Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data

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-bysequencing (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 (F HOM ) 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 (r 2 ± SD) between adjacent SNPs was 0.30 ± 0.35 over all scaffolds with an average distance of 51 kb between markers. The average r 2 < 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 F HOM 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.

Population Genomics of American Mink Using Whole Genome Sequencing Data

“…The average r 2 between adjacent markers were in range of 0.280 to 0.366 for different color-types, which was in agreement with the value of 0.300 ± 0.350 reported by Karimi et al [35] for American mink. Genomic selection and genome wide association studies (GWAS) rely on the assumption of the presence of LD between markers and the genes controlling the traits of interest [67].…”

“…The availability of chromosome-scale genome assembly for American mink can open more opportunities to reveal the genetic diversity and develop the genomic studies of this species. High correlation of 0.85 was found between FHOM and FROH, which was comparable with the values of 0.87, 0.89, and 0.83-0.95 reported in black American mink [35], four cattle breeds [65] and Italian local cattle [66], respectively. However, a lower correlation (0.47) was observed between FROH and FPED.…”

“…The F HOM ranged between −0.189 and −0.112 in different color-types ( Table 1 ), that were less than the average value of 0.150 obtained from 52,714 SNPs in black American mink [ 35 ]. This discrepancy can be due to the differences in the historical background, sampling approaches and the density of markers applied in these studies.…”

“…High percentage of reads mapped to the reference genome (on average, 98.24%) confirming the high efficiency of the whole genome sequence data in this study. The number of SNPs obtained in this study (8,150,569) was much higher than 52,714 and 34,816 SNPs that were extracted by GBS technique to study the LD pattern [ 35 ] and the genes associated with body size [ 57 ] in American mink, respectively. This is due to the fact that GBS is a restriction enzyme-based technique that can only sequence a reduced subset of genome [ 58 ].…”

“…Microsatellite DNA markers were also used to estimate the Ne in American mink based on the LD information [ 33 , 34 ]. Moreover, 13,321 SNPs extracted by genotyping-by-sequencing (GBS) was used to investigate the LD patterns and estimate the Ne of black American mink [ 35 ]. However, there is no study on the LD patterns and Ne of different color-types of American mink using the whole genome sequencing data.…”