Whole genome resequencing identifies candidate genes and allelic diagnostic markers for resistance to Ralstonia solanacearum infection in cultivated peanut (Arachis hypogaea L.)

    Zhang, C and Xie, W and Fu, H and Chen, Y and Chen, H and Cai, T and Yang, Q and Zhuang, Y and Zhong, X and Chen, K and Gao, M and Liu, F and Wan, Y and Pandey, M K and Varshney, R K and Zhuang, W (2023) Whole genome resequencing identifies candidate genes and allelic diagnostic markers for resistance to Ralstonia solanacearum infection in cultivated peanut (Arachis hypogaea L.). Frontiers in Plant Science (TSI), 13. 01-28. ISSN 1664-462X

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    Abstract

    Bacterial wilt disease (BWD), caused by Ralstonia solanacearum is a major challenge for peanut production in China and significantly affects global peanut field productivity. It is imperative to identify genetic loci and putative genes controlling resistance to R. solanacearum (RRS). Therefore, a sequencing-based trait mapping approach termed “QTL-seq” was applied to a recombination inbred line population of 581 individuals from the cross of Yueyou 92 (resistant) and Xinhuixiaoli (susceptible). A total of 381,642 homozygous single nucleotide polymorphisms (SNPs) and 98,918 InDels were identified through whole genome resequencing of resistant and susceptible parents for RRS. Using QTL-seq analysis, a candidate genomic region comprising of 7.2 Mb (1.8–9.0 Mb) was identified on chromosome 12 which was found to be significantly associated with RRS based on combined Euclidean Distance (ED) and SNP-index methods. This candidate genomic region had 180 nonsynonymous SNPs and 14 InDels that affected 75 and 11 putative candidate genes, respectively. Finally, eight nucleotide binding site leucine rich repeat (NBS-LRR) putative resistant genes were identified as the important candidate genes with high confidence. Two diagnostic SNP markers were validated and revealed high phenotypic variation in the different resistant and susceptible RIL lines. These findings advocate the expediency of the QTL-seq approach for precise and rapid identification of candidate genomic regions, and the development of diagnostic markers that are applicable in breeding disease-resistant peanut varieties.

    Item Type: Article
    Divisions: Center of Excellence in Genomics and Systems Biology
    CRP: UNSPECIFIED
    Uncontrolled Keywords: peanut, resistance to Ralstonia solanacearum, QTL-seq analysis, candidate genes, diagnostic markers
    Subjects: Mandate crops > Groundnut
    Others > Genetics and Genomics
    Depositing User: Mr Nagaraju T
    Date Deposited: 05 Feb 2024 04:49
    Last Modified: 05 Feb 2024 04:49
    URI: http://oar.icrisat.org/id/eprint/12428
    Official URL: https://www.frontiersin.org/articles/10.3389/fpls....
    Projects: Special Fund for Scientific and Technological Innovation of Fujian Agriculture and Forestry University
    Funders: National Science Foundation (NSF) of China, Science and Technology Foundation of Fujian Province of China, Guangdong Province Key Laboratory of Plant Molecular Breeding
    Acknowledgement: We would like to thank MogoEdit (https://www.mogoedit. com) for its English editing during the preparation of this manuscript.
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