Population Genomics of American Mink Using Whole Genome Sequencing Data.

Mehdi Sargolzaei,Karim Karimi,Younes Miar,Duy Ngoc Do

doi:10.3390/genes12020258

Mehdi Sargolzaei, Karim Karimi + Show 2 more

Open Access

https://doi.org/10.3390/genes12020258

Copy DOI

Journal: Genes	Publication Date: Feb 11, 2021
Citations: 9	License type: CC BY 4.0

Affiliation: University of Guelph, Dalhousie University

Abstract

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

Highlights

Characterizing the genetic structure is crucial to reveal the genetic diversity, domestication history, and genetic relationship of populations that eventually facilitate the development of efficient breeding strategies in domestic animals [1]
Sequencing technologies have provided the opportunity to use a large number of single nucleotide polymorphisms (SNPs) for investigation of genetic structure and diversity of livestock species, e.g., cattle [2,3], sheep [4], goat [5], and pig [6]
SNPs that were extracted by GBS technique to study the linkage disequilibrium (LD) pattern [35] and the genes associated with body size [57] in American mink, respectively

Summary

Introduction

Characterizing the genetic structure is crucial to reveal the genetic diversity, domestication history, and genetic relationship of populations that eventually facilitate the development of efficient breeding strategies in domestic animals [1]. Advances in DNA sequencing technologies have provided the opportunity to use a large number of single nucleotide polymorphisms (SNPs) for investigation of genetic structure and diversity of livestock species, e.g., cattle [2,3], sheep [4], goat [5], and pig [6]. These markers are efficient tools to measure the linkage disequilibrium (LD) across the genome [7]. Admixture between distinct populations can arise LD between two unlinked loci, those with different allele frequencies [10,11]

Methods

Results

Discussion

Conclusion