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 and Xiao-Hua Huang
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Dinh-Duy Vu: College of Forestry, Northwest A&F University, Yangling, Shaanxi, P.R China
Thi Tuyet-Xuan Bui: College of Forestry, Northwest A&F University, Yangling, Shaanxi, P.R China
Thi Hong-Nhung Nguyen: College of Forestry, Northwest A&F University, Yangling, Shaanxi, P.R China
Syed Noor Muhammad Shah: Department of Horticulture, Faculty of Agriculture, Gomal University Dera Ismail Khan Pakistan
Ngoc-Ha Vu: College of Forestry, Northwest A&F University, Yangling, Shaanxi, P.R China
Ya-Hong Zhu: College of Forestry, Northwest A&F University, Yangling, Shaanxi, P.R China
Lei Zhang: College of Forestry, Northwest A&F University, Yangling, Shaanxi, P.R China
Yi Zhang: College of Forestry, Northwest A&F University, Yangling, Shaanxi, P.R China
Xiao-Hua Huang: College of Forestry, Northwest A&F University, Yangling, Shaanxi, P.R China

Czech Journal of Genetics and Plant Breeding, 2018, vol. 54, issue 1, 17-25

Abstract: 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 (search for similar items in EconPapers)
Date: 2018
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Persistent link: https://EconPapers.repec.org/RePEc:caa:jnlcjg:v:54:y:2018:i:1:id:183-2016-cjgpb

DOI: 10.17221/183/2016-CJGPB

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