High-density genetic map using whole-genome re-sequencing for fine mapping and candidate gene discovery for disease resistance in peanut

Agarwal, G and Clevenger, J and Pandey, M K and Wang, H and Shasidhar, Y and Chu, Y and Fountain, J C and Choudhary, D and Culbreath, A K and Liu, X and Huang, G and Wang, X and Deshmukh, R and Holbrook, C C and Bertioli, D J and Ozias-Akins, P and Jackson, S A and Varshney, R K and Guo, B (2018) High-density genetic map using whole-genome re-sequencing for fine mapping and candidate gene discovery for disease resistance in peanut. Plant Biotechnology Journal (TSI). pp. 1-14. ISSN 1467-7644

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Abstract

Whole genome re‐sequencing (WGRS) of mapping populations has facilitated development of high‐density genetic linkage maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases in peanut causing significant yield loss. We generated WGRS data on a recombinant inbred line population, developed a SNP‐based high‐density genetic map, and conducted fine mapping, candidate gene discovery and marker validation for ELS, LLS and TSWV. The first sequence‐based high density map was constructed with 8,869 SNPs assigned to 20 linkage groups, representing 20 chromosomes, for the “T” population (Tifrunner × GT‐C20) with a map length of 3,120 cM and an average distance of 1.45 cM. The quantitative trait locus (QTL) analysis using high‐density genetic map and multiple season phenotyping data identified 35 main‐effect QTLs with phenotypic variation explained (PVE) from 6.32 to 47.63%. Among major effect QTLs mapped, there were two QTLs for ELS on B05 with 47.42% PVE and B03 with 47.38% PVE, two QTLs for LLS on A05 with 47.63% and B03 with 34.03% PVE, and one QTL for TSWV on B09 with 40.71% PVE. The epistasis and environment interaction analyses identified significant environmental effects on these traits. The identified QTL regions had disease resistance genes including R‐genes and transcription factors. KASP markers were developed for major QTLs and validated in the population, and are ready for further deployment in genomics‐assisted breeding in peanut.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes and Dryland Cereals
Uncontrolled Keywords: Arachis hypogaea ; Tomato spotted wilt virus; Whole genome re-sequencing; candidate gene discovery; early leaf spot; high-density genetic map; late leaf spot; quantitative trait loci; Whole genome re-sequencing
Subjects: Others > Crop Improvement
Others > Plant Breeding
Mandate crops > Groundnut
Others > Genetics and Genomics
Others > Plant Disease
Depositing User: Mr Ramesh K
Date Deposited: 23 Apr 2018 04:23
Last Modified: 21 May 2018 08:43
URI: http://oar.icrisat.org/id/eprint/10624
Official URL: http://dx.doi.org/10.1111/pbi.12930
Projects: UNSPECIFIED
Funders: UNSPECIFIED
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. 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, Bill & Melinda Gates Foundation (Tropical Legumes III), and World Bank-assisted Karnataka Watershed Development ProjectII of Government of Karnataka, India. This work has also been undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC). ICRISAT is a member of CGIAR Consortium. 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. The USDA is an equal opportunity provider and employer.
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