High resolution mapping of pleiotropic QTLs and candidate genes for seed quality using a whole genome resequencing approach in peanut (Arachis hypogaea L.)

Peanut ( Arachis hypogaea L.) is a major oilseed crop, and seed quality particularly total oil content, the balance between oleic and linoleic acids, and protein level is a primary target for breeding and health oriented improvement. Recent advances in peanut genomics, including high quality reference genomes, have created new opportunities for precision breeding; however, comprehensive high density linkage maps coupled with functional validation of quality related loci remain limited. In this study, we constructed a high density genetic linkage map comprising 4,746 bin markers spanning 3,328.40 cM, with an average marker interval of 0.70 cM. Using multi environment phenotypic data collected over four years, we identified 48 quantitative trait loci (QTLs) controlling eight seed quality traits, including oleic acid, linoleic acid, palmitic acid, total oil content, and protein content. Pleiotropy analysis revealed 20 QTL clusters, highlighting shared genetic control among multiple quality traits. Integrative genomic annotation further identified 20 candidate genes involved in fatty acid biosynthesis and lipid metabolism. Notably, haplotype analysis of Ahy_A09g042118 (AhFATB1) uncovered a functional non-synonymous SNP associated with significant variation in total oil content and fatty acid composition. The favorable haplotypes showed contrasting effects on oleic, linoleic, and palmitic acid accumulation without affecting protein content, indicating a key role of AhFATB1 in modulating carbon flux within seed lipid biosynthesis. Collectively, these findings elucidate the genetic architecture underlying peanut seed quality traits and provide valuable molecular targets for marker assisted selection, particularly for the development of high oil and high oleic peanut cultivars.