Analysis on SSR Information in Transcriptome and Development of EST-SSR Markers for Hybrid Cymbidium
ZHONG Huaiqin, LIN Rongyan, LIN Bing, WU Jianshe, FAN Ronghui, YE Xiuxian*
EST-SSR primers suitable for hybrid Cymbidium were developed and screened to provide reliable molecular markers for germplasm resource evaluation and study on genetic variation. In the present study, transcriptome data of hybrid Cymbidium was obtained by high-throughput sequencing technology. The SSR loci were screened and the EST-SSR markers were developed, and then the genetic diversity of different germplasm were analyzed. The results showed that a total of 18 603 SSR loci were mined from 31 724 Unigenes with a frequency of 58.64%. Mononucleotide repeat was the main type, accounted for as much as 65.10% of all SSRs, followed by dinucleotide repeat (23.56%) and trinucleotide repeat (10.76%). The dominant repeat elements were A/T, AG/CT, AT/AT and AG/CTT, accounting for 64.72%, 13.74%, 8.19% and 2.51% of the total loci, respectively. 565 pairs of SSR primers were found by Primer Premier 5.0 and 28 efficient pairs of primers were randomly selected from 64 valid pairs for polymorphism analysis. Thereinto, 16 pairs of primers showed clear and reproducible results indicating the high poly morphism among 40 different germplasms, with the average PIC was 0.789. Based on the amplified polymorphic SSR data, the 40 materials were divided into 4 major groups by UPGMA. The dendrogram results were accordance with the genetic backgrounds. In conclusion, the Unigenes generated from transcriptome data of hybrid Cymbidium can be used as an effective source to development EST-SSR markers. The SSR markers obtained in the study could be valuable candidate markers for improved varieties identification, genetic map construction, molecular marker-assisted breeding and functional gene mining of hybrid Cymbidium and other Cymbidium species.
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