Re-sequencing of 180 bitter gourd accessions uncovering the genetic basis of key horticultural traits

L.) is a valuable cucurbit crop, yet its genetic improvement has been hindered by limited genomic resources and understanding of trait genetics. Here, we performed whole-genome re-sequencing of a diverse panel of 180 bitter gourd accessions, generating an average coverage of 33.91× and identifying ~1.78 million high-quality single nucleotide polymorphisms (SNPs). Population structure analysis delineated the panel of 180 bitter gourd accessions into five distinct sub-populations, revealing moderate genetic diversity and varied linkage disequilibrium decay patterns across subgroups. We phenotyped the panel for four key horticultural yield related traits and conducted genome-wide association studies (GWAS). This identified several significant loci, including a major pleiotropic region on chromosome MC04 concurrently associated with single fruit weight (SFW), fruit length (FL), and fruit diameter (FD). Haplotype analysis of candidate genes within this interval (MC04g0117, MC04g0120, MC04g0121 and MC04g0126) demonstrated that Hap1 significantly enhanced SFW (20.46%-22.68%), FL (13.68%-16.09%), and FD (6.28%-8.44%) compared to Hap2. Notably, although GWAS did not initially link this region to fruit flesh thickness (FFT), haplotype partitioning revealed that Hap2 consistently increased FFT by 4.00%-4.31%, uncovering a previously hidden phenotypic effect. Furthermore, trait-specific loci were mapped, such as for SFW on MC08 (MC08g1837) and FFT on MC09 (MC09g_new0383, MC09g1204), with corresponding haplotypes conferring significant phenotypic advantages. Our study provides a comprehensive genomic variation map for bitter gourd, elucidates the genetic architecture of crucial yield-related traits, and identifies candidate genes with clear haplotype effects, thereby establishing a foundational resource for accelerating molecular breeding programs.