A recombination bin-map identified a major QTL for resistance to Tomato Spotted Wilt Virus in peanut (Arachis hypogaea)

Agarwal, G and Clevenger, J and Kale, S M and Wang, H and Pandey, M K and Choudhary, D and Yuan, M and Wang, X and Culbreath, A K and Holbrook, C C and Liu, X and Varshney, R K and Guo, B (2020) A recombination bin-map identified a major QTL for resistance to Tomato Spotted Wilt Virus in peanut (Arachis hypogaea). Scientific Reports (TSI), 9 (1). pp. 1-13. ISSN 2045-2322

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Tomato spotted wilt virus (TSWV) is a devastating disease to peanut growers in the South-eastern region of the United States. Newly released peanut cultivars in recent years are crucial as they have some levels of resistance to TSWV. One mapping population of recombinant inbred line (RIL) used in this study was derived from peanut lines of SunOleic 97R and NC94022. A whole genome re-sequencing approach was used to sequence these two parents and 140 RILs. A recombination bin-based genetic map was constructed, with 5,816 bins and 20 linkage groups covering a total length of 2004 cM. Using this map, we identified three QTLs which were colocalized on chromosome A01. One QTL had the largest effect of 36.51% to the phenotypic variation and encompassed 89.5 Kb genomic region. This genome region had a cluster of genes, which code for chitinases, strictosidine synthase-like, and NBS-LRR proteins. SNPs linked to this QTL were used to develop Kompetitive allele specific PCR (KASP) markers, and the validated KASP markers showed expected segregation of alleles coming from resistant and susceptible parents within the population. Therefore, this bin-map and QTL associated with TSWV resistance made it possible for functional gene mapping, map-based cloning, and marker-assisted breeding. This study identified the highest number of SNP makers and demonstrated recombination bin-based map for QTL identification in peanut. The chitinase gene clusters and NBS-LRR disease resistance genes in this region suggest the possible involvement in peanut resistance to TSWV.

Item Type: Article
Divisions: Research Program : Genetic Gains
Uncontrolled Keywords: Groundnut, Peanut, Tomato Spotted Wilt Virus, QTL for resistance, Arachis hypogaea, Plant Disease, SunOleic 97R, NC94022, 140 RILs,
Subjects: Mandate crops > Groundnut
Others > Genetics and Genomics
Others > Plant Disease
Others > Legume Crops
Depositing User: Mr Arun S
Date Deposited: 12 Dec 2019 06:09
Last Modified: 05 Sep 2020 05:18
URI: http://oar.icrisat.org/id/eprint/11348
Official URL: https://doi.org/10.1038/s41598-019-54747-1
Funders: U.S. Department of Agriculture Agricultural Research Service (USDA-ARS), The Peanut Foundation, The Georgia Peanut Commission, National Peanut Board, Bill & Melinda Gates Foundation (Tropical Legumes III)
Acknowledgement: We thank Billy Wilson, Stephanie Lee, Lucero Gutierrez, Sara Beth Pelham, Victoria Weaver, Frank Lin, Jake Weaver, and Joseph Harnage for technical assistance in the field and the laboratory. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. This work is partially supported by the U.S. Department of Agriculture Agricultural Research Service (USDA-ARS), the Peanut Foundation, the Georgia Peanut Commission, National Peanut Board, and Bill & Melinda Gates Foundation (Tropical Legumes III). The USDA is an equal opportunity provider and employer.
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