Identification of Simple Sequence Repeat Markers in the Mediterranean Saltbush (Atriplex halimus L.) Genome

The Mediterranean saltbush (Atriplex halimus L.) is a halophyte grows in deserts and salt marshes. This study was carried out to develop and characterize simple sequence repeat (SSR) markers in saltbush. Pooled genomic DNA from A. halimus genotypes was used for next generation sequencing. Reads were assembled into contigs and SSR motifs were retrieved. A total of 40202 repeat motifs were detected with an average length ranging between 18-24. The percentage contribution of repeat motifs for mononucleotide, dinucleotide, trinucleotide, tetranucleotide, pentanucleotide and hexanucleotide was 11.4%, 7.7%, 23.4%, 15.4%, 29.1% and 13.1%, respectively. The most frequent dinucleotide, trinucleotide and tetranucleotide motifs were AG, AAT and ATAC and their equivalent motifs, respectively. Sixty two SSRs (Genebank accession numbers KF614705 to KF614766) were selected and investigated in A. halimus and related species belonging to the Amaranthaceae family (Spinacia oleracea, Beta vulgaris and B. vulgaris subsp. cicla). Blast search of SSR markers revealed significant synteny between A. halimus and B. vulgaris. The authors would like to acknowledge the generous financial support by NPST program at King Saud University, Project Number 10-BIO1119-02, Saudi Arabia.