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United States Department of Agriculture

Agricultural Research Service

Title: Genbank-Derived Microsatellite Markers in Hops

Authors
item Bassil, Nahla
item Gilmore, Barbara
item Oliphant, James
item Henning, John
item Hummer, Kim

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 24, 2004
Publication Date: February 1, 2005
Citation: Bassil, N.V., Gilmore, B.S., Oliphant, J.M., Henning, J.A., Hummer, K.E. 2005. Genbank-derived microsatellite markers in hops. Acta Horticulturae. 668:47-52.

Interpretive Summary: Our objectives were to develop genetic tools for estimation of genetic diversity in a representative subset of European cultivars and North American accessions of hops maintained at the U.S. Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository, in Corvallis, OR. An internet-based data search method was used to identify useful sequences from an international database, and the resulting genetic tools were tested for their ability to estimate genetic diversity and to fingerprint 24 genotypes of hops.

Technical Abstract: A method was developed to identify microsatellite-containing sequences from existing hop entries in the Nucleotide GenBank database. We screened 45 genomic, mRNA and expressed sequence tag (EST) Humulus nuclear sequences and identified 7 that contained simple sequence repeats (SSRs). Primer pairs were designed for 16 sequences and the optimum annealing temperature was determined by gradient PCR. SSR primers were screened for polymorphism in a set of 24 accessions of hops. Ten primer pairs generated repeatable polymorphic bands and seemed to amplify single loci. The forward primers for these 10 loci were fluorescently labeled and capillary electrophoresis was used for size allele determination in 48 representative genotypes of European cultivars, European landraces, and wild North American material. These 10 polymorphic loci will be used for estimation of genetic diversity, cluster analysis and for their ability to identify hop accessions maintained at the U.S. Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, Oregon.

Last Modified: 9/10/2014
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