Horticultural, chemical and genetic diversity using SSR markers in Leek germplasm collection

•Kong Richard, G-1722 and Kumanovski accessions produced the highest yield.•Visok and G-1948 accessions had the highest allicin content.•Genetic diversity in leek germplasm was characterized with SSR markers for the first time.•Genetic clustering agreed with life form and biological status using different methodologies.•Two SSR markers associated with plant growth and another five associated with allicin. A total of twenty-three leek accessions, obtained from the German genebank in Gatersleben and the United States Department of Agriculture genebank, in addition to local genotype were phenotyped and genotyped to study the phenotypic and genetic diversity as well as population structure. Significant and broad variation was found among the accessions in terms of morphological (plant height and total yield), minerals content (nitrogen, phosphorus and sulfur) and bio-chemical (carbohydrates, phenols, thiosulfanates and allicin) traits. Our results identified promising accessions (Kong Richard, G-1722 and Kumanovski) for cultivation under Egyptian conditions, as they recorded the highest plant growth and yield. Also, a total of 152 alleles were obtained from 5 SSR polymorphic markers and high average number of alleles per locus (NA=30.4), heterozygosity per locus (Ho= 0.36) and polymorphism information content (PIC= 0.97) were reported, indicating that the used SSR primers were useful tool in detecting genetic variability among leek genotypes in the current leek collection. In addition, the genetic structure using multivariate, phylogenetic and model based methods generally and clearly separated these accessions into two different groups according to their life form (i.e., perennial vs. biennial genotypes). Moreover, Single Marker Analysis (SMA) identified candidate SSR markers associated with yield-related traits and allicin content. In conclusion, the results of the current research have provided important insights into the phenotypic and genetic diversity of leek's genebank accessions using morphological, minerals, bio-chemical content as well as SSR markers, for the first time, providing valuable information for researchers and breeders for future studies.