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ARS Home » Pacific West Area » Corvallis, Oregon » Forage Seed and Cereal Research Unit » Research » Publications at this Location » Publication #311047
Title: Simple SNP-based minimal marker genotyping for (Humulus lupulus L.) identification and variety validation

Author
item Henning, John
item COGGINS, JAMIE - Oregon State University
item PETERSON, MATTHEW - Oregon State University

Submitted to: BMC Research Notes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/21/2015
Publication Date: 10/6/2015
Citation: Henning, J.A., Coggins, J., Peterson, M. 2015. Simple SNP-based minimal marker genotyping for (Humulus lupulus L.) identification and variety validation. BMC Research Notes. 8(1):1-12. doi: 10.1186/s13104-015-1492-2.

Interpretive Summary: This study was performed in response to industries' need for varietal testing and identification of unknown or suspect hop lines. Currently used molecular or chemical techniques are not adequate for differentiation among closely related lines such as sister lines or clonal selection. A more recent molecular marker (SNPs) technology was tested to identify a small subset of markers that could easily differentiate between most if not all important hop varieties. A large set of SNP markers were tested across 121 different hop varieties. Data from this test was sorted for correlation to genetic diversity among the lines and a subset of 8 markers was identified as being sufficient for differentiating among all hop varieties in this study. Hop growers, brewers and merchants now have access to a widely adaptable molecular marker testing system to validate their varieties or get unknown samples tested.

Technical Abstract: Hop is a perennial crop with clonal propagation system for varietal distribution. Brewers and growers are highly concerned about variety purity and regularly seek genotype testing. Current means for genotyping are based upon SSRs OR AFLPs that are relatively accurate but cannot differentiate closely related lines. In addition, numerous and lengthy PCR steps are required to complete this process with only a few laboratories offering this service. A genotyping protocol based upon SNPs would enable rapid accurate testing that could be accomplished at multiple laboratories. This study arose from a larger whole genome association study of USDA-ARS hop germplasm consisting of approximately 121 unique hop varieties and germplasm. The original dataset that arose from this study identified 374829 SNPs. After filtering out SNPs and/or genotypes with significant amounts of missing data, 7120 high quality SNP markers across 116 genotypes were chosen for the study. Polymorphic information content was determined for each SNP and ranked according to the most informative to least informative. Genetic distance values were calculated for all individuals based upon the four most informative markers, then the combination of the first four markers with the next most informative marker and so on. This process was reiterated until a set of markers was identified that allowed for all genotypes in the study to be genetically differentiated from each other. This process resulted in a set of 8 SNP markers that differentiated all lines in the study. These SNPs were then aligned with a genome assembly, and DNA sequence both upstream and downstream were used to identify primer sequences that can be used to amplify the 8 SNPs. This study provides a valuable tool for the identification and validation of hop varieties and accessions. The tool can be used at any genetics laboratory that utilizes SNP-marker technology. Brewers, merchants and hop growers now have the capability to have unknown or known hop samples validated or identified in a timely manner for minimal costs.