Identification of a pleiotropic QTL and development of KASP markers for 100-pod weight, 100-seed weight, and shelling percentage in peanut

High yield remains the primary objective of peanut breeding. Key yield components, 100-pod weight (HPW), 100-seed weight (HSW), and shelling percentage (SP), are critical determinants of overall productivity. This study aimed to construct a high-density linkage map using resequencing data from recombinant inbred lines (RILs) derived from a cross between ‘Silihong’ (Arachis hypogaea var. fastigiate) and ‘Jinonghei 3’ (A. hypogaea var. hypogaea). The resulting map comprised 4,499 bins distributed across 20 chromosomes, spanning a total length of 1,712.32 cM with an average inter-marker distance of 0.38 cM. A total of 46 quantitative trait loci (QTLs) were identified across three environments. Major QTLs, including qHPW5.2, qHPW18.1, qSP7.1, qSP8.1, qSP8.2, qSP18.1, and qSP18.2, explained phenotypic variation (PVE) of 12.04, 11.41, 16.53, 24.17, 10.49, 10.82, and 29.89%, respectively. Fourteen QTLs detected across multiple environments were considered stable. Notably, one QTL region (qHPW7, qHSW7.1, and qSP7) was associated with all three traits, accounting for PVE values of 8.91, 9.04, and 16.53% for HPW, HSW, and SP, respectively. To validate the accuracy of QTL mapping, a genome-wide association study (GWAS) was conducted using the US mini-core collection. Across two environments, 115 single-nucleotide polymorphisms (SNPs) were significantly associated with HPW, HSW, and SP in the association panel. Six SNPs were linked to two traits, explaining an average phenotypic variation of 13.84%. Integration of both mapping populations revealed that AX-176802178, detected on chromosome 7 in the association panel and associated with SP, was located within the confidence interval of QTL qSP7 defined by the recombined inbred lines (RIL) population. Furthermore, three KASP markers were developed and validated in peanut landraces and cultivated varieties. These findings provide valuable insights into the genetic architecture underlying HPW, HSW, and SP, and offer useful molecular tools for marker-assisted selection in peanut breeding programs.