Genomic variation in 271 diverse accessions of Cannabis sativa L. in China

Cannabis sativa L., a multipurpose plant with historical significance in food, textile, and medicinal applications, exhibits undercharacterized genomic diversity within Chinese germplasm despite its widespread cultivation. To address this knowledge gap, we performed whole-genome resequencing of 271 geographically diverse accessions spanning 29 populations across 12 Chinese provinces, achieving an average depth of 7.08×. Comparative genomic analysis against the reference assembly revealed 2,699,120 single nucleotide polymorphisms (SNPs) and 42,201 insertion-deletion mutations (InDels), providing the most comprehensive variant catalog for Chinese cannabis to date. Phylogenetic reconstruction delineated five distinct genetic clusters, with principal component analysis (PCA) and population structure results demonstrating strong concordance between genetic relatedness and geographical origins. Genome-wide selective sweep scans revealed distinct signatures of selection across populations, identifying 3,299 candidate genes underlying north-south population differentiation in Xinjiang, 3,215 genes at the Xinjiang-Xizang divergence interface, and 3,404 genes distinguishing southwestern versus northeastern domestication trajectories. Genome-wide association studies (GWAS) identified CBDAS as a robust candidate gene associated with CBD content, with significant signals localized on chromosome 1. For THC, while several suggestive loci were identified, no definitive candidate gene could be confidently assigned based on functional annotations, highlighting the complex genetic architecture of THC biosynthesis. This study establishes a foundational genomic resource for molecular breeding programs while offering critical insights into the genetic basis of chemotypic variation, with dual implications for narcotics control and agricultural improvement.