Overview
TitleHigh-Density Genetic Map Using Whole-Genome Resequencing for Fine Mapping and Candidate Gene Discovery for Disease Resistance in Peanut
AuthorsAgarwal G, Clevenger J, Pandey MK, Wang H, Shasidhar Y, Chu Y, Fountain JC, Choudhary D, Culbreath AK, Liu X, Huang G, Wang X, Deshmukh R, Holbrook CC, Bertioli DJ, Ozias-Akins P, Jackson SA, Varshney RK, Guo B
TypeJournal
Media TitlePlant Biotechnology Journal
VolumeN/A
IssueN/A
Year2018
Page(s)N/A
CitationAgarwal G, Clevenger J, Pandey MK, Wang H, Shasidhar Y, Chu Y, Fountain JC, Choudhary D, Culbreath AK, Liu X, Huang G, Wang X, Deshmukh R, Holbrook CC, Bertioli DJ, Ozias-Akins P, Jackson SA, Varshney RK, 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. NULL:NULL NULL

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 x 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.
Maps
This publication contains information about 1 maps:
Map Name
TT_Tifrunner_x_GT-C20_c
Features
This publication contains information about 7,220 features:
Feature NameUniquenameType
B09_5189475B09_5189475genetic_marker
B09_5098788B09_5098788genetic_marker
B09_5008296B09_5008296genetic_marker
B09_4865954B09_4865954genetic_marker
B09_4784841B09_4784841genetic_marker
B09_4760350B09_4760350genetic_marker
B09_4624873B09_4624873genetic_marker
B09_4572633B09_4572633genetic_marker
B09_4485808B09_4485808genetic_marker
B09_4438072B09_4438072genetic_marker
B09_4320967B09_4320967genetic_marker
B09_4273247B09_4273247genetic_marker
B09_4247303B09_4247303genetic_marker
B09_4137374B09_4137374genetic_marker
B09_3950509B09_3950509genetic_marker
B09_3930319B09_3930319genetic_marker
B09_3847590B09_3847590genetic_marker
B09_3704628B09_3704628genetic_marker
B09_3666828B09_3666828genetic_marker
B09_3561093B09_3561093genetic_marker
B09_3549770B09_3549770genetic_marker
B09_3505099B09_3505099genetic_marker
B09_3464701B09_3464701genetic_marker
B09_3456278B09_3456278genetic_marker
B09_3302241B09_3302241genetic_marker

Pages

Properties
Additional details for this publication include:
Property NameValue
Publication Speciesarachis
URLhttps://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.12930
KeywordsWhole-genome resequencing, High-density genetic map, Quantitative trait loci, Early leaf spot, Late leaf spot, Tomato spotted wilt virus
Cross References
This publication is also available in the following databases:
DatabaseAccession
DOI: Document Object IdentifierDOI:10.1111/pbi.12930
PMID: PubMedPMID:29637729
Stocks
This publication contains information about 1 stocks:
Stock NameUniquenaemType
TT_Tifrunner_x_GT-C20_cTT_Tifrunner_x_GT-C20_cCultivar