Isolation and characterization of polymorphic microsatellite markers in Toxicodendron vernicifluum

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.:

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

References:

Aggarwal Ramesh K., Hendre Prasad S., Varshney Rajeev K., Bhat Prasanna R., Krishnakumar V., Singh Lalji (2007): Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theoretical and Applied Genetics, 114, 359-372 https://doi.org/10.1007/s00122-006-0440-x

Botstein D., White R.L., Skolnick M., Davis R.W. (1980): Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Medical Genetics, 32: 314–331.

Cho Namki, Choi Ji Hoon, Yang Heejung, Jeong Eun Ju, Lee Ki Yong, Kim Young Choong, Sung Sang Hyun (2012): Neuroprotective and anti-inflammatory effects of flavonoids isolated from Rhus verniciflua in neuronal HT22 and microglial BV2 cell lines. Food and Chemical Toxicology, 50, 1940-1945 https://doi.org/10.1016/j.fct.2012.03.052

Clarke K.R., Gorley R.N. (2001): Primer (Plymouth Routines in Multivariate Ecological Research) v5: User Manual. Plymouth, PRIMER-E, Ltd.

Excoffier L., Laval G., Schneider S. (2005): Arlequin v. 3.1. an integrated software package for population genetics data analysis. Evolutionary Bioinformatics online, 1: 47–50.

Goudet J. (1995): FSTAT (Version 1.2): A Computer Program to Calculate F-Statistics. Journal of Heredity, 86, 485-486 https://doi.org/10.1093/oxfordjournals.jhered.a111627

Hashida Koh, Tabata Masanobu, Kuroda Katsushi, Otsuka Yuichiro, Kubo Satoshi, Makino Rei, Kubojima Yoshitaka, Tonosaki Mario, Ohara Seiji (2014): Phenolic extractives in the trunk of Toxicodendron vernicifluum: chemical characteristics, contents and radial distribution. Journal of Wood Science, 60, 160-168 https://doi.org/10.1007/s10086-013-1385-8

He Xudong, Zheng Jiwei, Zhou Jie, He Kaiyue, Shi Shizheng, Wang Baosong (2015): Characterization and comparison of EST-SSRs in Salix, Populus, and Eucalyptus. Tree Genetics & Genomes, 11, - https://doi.org/10.1007/s11295-014-0820-3

Hsu Tsai-Wen, Shih Huei-Chuan, Kuo Chia-Chi, Chiang Tzen-Yuh, Chiang Yu-Chung (2013): Characterization of 42 Microsatellite Markers from Poison Ivy, Toxicodendron radicans (Anacardiaceae). International Journal of Molecular Sciences, 14, 20414-20426 https://doi.org/10.3390/ijms141020414

Kalia Rajwant K., Rai Manoj K., Kalia Sanjay, Singh Rohtas, Dhawan A. K. (2011): Microsatellite markers: an overview of the recent progress in plants. Euphytica, 177, 309-334 https://doi.org/10.1007/s10681-010-0286-9

Kaur Sukhjiwan, Pembleton Luke W, Cogan Noel OI, Savin Keith W, Leonforte Tony, Paull Jeffrey, Materne Michael, Forster John W (2012): Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics, 13, 104- https://doi.org/10.1186/1471-2164-13-104

Kim Ki Hyun, Moon Eunjung, Choi Sang Un, Pang Changhyun, Kim Sun Yeou, Lee Kang Ro (2015): Identification of cytotoxic and anti-inflammatory constituents from the bark of Toxicodendron vernicifluum (Stokes) F.A. Barkley. Journal of Ethnopharmacology, 162, 231-237 https://doi.org/10.1016/j.jep.2014.12.071

Kumpatla Siva P, Mukhopadhyay Snehasis (2005): Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome, 48, 985-998 https://doi.org/10.1139/g05-060

Lee J.-C., Lee K.-Y., Kim J., Na C.-S., Jung N.-C., Chung G.-H., Jang Y.-S. (2004): Extract from Rhus verniciflua Stokes is capable of inhibiting the growth of human lymphoma cells. Food and Chemical Toxicology, 42, 1383-1388 https://doi.org/10.1016/j.fct.2004.03.012

Li Y.-C. (2004): Microsatellites Within Genes: Structure, Function, and Evolution. Molecular Biology and Evolution, 21, 991-1007 https://doi.org/10.1093/molbev/msh073

Liu Mingying, Qiao Guirong, Jiang Jing, Yang Huiqin, Xie Lihua, Xie Jinzhong, Zhuo Renying, Janssen Paul Jaak (2012): Transcriptome Sequencing and De Novo Analysis for Ma Bamboo (Dendrocalamus latiflorus Munro) Using the Illumina Platform. PLoS ONE, 7, e46766- https://doi.org/10.1371/journal.pone.0046766

Liu Z., Chen T., Ma L., Zhao Z., Zhao P., Nan Z., Wang Y. (2013): Global transcriptome sequencing using the illumina platform and the development of ESTSSR markers in autotetraploid alfalfa. PLoS ONE, 8: e83549.

PEAKALL ROD, SMOUSE PETER E. (2006): genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288-295 https://doi.org/10.1111/j.1471-8286.2005.01155.x

STOECKEL SOLENN, GRANGE JÉRÔME, FERNÁNDEZ-MANJARRES JUAN F., BILGER ISABELLE, FRASCARIA-LACOSTE NATHALIE, MARIETTE STÉPHANIE (2006): Heterozygote excess in a self-incompatible and partially clonal forest tree species -Prunus avium L.. Molecular Ecology, 15, 2109-2118 https://doi.org/10.1111/j.1365-294X.2006.02926.x

Vieira Maria Lucia Carneiro, Santini Luciane, Diniz Augusto Lima, Munhoz Carla de Freitas (2016): Microsatellite markers: what they mean and why they are so useful. Genetics and Molecular Biology, 39, 312-328 https://doi.org/10.1590/1678-4685-GMB-2016-0027

Wei Wenliang, Qi Xiaoqiong, Wang Linhai, Zhang Yanxin, Hua Wei, Li Donghua, Lv Haixia, Zhang Xiurong (2011): Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics, 12, - https://doi.org/10.1186/1471-2164-12-451

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Czech Academy of Agricultural Sciences

Isolation and characterization of polymorphic microsatellite markers in Toxicodendron vernicifluum

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.:

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