Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions
Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where cattle farming has been traditionally practiced. In this study, we performed whole-genome sequencing to genetically characterize three rare native breeds Eastern Finncattle, Weste...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2018.00728/full |
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| author | Melak Weldenegodguad Melak Weldenegodguad Ruslan Popov Kisun Pokharel Innokentyi Ammosov Yao Ming Zoya Ivanova Juha Kantanen |
| author_facet | Melak Weldenegodguad Melak Weldenegodguad Ruslan Popov Kisun Pokharel Innokentyi Ammosov Yao Ming Zoya Ivanova Juha Kantanen |
| author_sort | Melak Weldenegodguad |
| collection | DOAJ |
| description | Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where cattle farming has been traditionally practiced. In this study, we performed whole-genome sequencing to genetically characterize three rare native breeds Eastern Finncattle, Western Finncattle and Yakutian cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian taurine cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European taurine breeds. This result is in contrast to the results of marker-based cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic taurine cattle may have been higher than that of the European cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on cattle genomes and on the value of the adapted breeds for the conservation of cattle genetic resources. |
| first_indexed | 2024-12-11T13:44:06Z |
| format | Article |
| id | doaj.art-b1d2394c2ed64846919a7c3cfd80c4ee |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-11T13:44:06Z |
| publishDate | 2019-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-b1d2394c2ed64846919a7c3cfd80c4ee2022-12-22T01:04:37ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-01-01910.3389/fgene.2018.00728419462Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming RegionsMelak Weldenegodguad0Melak Weldenegodguad1Ruslan Popov2Kisun Pokharel3Innokentyi Ammosov4Yao Ming5Zoya Ivanova6Juha Kantanen7Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, FinlandDepartment of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, FinlandYakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), Yakutsk, RussiaDepartment of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, FinlandBoard of Agricultural Office of Eveno-Bytantaj Region, Batagay-Alyta, RussiaBGI-Genomics, BGI-Shenzhen, Shenzhen, ChinaYakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), Yakutsk, RussiaDepartment of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, FinlandNorthern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where cattle farming has been traditionally practiced. In this study, we performed whole-genome sequencing to genetically characterize three rare native breeds Eastern Finncattle, Western Finncattle and Yakutian cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian taurine cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European taurine breeds. This result is in contrast to the results of marker-based cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic taurine cattle may have been higher than that of the European cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on cattle genomes and on the value of the adapted breeds for the conservation of cattle genetic resources.https://www.frontiersin.org/article/10.3389/fgene.2018.00728/fulladaptationdemographic historyFinncattleindelsselective sweepsSNPs |
| spellingShingle | Melak Weldenegodguad Melak Weldenegodguad Ruslan Popov Kisun Pokharel Innokentyi Ammosov Yao Ming Zoya Ivanova Juha Kantanen Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions Frontiers in Genetics adaptation demographic history Finncattle indels selective sweeps SNPs |
| title | Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions |
| title_full | Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions |
| title_fullStr | Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions |
| title_full_unstemmed | Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions |
| title_short | Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions |
| title_sort | whole genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions |
| topic | adaptation demographic history Finncattle indels selective sweeps SNPs |
| url | https://www.frontiersin.org/article/10.3389/fgene.2018.00728/full |
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