Genetic mapping and diagnostic marker development for a co-localization interval conferring resistance to both Aspergillus flavus infection and aflatoxin production in peanut

Aflatoxin contamination caused by Aspergillus flavus threatens the development of peanut industry, breeding aflatoxin-resistant peanut varieties are highly needed. In this study, a recombinant inbred line (RIL) population was developed from a cross between Zhonghua 16 and Kainong H03-3—a high oleic acid peanut line exhibiting resistance to both A. flavus infection and aflatoxin production. Using this RIL population, a high-density genetic map was constructed and employed to identify quantitative trait loci (QTLs) associated with resistance to A. flavus infection (described as percentage seed infection index, PSII) and aflatoxin production (described as aflatoxin content, ATC) across four environments. Three QTLs for PSII and ATC were detected, among which novel QTLs with major effect for both traits were co-localized in chromosome B06, explaining 20.71% and 22.73% of phenotypic variance for PSII and ATC, respectively. Within this co-localized genomic region, 13 candidate genes exhibited strong co-expression patterns linked to both PSII and ATC. Among them, Chr16g3738, harboring a non-synonymous variant in its exon, was used to develop a diagnostic KASP marker KASP-Chr16g3738. Validation of KASP-Chr16g3738 in a peanut germplasm panel and a breeding population (Jihua 6×Kaixuan 01–6) demonstrated that the favorable allele of the candidate gene was associated with a reduction of 15.27–56.67% in PSII and 27.59–72.76% in ATC. This study was the first report in identification of a genomic interval co-localized with QTLs conferring resistance to both A. flavus infection and aflatoxin production, and provides an efficient marker-assisted selection approach for accelerating improvement of resistance to aflatoxin in peanut.