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Identification of novel EST-SSR markers by transcriptome sequencing in ridgetail white prawn Exopalaemon carinicauda

Jiajia Wang, Qianqian Ge, Jitao Li, Haiyu Gao, Jian Li, Fazhen Zhao
Genes & genomics 2018 v.40 no.2 pp. 207-215
transcriptomics, microsatellite repeats, loci, DNA primers, gene ontology, breeding, expressed sequence tags, mariculture, polymerase chain reaction, genomics, shrimp, genetic variation, genetic markers, China
The ridgetail white prawn Exopalaemon carinicauda is one of the major commercial mariculture species in eastern China. However, only limited molecular markers are currently available due to the lack of genome information, which hinders its genetic and breeding studies. In this study, we identified new simple sequence repeats from transcriptome sequences by Illumina Hiseq 2500 platform. A total of 14273 SSR loci were identified from 130,082 assembled transcripts, with 6590 pairs of PCR primers designed. A total of 12,155 sequences containing SSR were predicted; and 2764 (22.74%) transcripts had significant matches to the NCBI non redundant protein (Nr) database. 11,563 transcripts were assigned into gene ontology (GO) categories. A set of 200 primers selected randomly were synthesized, of which 152 (76.0%) were successfully amplified. Further test with 60 pairs of polymorphic SSR primers to evaluate the genetic diversity of 30 wild populations and 43 loci were polymorphic, which had a polymorphic information content between 0.204 and 0.911. The results enriched genomic resources of E. carinicauda and provided powerful information for future conservation and breeding researches.