Identification of two QTLs and development of KASP molecular markers for seed coat cracking tolerance in peanut...

The peanut seed coat serves as a vital protective layer, but the occurrence of fine cracks breaches this integrity, thereby impairing visual quality and elevating the risk of pathogen infection and postharvest mycotoxin contamination. However, knowledge on genetic factors underlying seed coat cracking (SCC) tolerance remains limited. In this study, a population of 521 recombinant inbred line (RIL) was used to identify genetic regions associated with SCC tolerance across three environments. Quantitative trait locus (QTL) mapping identified two stable QTLs on chromosomes 7 and 16, qSCCA07 and qSCCA16, explaining 3.91%-11.83% and 3.63%-7.43% of phenotypic variation, respectively. Besides, the two QTL regions were refined to 272.90 kb and 626.75 kb, respectively, by constructing a high-density genetic map using Kompetitive Allele-Specific PCR (KASP) markers. The QTL-linked markers YZ9102_chr07_1027286 and YZ9102_chr16_12140367 were validated in the RIL population and a germplasm collection. Overall, genomic regions and molecular markers reported in this study provided novel insights into the genetic basis of SCC tolerance, and basis for marker-assisted selection.

The online version contains supplementary material available at 10.1007/s11032-026-01689-y.