Population Genomics of American Mink Using Whole Genome Sequencing Data
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 Agricult...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-02-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/2/258 |
| _version_ | 1797411449763528704 |
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| author | Karim Karimi Duy Ngoc Do Mehdi Sargolzaei Younes Miar |
| author_facet | Karim Karimi Duy Ngoc Do Mehdi Sargolzaei Younes Miar |
| author_sort | Karim Karimi |
| collection | DOAJ |
| description | 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 (<i>p</i> < 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 (<i>Ne</i>) 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 <i>r</i><sup>2</sup> 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. |
| first_indexed | 2024-03-09T04:46:14Z |
| format | Article |
| id | doaj.art-b6313b2a49374c31999e7abfc2902a28 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T04:46:14Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-b6313b2a49374c31999e7abfc2902a282023-12-03T13:15:46ZengMDPI AGGenes2073-44252021-02-0112225810.3390/genes12020258Population Genomics of American Mink Using Whole Genome Sequencing DataKarim Karimi0Duy Ngoc Do1Mehdi Sargolzaei2Younes Miar3Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, CanadaDepartment of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, CanadaDepartment of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, CanadaDepartment of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, CanadaCharacterizing 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 (<i>p</i> < 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 (<i>Ne</i>) 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 <i>r</i><sup>2</sup> 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.https://www.mdpi.com/2073-4425/12/2/258American minklinkage disequilibriumpopulation structurewhole genome sequencing |
| spellingShingle | Karim Karimi Duy Ngoc Do Mehdi Sargolzaei Younes Miar Population Genomics of American Mink Using Whole Genome Sequencing Data Genes American mink linkage disequilibrium population structure whole genome sequencing |
| title | Population Genomics of American Mink Using Whole Genome Sequencing Data |
| title_full | Population Genomics of American Mink Using Whole Genome Sequencing Data |
| title_fullStr | Population Genomics of American Mink Using Whole Genome Sequencing Data |
| title_full_unstemmed | Population Genomics of American Mink Using Whole Genome Sequencing Data |
| title_short | Population Genomics of American Mink Using Whole Genome Sequencing Data |
| title_sort | population genomics of american mink using whole genome sequencing data |
| topic | American mink linkage disequilibrium population structure whole genome sequencing |
| url | https://www.mdpi.com/2073-4425/12/2/258 |
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