Identification and development of EST-SSR markers in Tamarix hispida based on transcriptome sequencing

Expressed sequence tag-simple sequence repeats (EST-SSR) may provide a molecular basis for plant adaptation. In this study, we sequenced five individual transcriptomes of Tamarix hispida from different locations, and identified 1 187 polymorphic EST-SSRs. Of the identified SSRs, tri-nucleotide repeats were the most common (54.42%), followed by dinucleotide repeats (37.66%). A total of 500, 176, and 211 EST-SSRs were located in coding region, 3′ untranslated regions (UTRs), and 5′ UTRs in 829 transcripts, respectively. AGC/GCT, AT/AT, and AG/CT were the most abundant repeats in each gene region. Gene ontology functional annotation showed that the identified SSR-containing sequences were enriched in "regulation of transcription" , "transcription factor activity", and "nucleus" terms. KEGG pathway analysis showed that "metabolic pathways" was the most common and abundant term, followed by "plant hormone signal transduction". Using polymerase chain reaction amplification, sequencing, and capillary electrophoresis validation, 13 out of the 15 randomly selected polymorphic SSR markers were developed. The results of this study lay the foundation for the investigation of population genetics and adaptation evolution mechanisms underlying SSR variations in T. hispida.