Sex chromosome-aware GWAS reveals XY-linked agronomic architecture and breeding targets in cannabis

Cannabis sativa is a dioecious crop whose male plants carry a Y chromosome entirely excluded from every genome-wide association study (GWAS) published to date, despite its direct relevance to agronomic trait variation. Here, we present the first sex chromosome-aware GWAS of cannabis, integrating both ChrX and ChrY across 145 landrace accessions and 27 agronomic traits. By combining SNP-based GWAS with sex-stratified k -mer association analysis, we identified 16 genome-wide significant markers: e