De novo transcriptome assembly and SSR marker development in apricot (Prunus armeniaca)

Abstract

Apricot (Prunus armeniaca) is an important fruit crop worldwide. We have performed a de novo transcriptome assembly for7 apricot accessions (‘Stark Early Orange’ (SEO), ‘Hacıhaliloğlu’ (HH), ‘Perfection’, ‘Iğdır’, ‘Roxana’, ‘Esen1’, and ‘Esen2’), which yieldeda total number of transcripts ranging from 30,363 for ‘SEO’ to 59,751 for ‘Iğdır’. The pool of the reads produced from 7 accessions wereassembled into 85,766 transcripts, with an average of 1165.69 nt. Functional annotation (Gene Ontology- GO and Kyoto Encyclopediaof Genes and Genomes- KEGG) was performed successfully for the transcripts. Simple sequence repeats (SSRs) were searched in thetranscript pool and 14,722 di-, tri- tetra-, penta-, and hexanucleotide motif loci with a minimum of 5 repetitions for all motifs wereidentified. Primers were designed for 206 loci, and 72 of them were found to be polymorphic by amplifying diverse 24 apricot accessions,including 7 Plum Pox Virus (PPV)-resistant and 17 PPV-susceptible accessions. In order to test the amplification success of publiclyavailable genomic SSRs (gSSRs) for diverse apricot accessions, an additional 88 published Prunus gSSRs were characterized amplifyingthe same 24 apricots and only 54 (62%) produced polymorphic bands. The new EST-SSRs could be a reliable source of primers forcharacterization and mapping studies of apricots, especially because they mostly flank easily scorable tri- and tetranucleotide repeats.