Conservation Genomics of a Threatened Rhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs

Abstract

Though it is well-acknowledged that next generation sequencing (NGS) technologies can provide further insights into plant conservation management than traditional molecular markers, studies employing NGS to address conservation genomics and subsequent conservation strategies for threatened plants are still rare. Rhododendron is the largest genus of woody plants in China, and many species are threatened, however, to date there has been no conservation genetic research using NGS in this genus. In the present study, we investigated the conservation genetics of R. cyanocarpum , a threatened species endemic to the Cangshan Mountains in Yunnan, China, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. Due to the availability of sufficient SNPs, we were able to distinguish between neutral and putatively selected SNPs and were able to further investigate the genetic diversity, population structure, and differentiation in R. cyanocarpum , as well as make an estimation of its demographic history. A total of 6,584 SNPs were obtained, of which 5,729 were neutral (detected using Tajima’s D). In terms of the 5,729 neutral SNPs, R. cyanocarpum had a higher genetic diversity (π = 0.0702 ± 0.0017, H e = 0.0675 ± 0.0016) than other plant species assessed using Rad-seq methods, while population differentiation ( F st from 0.0314 to 0.0452) was weak. Interestingly, contrasting patterns of population structure were revealed from all neutral and selected SNPs, with distinct genetic clusters forming for all SNPs and neutral SNPs, but no distinct subgroups for selected ones. Moreover, we were able to detect changes in effective population size ( N e ) of R. cyanocarpum from 150,000 years ago, including a bottleneck event ca. 60,000 years ago, followed by recovery of N e over a short period, and a subsequent gradual decline in N e to date. Implications for conserving R. cyanocarpum based on these main results are then discussed.

Conservation Genomics of Wild Red Sage (Salvia miltiorrhiza) and Its Endangered Relatives in China: Population Structure and Interspecific Relationships Revealed From 2b-RAD Data

“…Recent demographic dynamics of S. miltiorrhiza was investigated following Liu et al (2020) . A python script easySFS 1 was used to generate the folded site frequency spectrum (SFS) formatted file with VCF files and sample list file, and demographic history was then inferred using the program Stairway plot v.0.2 ( Liu and Fu, 2015 ).…”

Chromosome‐level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation

“…However, with technological advances in next‐generation sequencing (NGS) and whole‐genome sequencing (WGS), we are able to analyze thousands of genetic markers, which allows us to answer important questions regarding conservation. Studies employing NGS or WGS to address conservation genomics and subsequently to develop conservation strategies for threatened plants are, however, still uncommon (Liu et al ., 2020).…”

Rhododendron kuomeianum (Ericaceae), a new species from northeastern Yunnan (China), based on morphological and genomic data

“…Next Generation Sequencing (NGS) offers a solution to these issues ( Hohenlohe et al, 2010 ). For example, restriction site-associated DNA sequencing (RAD-seq) has been widely used in non-model species (e.g., temperate bamboos) to resolve evolutionary relationships ( Heckenhauer et al., 2018 ; Zhang et al., 2018 ; Liu et al., 2020 ; Guo et al., 2020 ).…”