Systematical Identification and Primer Screening of EST-SSR Marker in Transcriptome of Caragana intermedia

doi:10.13560/j.cnki.biotech.bull.1985.2016.02.025

Abstract

Abstract: The aim of the study is to systematically identify and preliminary validate the SSR(simple sequence repeats)of EST(expr-essed sequence tags)in transcriptome database of Caragana intermedia for providing the basis in the further development of SSR molecular marker.Searching the SSR loci from Unigenes of the C.intermedia transcriptome by HiSeq²⁰⁰⁰ sequencing technology, total 45 706 SSR were obtained, accounting for 10.38% of the total Unigenes, averagely one SSR per 4.30 kb.Mononucleotide repeats were dominant in SSR with the ratio of 56.47%, bi- and tri-nucleotide repeats were 20.56% and 21.04%, and others were only 1.9%.Among all polynucleotide motifs, bi-nucleotide AG/CT were the most, second most was tri-nucleotide AAG/CTT.Totally 150 SSR primer pairs were randomly selected according to EST-SSR loci, PCR was verified by agarose gel electrophoresis, and 79 primer pairs showed clear amplified DNA fragments.While 21 out of the 79 primer pairs amplified single band, with a ratio of 14.0%.

Key words: Caragana intermedia, EST-SSR site reorganization, primer screening

WANG Guang-xia, YANG Qi, WANG Rui-gang, LI Guo-jing. Systematical Identification and Primer Screening of EST-SSR Marker in Transcriptome of Caragana intermedia[J]. Biotechnology Bulletin, 2016, 32(2): 178-184.

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