Local Ancestry and Selection in the Genomes of Russian Black Pied Cattle
The Russian Black Pied (RBP) is one of Russia’s most popular dairy cattle breeds. It was developed in the USSR during the 1930s by crossing Russian native cattle with Dutch cattle. Since the mid-1970s, the RBP has been cross-bred with Holstein cattle to enhance milk production. To trace haplotypes a...
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MDPI AG
2025-04-01
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| author | Alexander V. Igoshin Andrey A. Yurchenko Nikolay S. Yudin Denis M. Larkin |
| author_facet | Alexander V. Igoshin Andrey A. Yurchenko Nikolay S. Yudin Denis M. Larkin |
| author_sort | Alexander V. Igoshin |
| collection | DOAJ |
| description | The Russian Black Pied (RBP) is one of Russia’s most popular dairy cattle breeds. It was developed in the USSR during the 1930s by crossing Russian native cattle with Dutch cattle. Since the mid-1970s, the RBP has been cross-bred with Holstein cattle to enhance milk production. To trace haplotypes and selection signatures in the RBP genomes formed during cross-breeding and selection, we conducted local ancestry inference and scans for selection signatures in 12 resequenced RBP animals. Scans for selection using hapFLK and window-based F<i><sub>ST</sub></i> identified 65 putatively selected regions across the genome, with 4 identified by both methods. Candidate missense variants were detected within these regions, including <i>KIAA1755</i>, <i>CNBD1</i>, and <i>MPZL3</i>, which may be related to milk traits, pathogen resistance, and climate adaptation. Local ancestry inference and functional annotation analyses suggest that regions with a higher fraction of native haplotypes are enriched for genes associated with keratin filaments, antimicrobial defence, the immune system, protein digestion, and amino acid transporters. The results of our study could be utilised for conservation purposes and the improvement of this and other breeds. |
| format | Article |
| id | doaj-art-8d0421d7411f4c549e92a4fbf3fff3b2 |
| institution | DOAJ |
| issn | 2413-4155 |
| language | English |
| publishDate | 2025-04-01 |
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| spelling | doaj-art-8d0421d7411f4c549e92a4fbf3fff3b22025-08-20T03:16:39ZengMDPI AGSci2413-41552025-04-01725110.3390/sci7020051Local Ancestry and Selection in the Genomes of Russian Black Pied CattleAlexander V. Igoshin0Andrey A. Yurchenko1Nikolay S. Yudin2Denis M. Larkin3The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, RussiaINSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, 94800 Villejuif, FranceThe Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, RussiaRoyal Veterinary College, University of London, London NW1 0TU, UKThe Russian Black Pied (RBP) is one of Russia’s most popular dairy cattle breeds. It was developed in the USSR during the 1930s by crossing Russian native cattle with Dutch cattle. Since the mid-1970s, the RBP has been cross-bred with Holstein cattle to enhance milk production. To trace haplotypes and selection signatures in the RBP genomes formed during cross-breeding and selection, we conducted local ancestry inference and scans for selection signatures in 12 resequenced RBP animals. Scans for selection using hapFLK and window-based F<i><sub>ST</sub></i> identified 65 putatively selected regions across the genome, with 4 identified by both methods. Candidate missense variants were detected within these regions, including <i>KIAA1755</i>, <i>CNBD1</i>, and <i>MPZL3</i>, which may be related to milk traits, pathogen resistance, and climate adaptation. Local ancestry inference and functional annotation analyses suggest that regions with a higher fraction of native haplotypes are enriched for genes associated with keratin filaments, antimicrobial defence, the immune system, protein digestion, and amino acid transporters. The results of our study could be utilised for conservation purposes and the improvement of this and other breeds.https://www.mdpi.com/2413-4155/7/2/51Russian Black PiedRussian Black-and-Whitelocal ancestry inferencesignatures of selection |
| spellingShingle | Alexander V. Igoshin Andrey A. Yurchenko Nikolay S. Yudin Denis M. Larkin Local Ancestry and Selection in the Genomes of Russian Black Pied Cattle Sci Russian Black Pied Russian Black-and-White local ancestry inference signatures of selection |
| title | Local Ancestry and Selection in the Genomes of Russian Black Pied Cattle |
| title_full | Local Ancestry and Selection in the Genomes of Russian Black Pied Cattle |
| title_fullStr | Local Ancestry and Selection in the Genomes of Russian Black Pied Cattle |
| title_full_unstemmed | Local Ancestry and Selection in the Genomes of Russian Black Pied Cattle |
| title_short | Local Ancestry and Selection in the Genomes of Russian Black Pied Cattle |
| title_sort | local ancestry and selection in the genomes of russian black pied cattle |
| topic | Russian Black Pied Russian Black-and-White local ancestry inference signatures of selection |
| url | https://www.mdpi.com/2413-4155/7/2/51 |
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