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A Simple Strategy for Development of Single Nucleotide Polymorphisms from Non-Model Species and Its Application in Panax
Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China
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Received: 12 November 2013; in revised form: 9 December 2013 / Accepted: 13 December 2013 / Published: 17 December 2013
Abstract: Single nucleotide polymorphisms (SNPs) are widely employed in the studies of population genetics, molecular breeding and conservation genetics. In this study, we explored a simple route to develop SNPs from non-model species based on screening the library of single copy nuclear genes (SCNGs). Through application of this strategy in Panax, we identified 160 and 171 SNPs from P. quinquefolium and P. ginseng, respectively. Our results demonstrated that both P. ginseng and P. quinquefolium possessed a high level of nucleotide diversity. The number of haplotype per locus ranged from 1 to 12 for P. ginseng and from 1 to 9 for P. quinquefolium, respectively. The nucleotide diversity of total sites (πT) varied between 0.000 and 0.023 for P. ginseng and 0.000 and 0.035 for P. quinquefolium, respectively. These findings suggested that this approach is well suited for SNP discovery in non-model organisms and is easily employed in standard genetics laboratory studies.
Keywords: conservation genetics; Panax ginseng; Panax quinquefolium; single copy nuclear gene
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MDPI and ACS Style
Li, M.R.; Wang, X.F.; Zhang, C.; Wang, H.Y.; Shi, F.X.; Xiao, H.X.; Li, L.F. A Simple Strategy for Development of Single Nucleotide Polymorphisms from Non-Model Species and Its Application in Panax. Int. J. Mol. Sci. 2013, 14, 24581-24591.
Li MR, Wang XF, Zhang C, Wang HY, Shi FX, Xiao HX, Li LF. A Simple Strategy for Development of Single Nucleotide Polymorphisms from Non-Model Species and Its Application in Panax. International Journal of Molecular Sciences. 2013; 14(12):24581-24591.
Li, Ming R.; Wang, Xin F.; Zhang, Cui; Wang, Hua Y.; Shi, Feng X.; Xiao, Hong X.; Li, Lin F. 2013. "A Simple Strategy for Development of Single Nucleotide Polymorphisms from Non-Model Species and Its Application in Panax." Int. J. Mol. Sci. 14, no. 12: 24581-24591.