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_13038812B06_13038812genetic_marker
B06_12615620B06_12615620genetic_marker
B06_12605840B06_12605840genetic_marker
B06_12563381B06_12563381genetic_marker
B06_12455869B06_12455869genetic_marker
B06_12406540B06_12406540genetic_marker
B06_12329509B06_12329509genetic_marker
B06_12327023B06_12327023genetic_marker
B06_12300479B06_12300479genetic_marker
B06_11113946B06_11113946genetic_marker
B06_11099389B06_11099389genetic_marker
B06_11099373B06_11099373genetic_marker
B06_10878206B06_10878206genetic_marker
B06_10861546B06_10861546genetic_marker
B03_19784252B03_19784252genetic_marker
B03_19240971B03_19240971genetic_marker
B03_19001844B03_19001844genetic_marker
B03_19001826B03_19001826genetic_marker
B03_18974575B03_18974575genetic_marker
B03_18949190B03_18949190genetic_marker
B03_18642606B03_18642606genetic_marker
B03_18610241B03_18610241genetic_marker
B03_18610234B03_18610234genetic_marker
B03_18352306B03_18352306genetic_marker
B03_18183431B03_18183431genetic_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