Application of RAD Sequencing for Evaluating the Genetic Diversity of Domesticated Panax notoginseng (Araliaceae)

Abstract

Panax notoginseng, a traditional Chinese medicinal plant, has been cultivated and domesticated for approximately 400 years, mainly in Yunnan and Guangxi, two provinces in southwest China. This species was named according to cultivated rather than wild individuals, and no wild populations had been found until now. The genetic resources available on farms are important for both breeding practices and resource conservation. In the present study, the recently developed technology RADseq, which is based on next-generation sequencing, was used to analyze the genetic variation and differentiation of P. notoginseng. The nucleotide diversity and heterozygosity results indicated that P. notoginseng had low genetic diversity at both the species and population levels. Almost no genetic differentiation has been detected, and all populations were genetically similar due to strong gene flow and insufficient splitting time. Although the genetic diversity of P. notoginseng was low at both species and population levels, several traditional plantations had relatively high genetic diversity, as revealed by the He and π values and by the private allele numbers. These valuable genetic resources should be protected as soon as possible to facilitate future breeding projects. The possible geographical origin of Sanqi domestication was discussed based on the results of the genetic diversity analysis.

The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng

“…Pairwise sequentially Markovian coalescent (PSMC) analysis ( Li and Durbin, 2011 ) revealed a sharp decline in the effective population size of the mountain-dwelling P. notoginseng from 100,000 to 10,000 years ago consistent with the reduction of the atmospheric surface air temperature during this time ( Figure 2 E). Despite the relatively recent divergence time of extant ginseng species, P. notoginseng and P. ginseng have profoundly different disease resistance capabilities ( Chen et al., 2017b ; Lee et al., 2015 ; Mao et al., 2013 ; Ryu et al., 2014 ) and contemporary effective population sizes ( Jang et al., 2020 ; Li et al., 2011b ; Pan et al., 2016 ). Disease resistance genes ( R -genes) serve to detect and respond to plant pathogens ( Gururani et al., 2012 ).…”

The Identification of Araliaceae Species by ITS2 Genetic Barcoding and Pollen Morphology

“…Such an authentication appears necessary because of the popularity of Araliaceae on world trade markets. The quality of wild forms is typically higher than that in cultivated forms, which have lost many of their original traits due to genetic bottleneck-induced losses in genetic variation [31][32][33]. Hereupon, wild plants are of special interest to traders [34].…”

Seedling Selection Using Molecular Approach for Ex Situ Conservation of Critically Endangered Tree Species (Vatica bantamensis(Hassk.) Benth. & Hook. ex Miq.) in Java, Indonesia

“…These values were comparable to those reported for Panax spp. (Pan, Wang, Sun, Li, & Gong, 2016) and for Amorphophallus paeoniifolius (Araceae) studied with restriction site-associated DNA sequencing (RAD-seq) in China (Y. Gao et al, 2017).…”