Genetic diversity and population structure in onion (Allium cepa L.) accessions based on morphological and molecular approaches.

Bulb onion is cultivated throughout the world for consumption as vegetable and processed products. Although having high global demand and economic significance, information about genetic diversity and genomic resources is limited. This study investigated the variability of 96 accessions representing seventeen countries. Out of 145 SSR markers, 62 SSRs amplified and 15 SSRs gave consistent polymorphic bands. Fifty three alleles were detected with an average of 3.533 alleles per locus. PIC value ranged from 0.219 (ACM463) to 0.715 (ACM091). Structure and cluster analysis grouped the onion accessions into two clusters. Discriminant analysis of principal components, a tool that maximizes variation between groups while minimizing that within groups, assorted accessions into five clusters. Analysis of molecular variance revealed maximum variation within the populations than among the populations. Highest genetic differentiation (FST = 0.11045; p < 0.001) was observed between Europe and Japan populations whereas the lowest genetic differentiation (FST = 0.05714; p < 0.001) was recorded between India and Japan. Principal component analysis of morphological traits suggested two principal components cumulatively accounting for 74.4% of the total variance. First component (PC1) was positively and strongly correlated with bulbing whereas second component (PC2) had leaf colour with the highest coefficient. Clustering was not on the basis of bulb colour, bulb formation, or flowering but on the basis of geographical origin. Based on clustering, crossing of distantly related accessions can provide an insight about the hybrid vigour of these diverse accessions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01101-3.