Comprehensive analysis of copy number variation in diverse bitter gourd (Momordica charantia L.) accessions

Abstract

Copy number variation (CNV), a type of large-scale structural variation, contributes substantially to genetic diversity, impacting phenotypic traits and adaptive evolution in plants. In this study, genome re-sequencing of 146 bitter gourd (Momordica charantia L.) accessions revealed over 200,000 unique CNVs, consisting of 33,8031 deletions and 200,714 duplications. A total of 5763 CNV regions (CNVRs) were identified, spanning sizes ranging from 1 to over 400 kb, with notable enrichment on chromosomes 6 and 8. Functional annotation of 992 genes overlapping with CNVRs highlighted processes related to DNA repair, pathogen defense, metabolic regulation, and bioactive compound synthesis, including terpenes and antioxidants. Gene ontology and KEGG pathway enrichment analyses indicated roles in DNA integration, stress resilience, and metabolic pathways. A significant genetic differentiation influenced by domestication and regional adaptation was observed from clustering and population structure analyses. Hierarchical and PCA clustering identified distinct groups based on geographic origin, with a marked divergence between wild and cultivated varieties, particularly among accessions from China and Africa. This comprehensive CNV analysis provides valuable insights into the genetic diversity and adaptive mechanisms of bitter gourd, supporting breeding strategies, conservation efforts, and further exploration of its genomic potential for crop improvement.