Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds
Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorph...
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| Format: | Article |
| Language: | English |
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Wiley
2016-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2016/2152847 |
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| author | Laura Iacolina Astrid V. Stronen Cino Pertoldi Małgorzata Tokarska Louise S. Nørgaard Joaquin Muñoz Anders Kjærsgaard Aritz Ruiz-Gonzalez Stanisław Kamiński Deirdre C. Purfield |
| author_facet | Laura Iacolina Astrid V. Stronen Cino Pertoldi Małgorzata Tokarska Louise S. Nørgaard Joaquin Muñoz Anders Kjærsgaard Aritz Ruiz-Gonzalez Stanisław Kamiński Deirdre C. Purfield |
| author_sort | Laura Iacolina |
| collection | DOAJ |
| description | Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle (Bos taurus) and the European bison (Bison bonasus) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0.5–15 Mb to investigate ancient events and >15 Mb to address recent events (approximately three generations). For each length class, we chose a few chromosomes with a high number of ROH, calculated the percentage of times a SNP appeared in a ROH, and plotted the results. We selected areas with distinct patterns including regions where (1) all groups revealed an increase or decrease of ROH, (2) bison differed from cattle, (3) one cattle breed or groups of breeds differed (e.g., dairy versus meat cattle). Examination of these regions in the cattle genome showed genes potentially important for natural and human-induced selection, concerning, for example, meat and milk quality, metabolism, growth, and immune function. The comparative methodology presented here permits visual identification of regions of interest for selection, breeding programs, and conservation. |
| format | Article |
| id | doaj-art-2f4492f6f28548089ad94217f27ec9cc |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2016-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-2f4492f6f28548089ad94217f27ec9cc2025-02-03T05:52:03ZengWileyInternational Journal of Genomics2314-436X2314-43782016-01-01201610.1155/2016/21528472152847Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock BreedsLaura Iacolina0Astrid V. Stronen1Cino Pertoldi2Małgorzata Tokarska3Louise S. Nørgaard4Joaquin Muñoz5Anders Kjærsgaard6Aritz Ruiz-Gonzalez7Stanisław Kamiński8Deirdre C. Purfield9Department of Chemistry and Bioscience, Aalborg University, Section of Biology and Environmental Engineering, Fredrik Bajers Vej 7H, 9220 Aalborg, DenmarkDepartment of Chemistry and Bioscience, Aalborg University, Section of Biology and Environmental Engineering, Fredrik Bajers Vej 7H, 9220 Aalborg, DenmarkDepartment of Chemistry and Bioscience, Aalborg University, Section of Biology and Environmental Engineering, Fredrik Bajers Vej 7H, 9220 Aalborg, DenmarkMammal Research Institute Polish Academy of Sciences, Ul. Waszkiewicza 1, 17-230 Białowieża, PolandDepartment of Chemistry and Bioscience, Aalborg University, Section of Biology and Environmental Engineering, Fredrik Bajers Vej 7H, 9220 Aalborg, DenmarkDepartment of Chemistry and Bioscience, Aalborg University, Section of Biology and Environmental Engineering, Fredrik Bajers Vej 7H, 9220 Aalborg, DenmarkDepartment of Chemistry and Bioscience, Aalborg University, Section of Biology and Environmental Engineering, Fredrik Bajers Vej 7H, 9220 Aalborg, DenmarkDepartment of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, C/Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, SpainDepartment of Animal Genetics, University of Warmia and Mazury in Olsztyn, 10-718 Olsztyn, PolandAnimal & Biosciences Department, Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, County Cork, IrelandRuns of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle (Bos taurus) and the European bison (Bison bonasus) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0.5–15 Mb to investigate ancient events and >15 Mb to address recent events (approximately three generations). For each length class, we chose a few chromosomes with a high number of ROH, calculated the percentage of times a SNP appeared in a ROH, and plotted the results. We selected areas with distinct patterns including regions where (1) all groups revealed an increase or decrease of ROH, (2) bison differed from cattle, (3) one cattle breed or groups of breeds differed (e.g., dairy versus meat cattle). Examination of these regions in the cattle genome showed genes potentially important for natural and human-induced selection, concerning, for example, meat and milk quality, metabolism, growth, and immune function. The comparative methodology presented here permits visual identification of regions of interest for selection, breeding programs, and conservation.http://dx.doi.org/10.1155/2016/2152847 |
| spellingShingle | Laura Iacolina Astrid V. Stronen Cino Pertoldi Małgorzata Tokarska Louise S. Nørgaard Joaquin Muñoz Anders Kjærsgaard Aritz Ruiz-Gonzalez Stanisław Kamiński Deirdre C. Purfield Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds International Journal of Genomics |
| title | Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds |
| title_full | Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds |
| title_fullStr | Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds |
| title_full_unstemmed | Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds |
| title_short | Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds |
| title_sort | novel graphical analyses of runs of homozygosity among species and livestock breeds |
| url | http://dx.doi.org/10.1155/2016/2152847 |
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