Discovery of simple sequence repeat (SSR) markers in hazelnut (<i>Corylus avellana</i> L.) by transcriptome sequencing and SSR-based characterization of hazelnut cultivars
Musa Kavas, Kubilay Yıldırım, Zafer Seçgin, Gökhan Gökdemir
Abstract
Current cultivation and breeding strategy based on selections from local and wild vegetation does not meet the hazelnut demand. This situation would benefit from the development of high-yielding cultivars with greater tolerance to abiotic and biotic stress conditions. Molecular markers are useful tools to support these breeding efforts. In the current study, EST-SSR markers were developed from RNA-sequencing data obtained from three hazelnut varieties. The transcriptome sequences contained 86,542 unigenes and a total of 25,391 SSRs, most of which (50.9%) were di-nucleotide repeats. A set of 40 primer pairs were randomly selected to validate their usefulness for investigating genetic diversity in 19 C. avellana cultivars and one accession of Corylus colurna. Of the 40, 28 were highly polymorphic with average values of observed heterozygosity, polymorphism information content and number of alleles per locus of 0.45, 0.67 and 6.11, respectively. The principal coordinate and dendrogram analysis separated the C. colurna accession from the C. avellana cultivars, and separated the cultivars for date of leaf bud burst. These new EST-SSRs and others that could be developed from the transcriptome sequences increase the number of markers for cultivar fingerprinting and may be useful for identifying marker-trait associations and further genetic diversity analyses.