Development of new microsatellite markers (SSRs) for Humulus lupulus

Abstract

The number of informative markers available for hops currently limits breeding progress. Biotechnological improvement of hops therefore would benefit from a larger number of informative molecular markers. We expanded the pool of putative markers by developing new primer sets for SSR regions from genomic DNA extracted from eight US hop cultivars. From a library of 10,581 previously published hop ESTs we identified 1,007 SSRs. The SSRs were derived from 4,953 unique transcripts, consisting of 1,422 contigs and 3,531 singletons. Among them we identified 274 dinucleotide repeats, 519 trinucleotide repeats, 87 tetranucleotide repeats and 127 pentanucleotide repeats. Amplified bands were separated by agarose gel or capillary electrophoresis and visually scored for presence or absence of bands. Between 503 and 663 SSR amplifications were successful, depending on cultivar. Overall 952 (95.8%) of 1,007 SSRs were amplified successfully. As a demonstration of utility, a cluster analysis showed substantial congruence to previous studies of the cultivar’s genetic distances. The large number of demonstrated SSRs have the potential to increase the quality of molecular marker mapping experiments by increasing the map-density of markers. The SSRs presented have been selected for robustness of amplification and should, thus, be most useful in other laboratories. The primers and method to generate these polymorphic SSRs are presented here and have been deposited in Genbank (10315689–10316695, ProbeDB).