Okra (Abelmoschus spp.) is an important vegetable crop with complex genetic relationships among its cultivated and related species. To better understand their genetic diversity, we analyzed 440 accessions which consists of A. esculentus, A. caillei, A. manihot, and A. moschatus from the AVRDC headquarter genebank using genotyping-by-sequencing (GBS) and morphological traits. Principal component analysis (PCA) of SNP data showed that A. esculentus and A. caillei formed distinct clusters, while A. caillei was genetically closer to A. manihot, supporting the putative origin of A. caillei derived from this species. Variation along PC1 was greater in A. caillei cluster than in A. esculentus cluster, indicating higher within-species diversity. In contrast, morphological descriptors do not separate species well with PCA, likely due to environmental effects. Furthermore, A. caillei exhibited higher observed heterozygosity, lower inbreeding coefficient, and substantially greater nucleotide diversity (π), Watterson’s estimator (θ), and segregating sites compared to A. esculentus. Diversity profiles across scaffolds were broadly similar in A. caillei, A. manihot, and A. moschatus, but A. esculentus has relatively less diversity. Weighted fixation index (FST) analysis also indicated greater gene flow between A. caillei and A. manihot than between A. caillei and A. esculentus. This result reinforces the closer evolutionary relationship of A. caillei with A. manihot but also indicates the need for further studies on the relationship between A. caillei with A. esculentus. Overall, these findings highlight the distinct genetic differentiation between two main okra species A. esculentus and A. caillei, the greater genetic variability of A. caillei, and provide insights into the evolutionary origins of cultivated okra.
