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Fine-mapping and identifying candidate genes conferring resistance to Soybean mosaic virus strain SC20 in soybean

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The Mendelian gene conferring resistance to Soybean mosaic virus Strain SC20 in soybean was fine-mapped onto a 79-kb segment on Chr.13 where two closely linked candidate genes were identified and qRT-PCR verified.

Abstract

Soybean mosaic virus (SMV) threatens the world soybean production, particularly in China. A country-wide SMV strain system composed of 22 strains was established in China, among which SC20 is a dominant strain in five provinces in Southern China. Resistance to SC20 was evaluated in parents, F1, F2 and the F2:7 RIL (recombinant inbred line) population derived from a cross between Qihuang-1 (resistant) and NN1138-2 (susceptible). The segregation ratio of resistant to susceptible in the populations suggested a single dominant gene involved in the resistance to SC20 in Qihuang-1. A “partial genome mapping strategy” was used to map the resistance gene on Chromosome 13. Linkage analysis between 178 RILs and genetic markers showed that the SC20-resistance gene located at 3.9 and 3.8 cM to the flanking markers BARCSOYSSR_13_1099 and BARCSOYSSR_13_1185 on Chromosome 13. Subsequently, a residual heterozygote segregating population with 346 individuals was developed by selfing four plants heterozygous at markers adjacent to the tentative SC20-resistance gene; then, the candidate region was delimited to a genomic interval of approximately 79 kb flanked by the new markers gm-ssr_13-14 and gm-indel_13-3. Among the seven annotated candidate genes in this region, two genes, Glyma.13G194700 and Glyma.13G195100, encoding Toll Interleukin Receptor–nucleotide-binding–leucine-rich repeat resistance proteins were identified as candidate resistance genes by quantitative real-time polymerase chain reaction and sequence analysis. The two closely linked genes work together to cause the phenotypic segregation as a single Mendelian gene. These results will facilitate marker-assisted selection, gene cloning and breeding for the resistance to SC20.

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Acknowledgements

This work was financially supported through grants from the China National Key R & D Program for crop Breeding (2016YFD0100304, 2017YFD0101500), the Natural Science Foundation of China (31671718, 31571695), the MOE 111 Project (B08025), the MOE Program for Changjiang Scholars and Innovative Research Team in University (PCSIRT_17R55), the MOA CARS-04 program, the Jiangsu Higher Education PAPD Program, the Fundamental Research Funds for the Central Universities (Y0201600115) and the Jiangsu JCIC-MCP. The funders had no role in work design, data collection and analysis, or decision and preparation of the manuscript.

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Authors and Affiliations

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

    Adhimoolam Karthikeyan, Kai Li, Cui Li, Jinlong Yin, Na Li, Yunhua Yang, Yingpei Song, Rui Ren, Haijian Zhi & Junyi Gai

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

    Adhimoolam Karthikeyan, Kai Li, Cui Li, Jinlong Yin, Na Li, Yunhua Yang, Yingpei Song, Rui Ren, Haijian Zhi & Junyi Gai

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

    Adhimoolam Karthikeyan, Kai Li, Cui Li, Jinlong Yin, Na Li, Yunhua Yang, Yingpei Song, Rui Ren, Haijian Zhi & Junyi Gai

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

    Adhimoolam Karthikeyan, Kai Li, Cui Li, Jinlong Yin, Na Li, Yunhua Yang, Yingpei Song, Rui Ren, Haijian Zhi & Junyi Gai

  5. Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

    Kai Li, Haijian Zhi & Junyi Gai

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  1. Adhimoolam Karthikeyan
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  2. Kai Li
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  3. Cui Li
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  4. Jinlong Yin
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  5. Na Li
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  6. Yunhua Yang
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  7. Yingpei Song
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  8. Rui Ren
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  9. Haijian Zhi
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  10. Junyi Gai
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Correspondence to Junyi Gai.

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The experiments were performed in compliance with the current laws of China.

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Communicated by Henry T. Nguyen.

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Karthikeyan, A., Li, K., Li, C. et al. Fine-mapping and identifying candidate genes conferring resistance to Soybean mosaic virus strain SC20 in soybean. Theor Appl Genet 131, 461–476 (2018). https://doi.org/10.1007/s00122-017-3014-1

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