Discovery of genome-wideSNPs by RAD-seqand the genetic diversity of captive hog deer (Axis porcinus).

Wei Wang,Ang Chen,Lili Niu,Maozhong Fu,Jianqiu Yu,Hui Tang,Jun Yi,Yu Qu,Huijuan Yan,Tzen-Yuh Chiang

doi:10.1371/journal.pone.0174299

Abstract

The hog deer (Axis porcinus) is a small deer whose natural habitat is the wet or moist tall grasslands in South and Southeast Asia. Wild populations have dramatically decreased in recent decades. While wild hog deer were recently acknowledged to be extinct in China, a few captive populations have been maintained. In the present study, we successfully employed the restriction-site-associated DNA sequencing (RAD-seq) technique to generate a genome-wide profile of single-nucleotide polymorphisms (SNPs) in the captive population of hog deer from Chengdu Zoo, China (N = 11). Up to 4.7 million clean reads per sample were sequenced, and 11,155 SNPs and 8,247 haplotypes were simultaneously observed within more than 80% of sequenced individuals. In this population, the mean frequency of major alleles at each polymorphism site was 0.7903±0.0014, and the average nucleotide diversity (π) and inbreeding coefficient (FIS) were 0.3031±0.0015 and -0.0302±0.0062, respectively. Additionally, the Euclidean distance-based multidimensional scaling method revealed that the pairwise genetic relatedness was evenly distributed. However, the results of homologous searching by short reads did not provide any meaningful explanation of the phylogenetic relationship of hog deer, which should be further investigated. In conclusion, our results revealed current state of genetic diversity in this captive population of hog deer.Furthermore, these genome-wide SNPs would be useful for guiding the mating schedule to avoid sharp increase of inbreeding coefficient.

Highlights

The hog deer (Axis porcinus) is an endemic species of South and Southeast Asia and can be divided into the Southeast Asian subspecies (A.p.annamiticus) from China, Thailand, Laos, Cambodia and Vietnam, and the Indian subspecies (A.p.porcinus) distributed in Pakistan, Nepal, India, Bangladesh and Burma[1]
The historical record of wild hog deer in China was mainly found in Gengma and Cangyuan counties of Western Yunnan; the wild population is currently believed to be almost completely eliminated [5,6].there are still a few captive hog deer in China, most of which have been reared in Chengdu Zoo, Sichuan
We subsequently investigated genetic diversity at the population level based on these single-nucleotide polymorphisms (SNPs) (Table 2)

Summary

Introduction

The hog deer (Axis porcinus) is an endemic species of South and Southeast Asia and can be divided into the Southeast Asian subspecies (A.p.annamiticus) from China, Thailand, Laos, Cambodia and Vietnam, and the Indian subspecies (A.p.porcinus) distributed in Pakistan, Nepal, India, Bangladesh and Burma[1]. Genome-wide SNPs of captive hog deer is still controversial[3]. Such debates will be better resolved with the increasing availability of molecular and archaeological evidence. Because of its narrow habitat or other unknown factors, the wild population of hog deer has undergone a serious decline for decades; the hog deer has been included in the Red List at the Endangered level by the International Union for the Conservation of Nature(IUCN) since 2008 [4]. The historical record of wild hog deer in China was mainly found in Gengma and Cangyuan counties of Western Yunnan; the wild population is currently believed to be almost completely eliminated [5,6].there are still a few captive hog deer in China, most of which have been reared in Chengdu Zoo, Sichuan. Further knowledge is essential to develop an efficient conservation program

Methods

Results

Conclusion