Genetic identification of AhGH15, a gene under convergent selection during peanut growth habit domestication and breeding

Peanut (Arachis hypogaea), a globally important oilseed crop, exhibits contrasting growth habits between wild species (prostrate) and cultivated varieties (erect or spreading), but the underlying mechanism is unclear. In this study, we performed quantitative trait locus (QTL) mapping of two recombinant inbred line (RIL) populations of peanut using SNP arrays and bulk segregant analysis, which identified qGH15 on chromosome 15 as a major QTL regulating growth habit. Fine mapping using KASP markers narrowed the candidate region to a 151-kb interval, while analysis of a residual heterozygous line (RHL) further delimited qGH15 to a 38-kb interval containing a single candidate gene, which we designated as AhGH15. Genotyping of a natural population revealed multiple types of polymorphisms in this gene associated with the erect habit in cultivated varieties. Phylogenetic and pedigree analyses demonstrated that these polymorphisms were recurrently and convergently selected during peanut domestication and breeding, with modern hybridization accelerating their dissemination. Transcriptome deep sequencing and gene co-expression analysis via WGCNA revealed polymorphism-specific patterns of transcriptome regulation, with co-expressed gene modules differentially active between accessions with erect or prostrate growth habits. These findings establish AhGH15 as a key determinant of peanut growth habit and highlight its complex selection history during peanut improvement.