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High-density SNP map facilitates fine mapping of QTLs and candidate genes discovery for Aspergillus flavus resistance in peanut (Arachis hypogaea)

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Abstract

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Two novel resistant QTLs mapped and candidate genes identified for Aspergillus flavus resistance in cultivated peanut using SLAF-seq.

Abstract

Aflatoxin contamination in peanuts caused by Aspergillus flavus is a serious food safety issue for human health around the world. Host plant resistance to fungal infection and reduction in aflatoxin are crucial for mitigating this problem. Identification of the resistance-linked markers can be used in marker-assisted breeding for varietal development. Here we report construction of two high-density genetic linkage maps with 1975 SNP loci and 5022 SNP loci, respectively. Two consistent quantitative trait loci (QTL) were identified as qRAF-3-1 and qRAF-14-1, which located on chromosomes A03 and B04, respectively. QTL qRAF-3-1 was mapped within 1.67 cM and had more than 19% phenotypic variance explained (PVE), while qRAF-14-1 was located within 1.34 cM with 5.15% PVE. While comparing with the reference genome, the mapped QTLs, qRAF-3-1 and qRAF-14-1, were located within a physical distance of 1.44 Megabase pair (Mbp) and 2.22 Mbp, harboring 67 and 137 genes, respectively. Among the identified candidate genes, six genes with the same function were found within both QTLs regions. In addition, putative disease resistance RPP13-like protein 1 (RPP13), lipoxygenase (Lox), WRKY transcription factor (WRKY) and cytochrome P450 71B34 genes were also identified. Using microarray analysis, genes responded to A. flavus infection included coding for RPP13, pentatricopeptide repeat-containing-like protein, and Lox which may be possible candidate genes for resistance to A. flavus. The QTLs and candidate genes will further facilitate marker development and validation of genes for deployment in the molecular breeding programs against A. flavus in peanuts.

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Acknowledgements

Current work was supported by The National Science Foundation of People’s Republic of China (U1705233; 31601337; 31701463). The authors are thankful to Fujian Key Laboratory of Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China, for providing research facilities and technical guidance. Special acknowledgment to Meng Yang from Nextomics Biosciences Institute, Wuhan, China for his help in bioinformatics analysis.

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  1. Shahid Ali Khan and Hua Chen have equally contributed.

Authors and Affiliations

  1. Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Shahid Ali Khan, Hua Chen, Ye Deng, Yuhua Chen, Chong Zhang, Tiecheng Cai, Niaz Ali, Gandeka Mamadou, Dongyang Xie & Weijian Zhuang

  2. College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Shahid Ali Khan, Hua Chen, Yuhua Chen, Niaz Ali, Gandeka Mamadou & Weijian Zhuang

  3. College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Ye Deng, Chong Zhang, Tiecheng Cai, Dongyang Xie & Weijian Zhuang

  4. Crop Protection and Management Research Unit, USDA-ARS, Tifton, GA, 31793, USA

    Baozhu Guo

  5. Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, 502324, India

    Rajeev K. Varshney

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  1. Shahid Ali Khan
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Contributions

SAK and CH performed the research, generated data and wrote the manuscript. YC helped in experiment and resistance identification in 2016. ZC, DY and TC constructed the RIL mapping population used in the current research. NA and GM participated resistance evaluation and field experiment. GB and RKV contributed in data analysis and writing the manuscript. ZW designed the research project, supervised the experiments and modified the manuscript.

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Correspondence to Weijian Zhuang.

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On behalf of all contributing authors of the manuscript, the corresponding author states that there is no conflict of competing interest.

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Khan, S.A., Chen, H., Deng, Y. et al. High-density SNP map facilitates fine mapping of QTLs and candidate genes discovery for Aspergillus flavus resistance in peanut (Arachis hypogaea). Theor Appl Genet 133, 2239–2257 (2020). https://doi.org/10.1007/s00122-020-03594-0

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