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Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the pop...

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Autores principales: Zinovieva, Natalia Anatolievna, Dotsev, Arsen Vladimirovich, Sermyagin, Alexander Alexandrovich, Deniskova, Tatiana Evgenievna, Abdelmanova, Alexandra Sergeevna, Kharzinova, Veronika Ruslanovna, Sölkner, Johann, Reyer, Henry, Wimmers, Klaus, Brem, Gottfried
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7668599/
https://www.ncbi.nlm.nih.gov/pubmed/33196682
http://dx.doi.org/10.1371/journal.pone.0242200
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author Zinovieva, Natalia Anatolievna
Dotsev, Arsen Vladimirovich
Sermyagin, Alexander Alexandrovich
Deniskova, Tatiana Evgenievna
Abdelmanova, Alexandra Sergeevna
Kharzinova, Veronika Ruslanovna
Sölkner, Johann
Reyer, Henry
Wimmers, Klaus
Brem, Gottfried
author_facet Zinovieva, Natalia Anatolievna
Dotsev, Arsen Vladimirovich
Sermyagin, Alexander Alexandrovich
Deniskova, Tatiana Evgenievna
Abdelmanova, Alexandra Sergeevna
Kharzinova, Veronika Ruslanovna
Sölkner, Johann
Reyer, Henry
Wimmers, Klaus
Brem, Gottfried
author_sort Zinovieva, Natalia Anatolievna
collection PubMed
description Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (F(ST)) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.
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spelling pubmed-76685992020-11-19 Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis Zinovieva, Natalia Anatolievna Dotsev, Arsen Vladimirovich Sermyagin, Alexander Alexandrovich Deniskova, Tatiana Evgenievna Abdelmanova, Alexandra Sergeevna Kharzinova, Veronika Ruslanovna Sölkner, Johann Reyer, Henry Wimmers, Klaus Brem, Gottfried PLoS One Research Article Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (F(ST)) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds. Public Library of Science 2020-11-16 /pmc/articles/PMC7668599/ /pubmed/33196682 http://dx.doi.org/10.1371/journal.pone.0242200 Text en © 2020 Zinovieva et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Zinovieva, Natalia Anatolievna
Dotsev, Arsen Vladimirovich
Sermyagin, Alexander Alexandrovich
Deniskova, Tatiana Evgenievna
Abdelmanova, Alexandra Sergeevna
Kharzinova, Veronika Ruslanovna
Sölkner, Johann
Reyer, Henry
Wimmers, Klaus
Brem, Gottfried
Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis
title Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis
title_full Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis
title_fullStr Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis
title_full_unstemmed Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis
title_short Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis
title_sort selection signatures in two oldest russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7668599/
https://www.ncbi.nlm.nih.gov/pubmed/33196682
http://dx.doi.org/10.1371/journal.pone.0242200
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