From gene discovery to molecular tool: Characterization of a sucrose regulator and diagnostic KASP marker development for high-sucrose peanut breeding

Sucrose content dictates processing quality and consumer preference in edible peanuts, but its genetic control remains poorly characterized, limiting progress in breeding. In this study, using a breeding-informed F₂ population derived from a cross of high-sucrose germplasm JMT and elite cultivar Fushunsilihong (FSH) with normal-sucrose content, we integrated QTL mapping with functional genomics to decode the genetic architecture of sucrose accumulation. A major-effect locus (qSCB06) was precisely mapped to a 131-kb interval on chromosome B06 (148.03–148.16 Mb), accounting for 41.83% of the phenotypic variance (PVE). Comprehensive variant-to-function analysis identified five genes harboring exonic mutations, with Arahy.3URM83 validated as a key sucrose regulator through tissue-specific qRT-PCR profiling. To translate genomic discovery into breeding tools, we developed two cost-effective KASP markers (Arahy.06_115805462 and Arahy.06_148167024) that demonstrated 100% genotyping accuracy of F₂ individuals validated by SNP sequencing and 91.30% selection efficiency across 46 diverse cultivars. These markers enable rapid screening of sucrose-rich genotypes within 3 h, establishing a ready-to-implement molecular toolkit for expediting breeding of premium-quality peanuts. This work bridges gene discovery with field application, delivering both mechanistic insights and industrial solutions for flavor-driven peanut improvement.