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Rapid Identification of Soybean Resistance Genes to Soybean Mosaic Virus by SLAF-seq Bulked Segregant Analysis

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Abstract

Soybean mosaic virus (SMV) is one of the most harmful pathogens in soybeans, causing large yield losses. Therefore, it is very important to breed resistant soybean cultivars, but first we need to understand the genetics of soybean. Genetic maps are efficient tools in plant genetics and molecular-assisted breeding. In this study, a large-scale survey of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique was used to construct the fine gene mapping for two soybean cultivars. The cultivar Tianlong No. 1 (TL1) is resistant to the SC9 strain, but Zhexiandou No. 4 (ZXD4) is susceptible to this strain. All F1 individuals showed the susceptible phenotype for strain SC9. Among the 425 F2 plants derived from F1 individuals, 309 had the susceptible phenotype and 116 were resistant (χ2 = 1.1929, P = 0.725). The results indicated that TL1 harbors a recessive gene underlying resistance to strain SC9. A total of 28.91 million sequencing reads were obtained, with average sequencing depths of over 17-fold for TL1 and ZXD4 and 63-fold for the F2 offspring. In summary, 144,754 high-quality SLAFs were obtained, of which 30,578 were polymorphic. In all, 8738 SNPs were selected to construct the fine gene mapping with an average genetic distance of 1.30 cM between adjacent markers. Approximately 148 target genes were mapped in the intervening genomic region of chromosome 2. The results of this study will not only provide a fine gene mapping for SMV resistance research but will also serve as a robust tool for the molecular breeding of soybean.

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Funding

This work was supported by Zhejiang Basic Public Welfare Research Program (GN19C060001), Key Special Projects of China-EU Intergovernmental Science and Technology Cooperation of the Ministry of Science and Technology (2017YFE0111000), and the National Natural Science Foundation of China (31401400).

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Authors and Affiliations

  1. National Soybean Improvement Sub-center, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, People’s Republic of China

    Qinghua Yang, Hangxia Jin, Xiaomin Yu, Xujun Fu & Fengjie Yuan

  2. National Soybean Improvement Center, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

    Haijian Zhi

Authors
  1. Qinghua Yang
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  2. Hangxia Jin
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  3. Xiaomin Yu
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  4. Xujun Fu
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  5. Haijian Zhi
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  6. Fengjie Yuan
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Contributions

Conceived and designed the experiments: Qinghua Yang, Fengjie Yuan. Performed the experiments: Hangxia Jin, Xiaomin Yu. Analyzed the data: Xujun Fu and Haijian Zhi. Wrote the paper: Qinghua Yang, Fengjie Yuan.

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Correspondence to Fengjie Yuan.

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Key Message

• Soybean mosaic virus strain SC9 is very widespread and harmful. Resistance genes from cultivar Tianlong No. 1 were identified using the SLAF-seq technique; 8,738 SNPs were selected to construct an associated region with an average distance of 1.30 cM between markers. Approximately 148 target genes were mapped on chromosome 2.

Electronic Supplementary Material

ESM 1

Map information based on high-quality specific length amplified fragments obtained from population sequencing. (DOCX 18 kb)

ESM 2

Summary and functional annotation of unigenes, including NR, SwissProt, GO, COG and KEGG analysis. (XLS 144 kb)

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Yang, Q., Jin, H., Yu, X. et al. Rapid Identification of Soybean Resistance Genes to Soybean Mosaic Virus by SLAF-seq Bulked Segregant Analysis. Plant Mol Biol Rep 38, 666–675 (2020). https://doi.org/10.1007/s11105-020-01227-w

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