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Isolation and characterization of polymorphic microsatellite markers in Toxicodendron vernicifluum

Dinh-Duy Vu, Thi Tuyet-Xuan Bui, Thi Hong-Nhung Nguyen, Syed Noor Muhammad Shah, Ngoc-Ha Vu, Ya-Hong Zhu, Lei Zhang, Yi Zhang, Xiao-Hua Huang

https://doi.org/10.17221/183/2016-CJGPBCitation:Vu D.-D., Bui T.T.-X., Nguyen T.H.-N., Shah S.N.M., Vu N.-H., Zhu Y.-H., Zhang L., Zhang Y., Huang X.-H. (2018): Isolation and characterization of polymorphic microsatellite markers in Toxicodendron vernicifluum. Czech J. Genet. Plant Breed., 54: 17-25.
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A total 20 074 230 sequencing reads were generated by Illumina HiSeq™ 2500 from three different Toxicodendron vernicifluum tissue samples. In total, 48 693 unigenes with an average length of 703.34 bp were obtained by de novo assembly. 3392 potential EST-SSRs (expressed sequence tag-simple sequence repeat) were identified as potential molecular markers from unigenes with lengths exceeding 1 kb. A total of 80 pairs of PCR primers were randomly selected to validate the assembly quality and develop EST-SSR markers from genomic DNA. Of these primer pairs, 14 primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism within the lacquer tree population in Langao, Shaanxi province, China. There were high genetic diversities (number of alleles per locus (A) = 2.93, polymorphic information content (PIC) = 0.53, observed heterozygosity (Ho) = 0.62 and expected heterozygosity (He) = 0.85) in the lacquer tree natural population. The four loci were significantly deviated from Hardy-Weinberg equilibrium. These results suggested high homozygosity in the population and low or deficiency in heterozygosity (inbreeding coefficient (Fis) = 0.27). These polymorphic EST-SSR markers will provide the base for further studies of genetic structure and breeding in T. vernicifluum.

Keywords:

EST-SSRs; Illumina HiSeq™ 2500; genetic diversity; lacquer tree

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