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
B06_35531945B06_35531945genetic_marker
B06_34083116B06_34083116genetic_marker
B06_34083081B06_34083081genetic_marker
B06_33710759B06_33710759genetic_marker
B06_33663947B06_33663947genetic_marker
B06_32996122B06_32996122genetic_marker
B06_32052932B06_32052932genetic_marker
B06_31972025B06_31972025genetic_marker
B06_31559680B06_31559680genetic_marker
B06_31498239B06_31498239genetic_marker
B06_31384701B06_31384701genetic_marker
B06_31152073B06_31152073genetic_marker
B06_30824262B06_30824262genetic_marker
B06_30366161B06_30366161genetic_marker
B06_30291998B06_30291998genetic_marker
B06_29701468B06_29701468genetic_marker
B06_29654238B06_29654238genetic_marker
B06_29654217B06_29654217genetic_marker
B06_28872077B06_28872077genetic_marker
B06_28872074B06_28872074genetic_marker
B06_28220982B06_28220982genetic_marker
B06_27921791B06_27921791genetic_marker
B06_27784216B06_27784216genetic_marker
B06_27604358B06_27604358genetic_marker
B06_26162626B06_26162626genetic_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