Journal Article

High-resolution genetic and physical mapping reveals a peanut spotted wilt disease resistance locus, PSWDR-1, to Tomato spotted wilt virus (TSWV), within a recombination cold-spot on chromosome A01

Thompson, Ethan A., Wang, Xingjun, Holbrook, C. Corley, Wang, Hui, Korani, Walid, Culbreath, Albert, Zhao, Chuanzhi, Fountain, Jake C., Guo, Baozhu, Agarwal, Gaurav, Clevenger, Josh P., Wu, Dongliang

2025

Overview

Background Peanut ( Arachis hypogaea L.) is a vital global crop, frequently threatened by both abiotic and biotic stresses. Among the most damaging biotic stresses is Tomato spotted wilt virus (TSWV), which causes peanut spotted wilt disease resulting in significant yield loss. Developing TSWV-resistant cultivars is crucial to new cultivar release. Previous studies have used a subset of the “S” recombinant inbred line (RIL) population derived from SunOleic 97R and NC94022 and identified quantitative trait loci (QTLs) for resistance to TSWV. These studies utilized different genotyping techniques and found large consistent genomic regions on chromosome A01. The objective of this study was to fine map the QTL and identify candidate genes using the entire population of 352 RILs and high-density, high-quality peanut SNP arrays. Results We used both versions of the peanut SNP arrays with five years of disease ratings, and successfully mapped the long-sought peanut spotted wilt disease resistance locus, PSWDR-1 . QTL analyses identified two major QTLs, explaining 41.43% and 43.69% of the phenotypic variance within 3.6 cM and 0.28 cM intervals using the peanut Axiom_ Arachis -v1 and Axiom_ Arachis -v2 SNP arrays, respectively, on chromosome A01. These QTLs corresponded to 295 kb and 235 kb physical intervals. The unique overlap region of these two QTLs was 488 kb. A comparison of the genetic linkage map with the reference genome revealed a 1.3 Mb recombination “cold spot” (11.325–12.646 Mb) with only two recombination events of RIL-S1 and RIL-S17, which displayed contrasting phenotypes. Sequencing of these two recombinants confirmed the cold spot with only five SNPs detected within this region. Conclusions This study successfully identified a peanut spotted wilt disease resistance locus, PSWDR-1 , on chromosome A01 within a recombination “cold spot”. The PSWDR-1 locus contains three candidate genes, a TIR-NBS-LRR gene ( Arahy.1PK53M ), a glutamate receptor-like gene ( Arahy.RI1BYW ), and an MLO-like protein ( Arahy.FX71XI ). These findings provide a foundation for future functional studies to validate the roles of these candidate genes in resistance and application in breeding TSWV-resistant peanut cultivars.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Animal Genetics and Genomics / Arachis / Arachis - genetics / Arachis - virology / Arachis hypogaea / Arrays / Biomedical and Life Sciences / Chromosome 1 / Chromosome Mapping / Chromosomes / Chromosomes, Plant - genetics / Cultivars / Disease resistance / Disease Resistance - genetics / Diseases and pests / Environmental aspects / Gene mapping / Genes / Genetic aspects / Genetic linkage / Genomes / Genotyping / Glutamate receptors / Growth / Inbreeding / Intervals / Legumes / Life Sciences / Linkage and physical mapping / Microarrays / Microbial Genetics and Genomics / NBS-LRR gene / Peanut spotted wilt disease resistance locus / Peanuts / Phenotypes / Phenotypic variations / Physical Chromosome Mapping / Physical mapping / Plant breeding / Plant Diseases - genetics / Plant Diseases - virology / Plant Genetics and Genomics / Plant viruses / Polymorphism, Single Nucleotide / Proteomics / Quantitative Trait Loci / Recombinants / Recombination / Recombination cold spot / Recombination, Genetic / Single-nucleotide polymorphism / Stresses / Tomatoes / Tospovirus - physiology / TSWV / Wilt