Identification of Novel Single Nucleotide Polymorphisms (SNPs) in Deer (Odocoileus spp.) Using the BovineSNP50 BeadChip

Gwilym D Haynes,Emily K Latch,Casper Breuker

doi:10.1371/journal.pone.0036536

Gwilym D Haynes, Emily K Latch + Show 1 more

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https://doi.org/10.1371/journal.pone.0036536

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Journal: PloS one	Publication Date: May 8, 2012
Citations: 102	License type: CC BY 4.0

Affiliation: University of Wisconsin–Milwaukee

Abstract

Single nucleotide polymorphisms (SNPs) are growing in popularity as a genetic marker for investigating evolutionary processes. A panel of SNPs is often developed by comparing large quantities of DNA sequence data across multiple individuals to identify polymorphic sites. For non-model species, this is particularly difficult, as performing the necessary large-scale genomic sequencing often exceeds the resources available for the project. In this study, we trial the Bovine SNP50 BeadChip developed in cattle (Bos taurus) for identifying polymorphic SNPs in cervids Odocoileus hemionus (mule deer and black-tailed deer) and O. virginianus (white-tailed deer) in the Pacific Northwest. We found that 38.7% of loci could be genotyped, of which 5% (n = 1068) were polymorphic. Of these 1068 polymorphic SNPs, a mixture of putatively neutral loci (n = 878) and loci under selection (n = 190) were identified with the FST-outlier method. A range of population genetic analyses were implemented using these SNPs and a panel of 10 microsatellite loci. The three types of deer could readily be distinguished with both the SNP and microsatellite datasets. This study demonstrates that commercially developed SNP chips are a viable means of SNP discovery for non-model organisms, even when used between very distantly related species (the Bovidae and Cervidae families diverged some 25.1−30.1 million years before present).

Highlights

Single nucleotide polymorphisms (SNPs) are increasingly becoming the marker of choice for investigating contemporary and evolutionary genetic processes (e.g. [1,224])
A SNP panel including both selectively neutral loci and loci under selection could be beneficial in studies of non-model organisms, as neutral loci can be used to make inferences about long-term demographic processes whereas loci under selection can be used to differentiate recently diverged lineages or identify genomic regions involved in local adaptation, reproductive isolation or speciation [4,14,15]
Minor allele frequency (MAF) varied across loci and between lineages

Summary

Introduction

Single nucleotide polymorphisms (SNPs) are increasingly becoming the marker of choice for investigating contemporary and evolutionary genetic processes (e.g. [1,224]). SNPs have many advantages over more traditionally used allozymes, microsatellite loci and chain-termination (Sanger) sequencing of select loci. These include availability in high numbers, presence in coding and non-coding regions, low-scoring error rates, relative ease of calibration between different studies and conformation to simple models of mutation. SNPs are useful in researching the genetics of non-model organisms, and can be used in place of or in tandem with microsatellite markers to investigate kinship [10], individual identification [11], parentage inference [12] and population structure [13]. A SNP panel including both selectively neutral loci and loci under selection could be beneficial in studies of non-model organisms, as neutral loci can be used to make inferences about long-term demographic processes (e.g., migration) whereas loci under selection can be used to differentiate recently diverged lineages or identify genomic regions involved in local adaptation, reproductive isolation or speciation [4,14,15]

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