Origin And Domestication Of Cultivated Panax Ginseng

Panax ginseng C.A.Mey.is a medicinally important species within the genus Panax of Araliaceae family.As the symbol of traditional Chinese medicine,Chinese ginseng has been used as a herbal remedy to restore stamina and capacity and then known as the "king of herbs".In recent years,the medicinal value of ginseng has been well recongized and concered worldwide.Although extensive studies have been conducted in ginseng with respect to its pharmaceutical values and clinical effects,few investigations have focused on the origin and domestication of cultivated ginseng.Wild ginseng was widely distributed in northeastern China,Korean penisular and Russia Far East.Nowadays,however,only a few ginseng plants exist in natural environments due to the over exploitation of wild resources and the destruction of natural habitats.In contrast,domesticated ginseng is widely grown in northeastern China and the Korean peninsula and can be divided into four phenotypically divergent landraces,namely COMMON,BIANTIAO,SHIZHU and GAOLI.The major phenotypic differences between wild and cultivated ginseng and among the four ginseng landraces are the growth cycle and root morphologies.However,some basic questions of cultivated ginseng have not been solved so far,including the molecular authentication of progenitor of cultivated ginseng,genetic diversity of cultivated and wild ginseng,and the origin and domestication process of cultivated ginseng.The genetic diversity and population structure of cultivated and wild ginseng have been reported in previous studies based on random amplified polymorphic DNA(RAPD),amplified restriction fragment polymorphism(AFLP),and methylation-sensitive amplification polymorphism(MSAP).However,the origin and domestication history of genetic variation of Chinese ginseng remain unclear so far due to the limitation of the molecular markers used and the scarcity of wild ginseng samples.In this study,we employed DNA sequencing technique to study the phylogeny of genus Panax and address the origin and domestication of cultivated ginseng.To this end,we selected four chloroplast genes to infer the phylogenetic relationships among the Panax species.To identify the wild progenitor of cultivated ginseng,we analyzed the nucleotide polymorphisms between wild and cultivated ginseng based on 24 chloroplast genes.We also developed 49 single copy nuclear genes(SCNGs)from nuclear genome and sequenced these SCNGs at 137 individuals of 11 cultivated ginseng populations and 38 individuals of 9 wild ginseng populations.Based on the phylogenetic and population genetic analyes,we made the following conclusions:1.Through comparing the nucleotide polymorphisms of the 24 chloroplast genes between wild and cultivated ginseng,our study showned that no sygregation sites were found within the ginseng samples examined.In contrast,different haplotypes were observed among Panax species.We therefore selected the matK-trnK,rps16,psbI-psbK,and psbA-trnH genes to construct the phylogenetic tree of Panax.As expected,cultivated ginseng not only shares most of the mophological characteristics with wild ginseng,but also clusters together with wild ginseng in the phylogenetic tree,clearly indicating that cultivated ginseng was domesticated from the wild form of P.ginseng.Phylogenetic analysis also revealed that although the three geographically isolated species,P.ginseng,P.japonicus and P.quinquefolius,are distributed in northeastern Asia(excluding Japan),Japan and North America,respectively,they were formed through a single tetraploidization event.Besides,the topology of chloroplast tree showed that cholorplast genes exhibited good resolution for molecular authentication of Panax species which can be applied to identify the species P.ginseng from P.quinquefolius and other congeneric species.2.We explored a simple approach to devlope single copy nuclear genes from Panax by comparing the Panax ESTs with avalible Arabidopsis SCNGs database.A total of 49 primer pairs were designed from the P.ginseng nuclear genome.Transferability and polymorphism of these SCNGs were tested in P.ginseng and P.quinquefolius.Our results showed that 16 of these SCNGs possess high transferability between the two species.The maximum percetage of polymorphic sites constitutes as high as 4.4% of the alignment at the gene PZ8.High levels of transferability and polymorphism of these SCNGs in P.ginseng and P.quinquefolius suggested that they can be applied in future studies of phylogenetic and authentication.3.The three genes,PGN7,Z7 and Z14,were selected to sequence the 137 individuals of 11 cultivated ginseng populations and 38 individuals of 9 wild ginseng populations.Although the three nuclear genes showed difference in genetic variation pattern,high level of nucleotide diversity were found in all of the three genes.The neutrality tests revealed that cultivated ginseng showed obviously greater negative Tajima’s D and Fu and Li’s D and F values compared to wild ginseng,suggesting that there are more low frequency polymorphisms in cultivated ginseng.Of the three SCNGs,Z7 and Z14 genes showed relatively higher level of nucleotide diversity in cultivated gineng compared to wild ginseng.However,no significiant differences were found among the four landraces at nucleotide diversity.These results indicated that culivated ginseng might not have undergone a severe genetic bottleneck during the domestication process.In addition,statistical parsimony network analysis combined with geographical distribution revealed that all haplotypes of PGN7 gene are distributed into four major haplotype groups,wheares only two haplotype groups were found in Z7 and Z14 genes.These attributes indicated that some haplotypes exist across all cultivated and wild ginseng populations and each population also harbored some private haplotypes that derived the major haplotype groups.The observation of no significant difference in haplotype and geographical distribution pattern suggested the possibility of single origin of cultivated ginseng.4.The Hiseq 2000 platform was employed to sequence the 46 nuclear genes of 96 cultivated ginseng and 35 wild ginseng accessions.We divided these accessions into eight distinct libraries according to their genetic background and geographical locations.In detail,the five cultivated ginseng libraries include GAOLI(GL),BIANTIAO(BT),SHIZHU(SZ),southern COMMON,and northern COMMON ginseng populations.Similarly,wild ginseng accessions were divided into three libraries corresponding to the northern,southern,and domestication center populations,respectively.Our results revealed that cultivated ginseng harbored similar level of nucleotide diversity with wild ginseng(πcultivar=0.00781;πwild= 0.00754),confirming previous hypothesis that cultivated ginseng has not undergone genetic bottleneck during domestication process.The landrace COMMON ginseng possessed a relatively higher level of nonsynonymous and synonymous mutations compared to the other three landraces.The simulations of approximate Bayesian computation(ABC)demonstrated that cultivated ginseng diverged from wild ginseng some 1,498 years ago and bidirection gene flow were detected between wild and cultivated ginseng.In summary,our study employed chloroplast and nuclear genes to investigate the origin and domestication of cultivated ginseng.Our results from phylogenetic and population gnetic analyses demonstrated that cultivated ginseng diverged from its wild progenitor about 1,498 years ago.Altough the cultivated ginseng landraces showed morphological differences,artificial selection does not result in the decrease in nucleotide divetsity.