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

Authors : Muhammed Ali KÖSE, NECATİ ÇETİNSAĞ, KAHRAMAN GÜRCAN

Pages : 305-315

View : 16 | Download : 5

Publication Date : 2017-08-01

Article Type : Research Paper

Abstract :Apricot insert ignore into journalissuearticles values(Prunus armeniaca); is an important fruit crop worldwide. We have performed a de novo transcriptome assembly for 7 apricot accessions insert ignore into journalissuearticles values(`Stark Early Orange` insert ignore into journalissuearticles values(SEO);, `Hacıhaliloğlu` insert ignore into journalissuearticles values(HH);, `Perfection`, `Iğdır`, `Roxana`, `Esen1`, and `Esen2`);, which yielded a total number of transcripts ranging from 30,363 for `SEO` to 59,751 for `Iğdır`. The pool of the reads produced from 7 accessions were assembled into 85,766 transcripts, with an average of 1165.69 nt. Functional annotation insert ignore into journalissuearticles values(Gene Ontology- GO and Kyoto Encyclopedia of Genes and Genomes- KEGG); was performed successfully for the transcripts. Simple sequence repeats insert ignore into journalissuearticles values(SSRs); were searched in the transcript pool and 14,722 di-, tri- tetra-, penta-, and hexanucleotide motif loci with a minimum of 5 repetitions for all motifs were identified. 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 insert ignore into journalissuearticles values(PPV);-resistant and 17 PPV-susceptible accessions. In order to test the amplification success of publicly available genomic SSRs insert ignore into journalissuearticles values(gSSRs); for diverse apricot accessions, an additional 88 published Prunus gSSRs were characterized amplifying the same 24 apricots and only 54 insert ignore into journalissuearticles values(62%); produced polymorphic bands. The new EST-SSRs could be a reliable source of primers for characterization and mapping studies of apricots, especially because they mostly flank easily scorable tri- and tetranucleotide repeats.
Keywords : Microsatellite, molecular markers, functional annotation