Deciphering genetic diversity and population structure of onion (Allium cepa L.) using agro-morphological and molecular markers

Onion, a member of the Allium genus, stands out as the most extensively cultivated species in the Indian sub-continent, possessing remarkable potential for export. To enhance bulb yield, overall quality, and to fortify the resistance against both biotic and abiotic stresses, agro-morphological and molecular characterization is of utmost significance. Genetic diversity in 49 onion genotypes was assessed using six DUS descriptors, 19 quantitative traits along with 13 ISSR markers. Among DUS descriptors, bulb: basic color of dry skin exhibited the highest diversity index (1.44). Mahalanobis D2 statistic grouped the genotypes into seven clusters with the highest inter-cluster distance between clusters V and VII (364.35). A total of 78 fragments were produced from 13 polymorphic primers with a mean of six alleles per primer. The polymorphic information content (PIC) ranged from 0.42 (UBC 835) to 0.75 (UBC 825) with an average of 0.61 per primer. Cluster analysis using UPGMA algorithm divided genotypes into two major clusters, whereas the cluster tree identified three major groups. The structure analysis divided the population into two main groups. Based on genetic distance, Genotypes no. 13 (ON20-11) and 28 (ON20-49) were found most diverse and also exhibited considerable resistance to stemphylium blight and thrips incidence. Mantel’s test showed a moderate positive correlation between agro-morphological (DUS descriptors) and molecular data. Thus, integrated morphological and molecular characterization followed by hybridization can facilitate onion breeding programs to introgress desired traits like resistance to stemphylium blight and thrips incidence into elite cultivars.