape was evaluated by seed length-to-width (SLW), length-to-thickness (SLT) and width-to-thickness (SWT) ratios, in 2008–2010. A total of 59 main-effect quantitative trait loci (QTL) and 31 QTL-by-environment interactions were identified. Among them, 25 QTL were associated simultaneously with at least two traits; 80 QTL (90 %) could be confirmed by enriched compression mixed linear model analysis; and the size for a large number of detected QTL was minor, except for qSL-5, qSW-7e, qST-5-2 and qSLW-2. According to the estimates for the allelic effects of the detected QTL, elite alleles could be mined: for example, the 307-bp allele of QTL linked to satt453 was the best for seed length. These elite alleles could be used to design parental combinations; e.g., the cross of Zhenghezhibanzi and Nannongdahuangdou might improve seed length, and the combination of cultivars Lindou10, Deqingxiangzhudou, Ninghaixiazhidou, Zhenghezhibanzi, 0803, Shangqiu7605 and 0831 might pyramid 42 elite alleles.

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Acknowledgments

This work was supported by the National Key Basic Research Program of China grant 2011CB109306; the National Natural Science Foundation of China grant 30971848; the Fundamental Research Funds for the Central Universities grants KYT201002; a Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions and the Specialized Research Fund for the Doctoral Program of Higher Education grants 20100097110035 and 20120097110023.

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  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

    Yuan Niu, Yu Xu, Xiao-Fen Liu, Sheng-Xian Yang, Shi-Ping Wei, Fang-Teng Xie & Yuan-Ming Zhang

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  1. Yuan Niu
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  2. Yu Xu
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  7. Yuan-Ming Zhang
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Correspondence to Yuan-Ming Zhang.

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Niu, Y., Xu, Y., Liu, XF. et al. Association mapping for seed size and shape traits in soybean cultivars. Mol Breeding 31, 785–794 (2013). https://doi.org/10.1007/s11032-012-9833-5

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