Subspecies-specific haplotype signatures for customizing blanchability in groundnut (Arachis hypogaea L.) via haplotype-based breeding

Blanchability, the ease of seed coat removal after roasting, is a critical post-harvest trait in groundnut (Arachis hypogaea L.) that directly influences processing efficiency and product quality. Despite its economic value, limited genetic understanding restricts breeding efforts for customized blanchability in groundnut. Here, we integrate whole-genome resequencing of 184 diverse groundnut genotypes with multi-season phenotyping to dissect the haplotype-level genomic architecture of blanchability. Genome-wide association studies identify 26 significant single-nucleotide polymorphism-trait associations across multiple chromosomes, six of which are further validated using KASP markers, with two successfully validating the expected allelic effects across breeding lines and genotypes. Haplo-pheno analyses identify distinct subspecies-specific signatures for the major associations on chromosomes Ah01, Ah05, Ah06, and Ah17. Superior high-blanchability haplotypes (Ah01HapBL4, Ah05HapBL3, Ah06HapBL5, Ah06HapBL10, and Ah17HapBL6) are predominantly found in the fastigiata subspecies from South Asia and South America. In contrast, the low-blanchability haplotypes (Ah01HapBL2, Ah05HapBL6, Ah06HapBL3, Ah17HapBL2) are enriched in the hypogaea subspecies, mainly from Africa. These contrasting haplotypes offer the flexibility to achieve either high or low blanchability tailored to specific end-use applications. The availability of diagnostic markers and donor genotypes harboring multiple favorable haplotypes provides immediate tools for haplotype-based breeding. Collectively, this study introduces blanchability as a novel, customizable breeding target and establishes a translational framework to enhance the processing quality and industrial value of groundnut through haplotype-based breeding.