In silico mining, characterization and cross-species transferability of EST-SSR markers for European hazelnut (Corylus avellana L.)

Abstract

The European hazelnut (Corylus avellana L.) is one of the most important nut crops. In this work, we characterize functional microsatellite or simple sequence repeat (SSR) markers for genetic analysis and molecular breeding in this species. A total of 38,454 Betulaceae EST sequences from NCBI resulted in 1,282 non-redundant EST-SSRs. Dinucleotide repeats were the most abundant (63.9 %), followed by trinucleotides (33.8 %). The putative functions of the non-redundant EST-SSRs were classified according to gene ontology (GO) categories (biological process, molecular function, and cellular component). A total of 921 sequences showed significant hits with the non-redundant protein database, and GO categories were assigned to 696 (75.5 %) of them. Flanking primer pairs were designed for 78 di- and trinucleotide EST-SSRs from Alnus glutinosa L. (29), Betula pendula Roth (26), and Betula platyphylla Suckaczev (23). Further, 41 dinucleotide repeats selected from hazelnut transcriptome sequences were added. Thirty-six out 119 primer pairs generated amplification products in six hazelnut accessions and in the samples of the species from which they were isolated. Among them, 20 were polymorphic when tested on 18 hazelnut cultivars. Fifteen loci are suitable for mapping in a F1 population of ‘Tonda Gentile delle Langhe’ × ‘Merveille de Bollwiller’ and 11 of them were functionally annotated. The cross-species transferability of 36 EST-SSR loci within nine Corylus species was also performed. The success rate of markers transferability (excluding C. avellana) ranged from 11 to 100 %, with an average of 55 %. The EST-SSRs developed increase the number of markers currently available for hazelnut.