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
B10_86512405B10_86512405genetic_marker
B10_86512409B10_86512409genetic_marker
B10_89102170B10_89102170genetic_marker
B10_89912142B10_89912142genetic_marker
B10_90916467B10_90916467genetic_marker
B10_90929906B10_90929906genetic_marker
B10_91579899B10_91579899genetic_marker
B10_91824430B10_91824430genetic_marker
B10_95031264B10_95031264genetic_marker
B10_95653805B10_95653805genetic_marker
B10_96104139B10_96104139genetic_marker
B10_98079674B10_98079674genetic_marker
B10_98465132B10_98465132genetic_marker
B10_98870570B10_98870570genetic_marker
B10_99333742B10_99333742genetic_marker
KASP.A03_134198144KASP.A03_134198144genetic_marker
KASP.A05_20406182KASP.A05_20406182genetic_marker
KASP.A05_82270000KASP.A05_82270000genetic_marker
KASP.A06_14301316KASP.A06_14301316genetic_marker
KASP.B05_22527171KASP.B05_22527171genetic_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