Abstract
Knowledge of linkage disequilibrium (LD) patterns is necessary to determine the minimum density of markers required for genomic studies and to infer historical changes as well as inbreeding events in the populations. In this study, we used genotyping-by-sequencing (GBS) approach to detect single nucleotide polymorphisms (SNPs) across American mink genome and further to estimate LD, effective population size (Ne), and inbreeding rates based on excess of homozygosity (FHOM) and runs of homozygosity (ROH). A GBS assay was constructed based on the sequencing of ApeKI-digested libraries from 285 American mink using Illumina HiSeq Sequencer. Data of 13,321 SNPs located on 46 scaffolds was used to perform LD analysis. The average LD (r2 ± SD) between adjacent SNPs was 0.30 ± 0.35 over all scaffolds with an average distance of 51 kb between markers. The average r2 < 0.2 was observed at inter-marker distances of >40 kb, suggesting that at least 60,000 informative SNPs would be required for genomic selection in American mink. The Ne was estimated to be 116 at five generations ago. In addition, the most rapid decline of population size was observed between 100 and 200 generations ago. Our results showed that short extensions of homozygous genotypes (500 kb to 1 Mb) were abundant across the genome and accounted for 33% of all ROH identified. The average inbreeding coefficient based on ROH longer than 1 Mb was 0.132 ± 0.042. The estimations of FHOM ranged from −0.44 to 0.34 among different samples with an average of 0.15 over all individuals. This study provided useful insights to determine the density of SNP panel providing enough statistical power and accuracy in genomic studies of American mink. Moreover, these results confirmed that GBS approach can be considered as a useful tool for genomic studies in American mink.
Highlights
Linkage disequilibrium (LD) refers to the non-random association of alleles at two separate loci within a population (Weir, 1979)
The main objectives of this study were (1) to estimate the LD levels across the American mink genome using high-throughput single nucleotide polymorphisms (SNPs) makers obtained from GBS data, (2) to evaluate the recent and historical Ne based on the pattern of LD decay across the genome, and (3) to estimate the inbreeding levels in the studied population using genomic data
The GBS analysis generated a large number of SNPs in other livestock species including horse (30,429), cattle (13,396) and sheep (57,377), which were subsequently applied in revealing the genetic differentiation of the studied populations (Gurgul et al, 2019)
Summary
Linkage disequilibrium (LD) refers to the non-random association of alleles at two separate loci within a population (Weir, 1979). The existence of LD between causative variants and genetic markers is the critical assumption of the genomic studies exploring the association between phenotypes and genotypes (Goddard et al, 2016). Knowledge of LD extension is crucial to determine the required marker density to achieve adequate accuracy in both genome-wide association studies (GWAS) and genomic selection (Meadows et al, 2008; Rabier et al, 2016). LD patterns across the genome could be affected by evolutionary forces including migration, mutation, genetic drift, natural selection, population structure, and recombination rates (Ardlie et al, 2002). LD maps are useful tools to study the genetic diversity (McKay et al, 2007) and identify the selective sweeps in livestock populations (Gutiérrez-Gil et al, 2015). The Ne is a useful measure to evaluate the inbreeding levels, historical events, and conservation priorities in animal populations (Theodorou and Couvet, 2006)
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