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Discovery of SNP Markers in Expressed Genes of Hazelnut

TitleDiscovery of SNP Markers in Expressed Genes of Hazelnut
Publication TypeConference Paper
Year of Publication2010
AuthorsBryant, D. W., S. E. Fox, E. R. Rowley, H. D. Priest, R. Shen, W-K. Wong, and T. C. Mockler
Conference NameISHS Acta Horticulturae
Pagination859, 289-294
Date Published04/2010
Conference LocationCorvallis, OR
Keywordscandidate genes, corylus avellana, expressed sequence tags, hazelnut, high throughput RNA sequencing, RNA-seq, single nucleotide polymorphism, SNP

Polymorphisms associated with gene coding regions are useful tools for use as molecular markers, for example in marker-assisted breeding efforts. In particular, single nucleotide polymorphisms (SNPs) have emerged as a preferred marker for high-throughput genotyping studies. The objective of this study was to develop a set of SNPs for European hazelnut (Corylus avellana) by exploiting the exceptional depth and breadth of transcriptome sequencing made possible by high-throughput RNA sequencing (RNA-seq) using the Illumina Genome Analyzer platform. Bioinformatics tools were used to mine SNPs from a database of EST sequences derived from de novo assembly of Illumina RNA-seq reads representing hazelnut transcripts from multiple accessions. This resulted in the identification of 5,398 SNPs. This set of SNP markers for hazelnut provides a new resource for genetic mapping of important agronomic traits and will be useful markers for aligning future physical and genetic maps.