Revealing the Genetic Structure and Differentiation in Endangered Pinus bungeana by Genome-Wide SNP Markers

Qian Tian,Yousry A El-Kassaby,Wei Li

doi:10.3390/f13020326

Qian Tian, Yousry A El-Kassaby + Show 1 more

Open Access

https://doi.org/10.3390/f13020326

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Abstract

Understanding the genetic variation and differentiation of natural populations is essential for their protection, specifically if the species status is endangered as with Pinus bungeana. Here, we used 346,840 high density and strong specificity SNP loci to carry out genetic analyses (i.e., genetic diversity, genetic structure, phylogeny, and geographical differentiation) on 52 P. bungeana individuals from 5 populations (4 natural and one artificial) representing the main regions of the species distribution in China. Genetic diversity assessment indicated a trend of genetic diversity gradual decrease from west to east across the species distribution areas. Population genetic structure, PCA and phylogenetic analyses consistently indicated that populations in the central and eastern regions were clustered together, while those from the western regions were separated. Mantel test values indicated the presence of geographic isolation among populations, an important factor contributing to the observed genetic differentiation. The maximum likelihood tree and potential migration events inferred from TreeMix analysis indicated the presence of historical genetic exchanges between the west of Qinling Mountains and the Lvliang Mountains populations. Based on the generated genetic information, in situ and ex situ conservation strategies for P.bungeana germplasm resources are proposed, these strategies could be valuable for the conservation, protection and genetic improvement of this endangered species.

Highlights

Administration, College of Biological Sciences and Technology, Beijing Forestry University, Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Abstract: Understanding the genetic variation and differentiation of natural populations is essential for their protection, if the species status is endangered as with Pinus bungeana
We used high density and strong specificity Single Nucleotide Polymorphism (SNPs) loci to carry out genetic analysis on 52 P. bungeana individuals from 5 populations representing the main regions of the species distribution in China
Genetic diversity assessment indicated a trend of genetic diversity gradual decrease from west to east across the species distribution areas

Summary

Introduction

Administration, College of Biological Sciences and Technology, Beijing Forestry University, Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Abstract: Understanding the genetic variation and differentiation of natural populations is essential for their protection, if the species status is endangered as with Pinus bungeana. We used 346,840 high density and strong specificity SNP loci to carry out genetic analyses (i.e., genetic diversity, genetic structure, phylogeny, and geographical differentiation) on 52 P. bungeana individuals from 5 populations (4 natural and one artificial) representing the main regions of the species distribution in China. The average genetic diversity of P. bungeana natural populations is relatively low, but the degree of differentiation among populations is relatively high [4,9,10]. It is necessary to protect the genetic diversity of P. bungeana natural populations

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Conclusion