Population genomic analysis reveals genomic variations associated with domestication and key agronomic traits in bitter gourd (Momordica charantia)

Bitter gourd (Momordica charantia) is a widely cultivated vegetable and medicinal crop for its nutritional and pharmaceutical properties. Yet, the genomic basis of its domestication and key agronomic traits remains largely unexplored. Here, we present a high-quality, chromosome-level genome assembly specifically representing a smooth bitter gourd cultivar (Y1745), with a total assembly size of 327.14 Mb, a contig N50 of 11.33 Mb, and a scaffold N50 of 23.47 Mb. Comparative genomics reveals lineage-specific expansions of gene families related to stress responses and secondary metabolism. Population genomic analysis of 192 globally representative accessions identifies three distinct genetic groups (China, Southeast Asia, and South Asia Subcontinent), reflecting complex demographic histories, and uncovers strong signatures of selection associated with domestication and regional adaptation. In the genome-wide association study (GWAS) of 35 traits, we identify 893 significant trait-associated loci. Notably, two candidate genes (McWRKY and McFPF1-like 1) are associated with flowering time regulation, and one candidate gene (McEXLB1) with fruit size determination. Our work provides valuable genomic resources for understanding bitter gourd domestication and offers potential genetic targets for breeding.