Genetic Diversity Of Single Copy Nuclear Genes In Panax Ginseng And Panax Quinquefolium

Panax L.is the perennial herb of Araliaceae.Results from molecular phylogenetic analyses revealed that P.ginseng and P.quinquefolium are most closely related species within this genus.At present,the genetic diversity of related species has been widely used in population genetics,molecular breeding and conservation genetics.In this study,the genetic diversity of P.ginseng and P.quinquefolium was assessed based on single copy nuclear gene sequence(SCNGs).The main results are as follows:(1)Construction of Single Copy Nuclear Gene Database of P.ginseng.In this study,we collected Panax ESTs sequences from the NCBI database,performing a BLAST homology search against the constructed Arabidopsis SCNGs and screening sequences with high similarity to form the putative ginseng single copy sequence of P.ginseng.Then we designed the primers by screening single copy of the nuclear genes for amplifying the target fragments of P.ginseng.On the basis of these,we used the next-generation sequencing platform to sequence the PCR products of multiple genes from different individuals.We have obtained 58 SCNGs to construct the library of single copy nuclear gene.Among them,the developed primers can be used for the amplification of single copy nuclear gene sequence of other species of Panax L.(2)Nucleotide Diversity in P.ginseng and P.quinquefolium.In this study,we explored a simple and effective route to develop single nucleotide polymorphisms(SNPs)from P.quinquefolium and P.ginseng.We used the SNP molecular markers to amplify 16 SCNGs by 20 individuals of P.ginseng and 10 individuals of P.quinquefolium.By means of sequence alignment analysis,160 and 171 SNPs were developed in P.ginseng and P.quinquefolium,respectively.The number of haplotype per locus ranged from 1 to 12 for P.ginseng based on SNP,and The number of haplotype per locus ranged from 1 to 9 for P.quinquefolium.The nucleotide diversity of total sites(?T)varied between 0.000 and 0.023 for P.ginseng and 0.000 and 0.035 for P.quinquefolium,respectively.So ?T are 0.007 and 0.017 for P.ginseng and P.quinquefolium,respectively.Our results showed that both the two Panax species exhibited relatively high level of nucleotide diversity.Notably,we found that P.quinquefolium showed relatively higher nucleotide diversity at both total sites and nonsynonmous sites in comparison with P.ginseng.These results contribute to P.ginseng and P.quinquefolium germplasm resources protecting and molecular breeding to provide the theoretical basis.The development of SCNGs of P.ginseng will provide effective datas for the phylogenetic of Panax L.and domestication.