Deciphering morpho-molecular diversity and population structure in ridge gourd (Luffa acutangula (L.) Roxb.) germplasm for breeding applications

• Key yield traits showed high heritability (96.9%) and genetic advance, indicating strong selection potential. • High Shannon diversity (H′ = 0.60–0.94) indicated substantial phenotypic variation in ridge gourd germplasm. • Flowering time and sex ratio were the main drivers of yield-related variation. • SSR markers revealed high genetic diversity within 200 ridge gourd accessions. • Morphological and molecular clustering were independent of collection site in 200 ridge gourd accessions. Ridge gourd ( Luffa acutangula (L.) Roxb.) is a popularly grown cucurbitaceous crop cultivated across Southeast Asia for its young, immature fruits. This study evaluated genetic variability among 200 germplasm accessions sown in Augmented Block Design during Spring-summer season in 2021–22. Descriptive statistics showed substantial phenotypic variation was supported by Shannon diversity index. Euclidian clustering for quantitative traits divided the germplasm into six distinct morphological clusters, each exhibiting unique trait combinations. Among these, Cluster V comprised accessions with superior fruit traits, which contributed directly to enhanced yield potential. The first five principal components together accounted for 64.4% of the total cumulative variation. High value of genetic advance and genetic advance as percent of mean observed for fruit length, fruit width, number of fruits per vine, seed number per fruit and 100-seed weight. Estimates of heritability were also observed high for these key traits. Positive correlation observed between number of fruits per plant with days to 50% flowering and days to first female flower indicating selection of late maturing accessions for high yielding varieties. Molecular characterization using 18 simple sequence repeat (SSR) markers revealed 94 alleles, with allele sizes ranging from 90 to 384 bp and polymorphic information content (PIC) values between 0.35 and 0.83. A dendrogram constructed from SSR profiles categorized entire set into three major clusters, with further sub-clustering reflecting genetic relatedness among genotypes. Additionally, population structure analysis using STRUCTURE software grouped the accessions into two distinct subpopulations irrespective of geographical location. Findings highlight the potential of diverse germplasm as a parent in hybridization program through targeted breeding.