Quantitative trait loci mapping disease resistance to TSWV, leaf spots, and aflatoxin contamination of peanut (Arachis hypogaea L.) using whole-genome re-sequencing

We used a recombinant inbred line (RIL) population derived from the cross between SunOleic 97R and NC94022, and conducted whole genome re-sequencing (WGRS). Using single nucleotide polymorphism (SNP) markers, a genetic linkage bin-map containing 5,816 bins and 20 linkage groups was constructed. We identified three major QTLs on chromosome A0l using this bin-map. One of the QTLs with the largest contribution of 36.51 % to the phenotypic variation encompassed 89.5 Kb region on the physical map. A cluster of genes coding for chitinase family protein, strictosidine synthase-like protein, and LRR receptor kinase were identified in this physical region. SNPs associated with this QTL were used to develop Kompetitive allele specific PCR (KASP) markers, and the validated KASP markers showed expected segregation of alleles coming from resistant and susceptible parents within the population. Therefore, this genetic bin-map based identification of QTL linked to TSWV resistance can be further used for functional gene mapping, cloning, and marker-assisted selection for TSWV resistance breeding. This study has not only identified the highest number of SNPs, it also demonstrated the use of genetic bin map based QTL analysis in an allotetraploid like peanut. Presence of chitinase gene clusters and other disease resistance related genes in this QTL region suggest them to be the potential candidate genes with their involvement in TSWV resistance.