Record Details

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

OAR@ICRISAT

View Archive Info
 
 
Field Value
 
Relation http://oar.icrisat.org/10925/
http://dx.doi.org/10.1111/pbi.12930
10.1111/pbi.12930
 
Title High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut
 
Creator Agarwal, G
Clevenger, J
Pandey, M K
Wang, H
Shasidhar, Y
Chu, Y
Fountain, J C
Choudhary, D
Culbreath, A K
Liu, X
Huang, G
Wang, X
Deshmukh, R
Holbrook, C C
Bertioli, D J
Ozias-Akins, P
Jackson, S A
Varshney, R K
Guo, B
 
Subject Groundnut
Genetics and Genomics
 
Description 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.
 
Publisher Wiley
 
Date 2018
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/10925/1/High-density%20genetic%20map%20using%20whole-genome.pdf
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 resequencing for fine mapping and candidate gene discovery for disease resistance in peanut. Plant Biotechnology Journal (TSI), 16 (11). pp. 1954-1967. ISSN 14677644