HOP EST RESOURCES FOR MARKER DEVELOPMENT

Abstract

The first large dataset of hop EST sequences has recently become available to the hop research community. In this work we assembled all single pass hop EST sequences into tentative consensus sequences and used this information for development of molecular markers. A total of 14,944 EST sequences were acquired in a total length of 7,786,981 bp. After vector clipping, polyA clipping and removal of low-quality and short sequences, the remaining 14,731 sequences were clustered using the TGICL tool. Clustering yielded 1,318 contigs and only 76 singletons in a total length of 1,067,770 bp. A total of 13 clusters contained more than 100 EST sequences each. The 20 contigs with the highest number of ESTs clustered together were compared with blastn or blastx algorithms for simple annotation. The most abundant were ribosomal DNA and chloroplast transcripts. All sequences were subsequently screened for the presence of microsatellite motifs (2-10 bp motifs) and 235 contained such motifs. The most common type of repeat was dinucleotide (131), followed by trinucleotide (118). PCR primers were developed for chalcone synthase (CHS) and valerophenone synthase (VPS) genes and the sequences were checked for the presence of single nucleotide polymorphisms (SNPs). Markers were found in both genes and will be further used to map the two genes in the hop linkage map.