Genome-Wide Variation Patterns Uncover the Origin and Selection in Cultivated Ginseng (Panax ginseng Meyer)

Abstract

Chinese ginseng (Panax ginseng Meyer) is a medicinally important herb and plays crucial roles in traditional Chinese medicine. Pharmacological analyses identified diverse bioactive components from Chinese ginseng. However, basic biological attributes including domestication and selection of the ginseng plant remain under-investigated. Here, we presented a genome-wide view of the domestication and selection of cultivated ginseng based on the whole genome data. A total of 8,660 protein-coding genes were selected for genome-wide scanning of the 30 wild and cultivated ginseng accessions. In complement, the 45s rDNA, chloroplast and mitochondrial genomes were included to perform phylogenetic and population genetic analyses. The observed spatial genetic structure between northern cultivated ginseng (NCG) and southern cultivated ginseng (SCG) accessions suggested multiple independent origins of cultivated ginseng. Genome-wide scanning further demonstrated that NCG and SCG have undergone distinct selection pressures during the domestication process, with more genes identified in the NCG (97 genes) than in the SCG group (5 genes). Functional analyses revealed that these genes are involved in diverse pathways, including DNA methylation, lignin biosynthesis, and cell differentiation. These findings suggested that the SCG and NCG groups have distinct demographic histories. Candidate genes identified are useful for future molecular breeding of cultivated ginseng.

Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

“…To analyze population structure, various methods such as STRUCTURE and principal coordinates analysis have been used for ginseng germplasm [19,20,58]. In this study, STRUCTURE and DAPC used to analyze the population structure of 1109 ginseng accessions appeared to provide complementary information.…”

“…Genetic diversity of germplasm can be investigated using various techniques, including analysis of morphological and agricultural traits [13], isozymes [14], biochemical characteristics [15], and molecular markers [14][15][16]. In recent years, the development of various chemical and molecular techniques for differentiation among P. ginseng samples has received attention [10,[17][18][19][20]. Gepts has reported that DNA markers are the most reliable ones for distinguishing variations of alleles because these markers are not influenced by environmental or physiological factors [21].…”

Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax

“…In the case of P. notoginseng , for example, increasing in specific leaf area and chlorophyll content are negatively correlated with the growth irradiance level (Chen et al, 2014 , 2016 ). Likewise, cytoplasmic proteins of P. ginseng encoded by both cytoplasmic and nuclear genomes are the targets of selection during local adaptation and domestication processes (Li et al, 2017 ). These attributes together suggest that cytoplasmic genes may have evolved non-neutrally in the Panax species.…”

“…All these Panax species are shade-demanding perennial herbs and inhabit the cool shaded habitats (Liu and Xiao, 1992 ; Chen et al, 2014 , 2016 ). In the case of the agro-economically important species P. ginseng , while cultivated ginseng harbored similar level of nucleotide diversity compared to the wild ginseng in the nuclear genome, obviously lower sequence polymorphisms were found in the chloroplast genome of cultivated ginseng (Li et al, 2015 , 2017 ). Specifically, cytoplasmic genomes as well as the cytoplasmic proteins encoded by the nuclear genome are the targets of selection in the cultivated ginseng during local adaptation and domestication processes (Li et al, 2017 ).…”

“…In the case of the agro-economically important species P. ginseng , while cultivated ginseng harbored similar level of nucleotide diversity compared to the wild ginseng in the nuclear genome, obviously lower sequence polymorphisms were found in the chloroplast genome of cultivated ginseng (Li et al, 2015 , 2017 ). Specifically, cytoplasmic genomes as well as the cytoplasmic proteins encoded by the nuclear genome are the targets of selection in the cultivated ginseng during local adaptation and domestication processes (Li et al, 2017 ). Similarly, the increase in specific leaf area and chlorophyll content of the species P. notoginseng is negatively correlated with the growth irradiance level (Chen et al, 2014 , 2016 ).…”