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

G. Agarwal; J. Clevenger; M.K. Pandey; H. Wang; Y. Shasidhar; Y. Chu; J.C. Fountain; D. Choudhary; A.K. Culbreath; X. Liu; G. Huang; X. Wang; R. Deshmukh; C.C. Holbrook; D.J. Bertioli; P. Ozias-Akins; S.A. Jackson; R.K. Varshney; B. Guo

doi:10.1111/pbi.12930

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

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

G. Agarwal, J. Clevenger, M.K. Pandey, H. Wang, Y. Shasidhar, Y. Chu, J.C. Fountain, D. Choudhary, A.K. Culbreath, X. Liu, …

Plant Biotechnology Journal, Vol.16(11), pp.1954-1967

2018

DOI: https://doi.org/10.1111/pbi.12930

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Abstract

Whole‐genome resequencing (WGRS) of mapping populations has facilitated development of high‐density genetic 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 8869 SNPs assigned to 20 linkage groups, representing 20 chromosomes, for the ‘T’ population (Tifrunner × GT‐C20) with a map length of 3120 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.

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Title: High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut
Authors/Creators: G. Agarwal (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
J. Clevenger (Author/Creator) - Applied Genetic Technologies (United States)
M.K. Pandey (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
H. Wang (Author/Creator) - Agricultural Research Service
Y. Shasidhar (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
Y. Chu (Author/Creator) - University of Georgia
J.C. Fountain (Author/Creator) - Agricultural Research Service
D. Choudhary (Author/Creator) - Agricultural Research Service
A.K. Culbreath (Author/Creator) - University of Georgia
X. Liu (Author/Creator) - BGI (United States)
G. Huang (Author/Creator) - BGI (United States)
X. Wang (Author/Creator) - Shandong Academy of Agricultural Sciences
R. Deshmukh (Author/Creator) - Université Laval
C.C. Holbrook (Author/Creator) - Agricultural Research Service
D.J. Bertioli (Author/Creator) - Applied Genetic Technologies (United States)
P. Ozias-Akins (Author/Creator) - University of Georgia
S.A. Jackson (Author/Creator) - Applied Genetic Technologies (United States)
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
B. Guo (Author/Creator) - Agricultural Research Service
Publication Details: Plant Biotechnology Journal, Vol.16(11), pp.1954-1967
Publisher: Blackwell Publishing Inc.
Identifiers: 991005542752507891
Copyright: © 2018 The Authors.
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Biotechnology & Applied Microbiology; Plant Sciences
ESI research areas: Plant & Animal Science