Genetic Diversity on a Rare Terrestrial Orchid, Habenaria linearifolia in South Korea: Implications for Conservation Offered by Genome-Wide Single Nucleotide Polymorphisms.

Soo-Rang Lee,Su-Young Jung,Tae-Young Choi

doi:10.3389/fpls.2022.772621

Soo-Rang Lee, Su-Young Jung + Show 1 more

Open Access

https://doi.org/10.3389/fpls.2022.772621

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Abstract

Monitoring intraspecific diversity offers invaluable insights on conservation practices as the variation is the product of species evolution. Accordingly, the role of population genetic diversity has drawn great attention over the last century responding to the biodiversity loss induced by a series of anthropogenic changes. Orchids are one of the most diverse, yet ironically most rapidly disappearing plant groups due to the specialized habitat preferences. Thus, population-level genetic diversity studies may offer a powerful tool for orchid conservation programs. Using the 3 restriction site-associated DNA (3RAD) approach, 2,734 genome-wide single nucleotide polymorphisms (SNPs) were isolated. With the 2,734 SNPs, we investigated genetic diversity and population structure on 72 individuals of Habenaria linearifolia and Habenaria cruciformis in South Korea. Overall, the genetic diversity was well maintained in South Korean Habenaria, but high FST values were estimated suggesting large population diversification with limited gene flow. Bayesian assignment analysis revealed a morphologically cryptic diversity pattern in Jeju Island populations, which might serve as an evolutionarily significant unit.

Highlights

Monitoring the population-level genetic diversity for a species offers invaluable insights into conservation practices as the variation directly reflects the evolutionary and ecological process that the species has experienced (Olson et al, 2016; Mimura et al, 2017; Schierenbeck, 2017; de Kort et al, 2021)
From the initial single nucleotide polymorphisms (SNPs) call, we isolated over 91K SNPs
After a series of pruning steps with the thresholds described, 2,734 SNPs were retained for the downstream analyses

Summary

Introduction

Monitoring the population-level genetic diversity for a species offers invaluable insights into conservation practices as the variation directly reflects the evolutionary and ecological process that the species has experienced (Olson et al, 2016; Mimura et al, 2017; Schierenbeck, 2017; de Kort et al, 2021). Biodiversity encompasses variations at all levels from the infraspecific to the community, yet infraspecific diversity, including population-level genetic variation, has been relatively underestimated despite its rate of loss exceeding that of higher-level diversity (Mimura et al, 2017; Kooyman et al, 2020). Lee et al (2018) suggested risk in deleting a rare myrmecochorous herb, Plagiorhegma dubium from the Red List of South Korea based on the pattern of population genetic diversity of simple sequence repeat data despite the recent growth of census population sizes.

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