Genic SSRs for European and North American Hop (Humulua lupulus L.)

Authors: Bassil, Nahla; Gilmore, Barbara; Oliphant, James - Jim; Hummer, Kim; Henning, John

Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/4/2007
Publication Date: 12/20/2007
Citation: Bassil, N.V., Gilmore, B.S., Oliphant, J.M., Hummer, K.E., Henning, J.A. 2007. Genic SSRs for European and North American Hop (Humulua lupulus L.). Genetic Resources and Crop Evolution. Available: www.springerlink.com/content/d000k04454n55v2p/fulltext.pdf

Interpretive Summary: Hop is an important crop in the Pacific Northwest and a collection is preserved at the U.S. Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository, in Corvallis, OR. Our objectives were to evaluate genetic tools for estimation of genetic diversity and for genotype identification in a representative subset of European (EU) and North American (NA) accessions. The EU group contained 14 cultivated varieties and 10 wild genotypes while the NA group consisted of 22 wild genotypes collected from two geographic areas of the US: North Central (NC) and Southwestern (SW). We used eight microsatellite or simple sequence repeat (SSR) markers present in 7 hop genes. Based on SSR analysis, the hop genotypes formed two groups: a European and a North American group. These 8 SSRs were useful in uniquely identifying each accession with the exception of two sets of European landraces and a pair of Japanese cultivars, ‘Shinshuwase’ and ‘Kirin II’. An accession from Manitoba grouped with the EU cluster reflecting its similarity to older Manitoba germplasm used to develop ‘Brewers Gold’ and the genotypes arising from this cultivar. Cultivars grouped closely with one of their immediate parents. ‘Perle’ grouped with its parent ‘Northern Brewer’ and ‘Willamette’ grouped with its parent ‘Fuggle H’. Wild American accessions were grouped based on geographical location into two groups: a North Central group and a Southwestern group. These eight SSRs will be valuable for genotype identification in European and wild American germplasm and may potentially prove useful for facilitating cultivar selection in hop.

Technical Abstract: Eight genic SSR loci were evaluated for genetic diversity assessment and genotype identification in Humulus lupulus L. from Europe and North America. Genetic diversity, as measured by three diversity indices, was significantly lower in European cultivars than in North American wild accessions. Neighbor Joining cluster analysis separated the hop genotypes into European and North American groups. These eight SSRs were useful in uniquely identifying each accession with the exception of two sets of European landraces and a pair of Japanese cultivars, ‘Shinshuwase’ and ‘Kirin II’. An accession from Manitoba grouped with the European (EU) cluster reflecting the group’s genetic similarity to older Manitoba germplasm used to develop ‘Brewers Gold’ and the gene pool arising from this cultivar. Cultivars grouped closely with one of their immediate parents. ‘Perle’ grouped with its parent ‘Northern Brewer’ and ‘Willamette’ grouped with its parent ‘Fuggle H’. Wild American accessions were divided into two subgroups: a North Central group containing mostly H. lupulus var. lupuloides and a Southwestern group containing H. lupulus var. neomexicanus accessions. These eight SSRs will be valuable for genotype identification in European and wild American germplasm and may potentially prove useful for marker-assisted selection in hop. PCR products from four previously reported primer pairs that amplify the same intronic SSR regions as do the genic SSRs in this study were compared in eight common cultivars. Different primer pairs generated robust markers at the chs2 and chi loci. However, only the HLC-004B and HLC-006 primer pairs amplified successfully at the chs3 and chs4 loci.