John A. Henning

Genic SSRs for European and North American hop (Humulus lupulus L.)

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.

Potential Heterotic Crosses in Hops as Estimated by AFLP-Based Genetic Diversity and Coefficient of Coancestry

Hop is a dioecious perennial with female plants grown commercially for brewing purposes. Parent selection in hop breeding on the basis of heterotic potential has not been reported in literature even though dominance has been reported in hops for several economically important traits. The objectives of this study were to determine if amplified fragment length polymorphism (AFLP)-based genetic distance among male and female accessions accurately reflect pedigree relationships and present information on potential heterotic crosses in hop. Nineteen cultivars were analyzed for genetic distance to 82 male accessions representing the assumed diversity of U.S. hops. Genetic distances (GD) between male/female pairs were estimated using AFLP (490 polymorphic bands). Distance estimates comparing males with females ranged from 0.169 to 0.62 with an overall average of 0.306. For each hop female, the 10 most genetically diverse and 10 most genetically similar males were identified and grouped. Coefficients of coancestry (COA) for each male/female pair within these groups were calculated using pedigree analysis. Values of COA for the genetically similar pairs (COAavg = 0.046) were significantly higher than the COA for the diverse pairs (COAavg = 0.013), suggesting that choosing male/female pairs on the basis of AFLP-based genetic distance may predict heterotic potential in crosses when GD >0.36.

Statistical Modeling of Epistasis and Linkage Decay using Logic Regression

Logic regression has been recognized as a tool that can identify and model non-additive genetic interactions using Boolean logic groups. Logic regression, TASSEL-GLM and SAS-GLM were compared for analytical precision using a previously characterized model system to identify the best genetic model explaining epistatic interaction of vernalization-sensitivity in barley. A genetic model containing two molecular markers identified in vernalization response in barley was selected using logic regression while both TASSEL-GLM and SAS-GLM included spurious associations in their models. The results also suggest the logic regression can be used to identify dominant/recessive relationships between epistatic alleles through its use of conjugate operators.