Genetic structure and differentiation in hop (Humulus lupulus L.) as inferred from microsatellites

A set of 67 wild and cultivated hop accessions, representative of hop diversity, was genotyped with 29 SSR markers in order to investigate the population structure and genetic diversity among hop genotypes. A total of 314 alleles was detected, with an average of 10.8 alleles per locus and an average PIC content of 0.607. Model-based clustering placed the accessions into five germplasm groups. A distance-based tree showed good agreement with five germplasm groups, and additionally assigned accessions omitted from model-based analysis into two additional germplasm groups. The 67 hop accessions were thus subdivided in seven germplasm groups, with three corresponding to major breeding groups and four to wild hops. This finding is in accordance with two biogeographically separated hop germplasms (European and North American origin) and with the known history of the accessions. North American hop germplasm was partitioned into native and cultivated germplasm groups. European germplasm was divided into two groups of hop cultivars representing distinguishable European germplasms and three new groups of native hops, which were differentiated for the first time by this analysis. Admixture analysis showed shares of various ancestries in hop cultivars, mostly congruent with pedigree data, and the introgression of various ancestries in some native hops. The above results have so far given the most detailed insight to date into the population structure of hop diversity, which is important for its effective use in hop breeding.