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Using presence/absence variation markers to identify the QTL/allele system that confers the small seed trait in wild soybean (Glycine soja Sieb. & Zucc.)

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Abstract

Glycine soja has the potential to improve upon the cultivated soybean (G. max) in protein content, resistance/tolerance to stresses, and other traits, but its small 100-seed weight (100SW) is usually undesired. To explore the 100SW QTL-allele system of G. soja, the recombinant inbred line population NJRINY with 286 lines was developed from a cross between G. max (NN86-4, 17.9 g) and G. soja (PI342618B, 1.1 g) and was tested over 4 years. The genetic linkage map was constructed with 181 PAV (presence/absence variation) and 42 SSR markers. The quantitative trait locus (QTL) mapping results showed that the wild genetic system of 100SW was composed of three groups of QTLs, including (1) 15 additive QTLs, which accounted for 55.1 % of the phenotypic variation (PV), with each locus contributing 1.5–8.1 % of the PV and all of the wild alleles having negative effects (−0.1 to −0.5 g); (2) 17 epistatic QTL pairs, which accounted for 19.0 % of the PV, with epistatic effects positive for parental type (0.1–0.2 g) and negative for recombinants and all of the QTLs in epistatic pairs having simultaneously additive effects except one pair (SW16); (3) a collection of unmapped minor QTLs that accounted for 22.9 % of the PV. Among the detected total additive and/or epistatic QTLs, 12 QTLs have been reported in the literature, but five of the QTLs and all of the epistatic pairs have not been reported before. The results can be used for marker-assisted breeding for 100SW.

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Acknowledgments

This research was supported by the National Key Basic Research Program of China (2011CB1093), National Hightech R&D Program of China (2011AA10A105, 2012AA101106), MOE 111 Project (B08025), MOE Program for Changjiang Scholars and Innovative Research Team in University (PCSIRT13073), MOA Public Profit Program (201203026-4), Jiangsu Higher Education PAPD Program, and Jiangsu JCIC-MCP program.

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    Authors and Affiliations

    1. Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

      Wubin Wang, Xuliang Li, Shixuan Chen, Shiyu Song, Junyi Gai & Tuanjie Zhao

    2. National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China

      Wubin Wang, Xuliang Li, Shixuan Chen, Shiyu Song, Junyi Gai & Tuanjie Zhao

    3. Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China

      Wubin Wang, Xuliang Li, Shixuan Chen, Shiyu Song, Junyi Gai & Tuanjie Zhao

    4. National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

      Wubin Wang, Xuliang Li, Shixuan Chen, Shiyu Song, Junyi Gai & Tuanjie Zhao

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    1. Wubin Wang
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    Correspondence to Junyi Gai or Tuanjie Zhao.

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    Wubin Wang and Xuliang Li have contributed equally to this work.

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    Wang, W., Li, X., Chen, S. et al. Using presence/absence variation markers to identify the QTL/allele system that confers the small seed trait in wild soybean (Glycine soja Sieb. & Zucc.). Euphytica 208, 101–111 (2016). https://doi.org/10.1007/s10681-015-1591-0

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