Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds
It is known that different species of animals, when living in the same environmental conditions, can form similar phenotypes. The study of the convergent evolution of several species under the influence of the same environmental factor makes it possible to identify common mechanisms of genetic adapt...
Published in: | Vavilov Journal of Genetics and Breeding |
---|---|
Main Authors: | , |
Format: | Article in Journal/Newspaper |
Language: | English Russian |
Published: |
Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2023
|
Subjects: | |
Online Access: | https://doi.org/10.18699/VJGB-23-56 https://doaj.org/article/80c370dc0a89462f9834eb76e20c16af |
id |
ftdoajarticles:oai:doaj.org/article:80c370dc0a89462f9834eb76e20c16af |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:80c370dc0a89462f9834eb76e20c16af 2024-02-11T09:58:48+01:00 Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds N. S. Yudin D. M. Larkin 2023-09-01T00:00:00Z https://doi.org/10.18699/VJGB-23-56 https://doaj.org/article/80c370dc0a89462f9834eb76e20c16af EN RU eng rus Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders https://vavilov.elpub.ru/jour/article/view/3865 https://doaj.org/toc/2500-3259 2500-3259 doi:10.18699/VJGB-23-56 https://doaj.org/article/80c370dc0a89462f9834eb76e20c16af Вавиловский журнал генетики и селекции, Vol 27, Iss 5, Pp 463-470 (2023) signatures of selection adaptation cold cattle sheep local breed russia whole genome sequencing Genetics QH426-470 article 2023 ftdoajarticles https://doi.org/10.18699/VJGB-23-56 2024-01-14T01:50:16Z It is known that different species of animals, when living in the same environmental conditions, can form similar phenotypes. The study of the convergent evolution of several species under the influence of the same environmental factor makes it possible to identify common mechanisms of genetic adaptation. Local cattle and sheep breeds have been formed over thousands of years under the influence of domestication, as well as selection aimed at adaptation to the local environment and meeting human needs. Previously, we identified a number of candidate genes in genome regions potentially selected during domestication and adaptation to the climatic conditions of Russia, in local breeds of cattle and sheep using whole genome genotyping data. However, these data are of low resolution and do not reveal most nucleotide substitutions. The aim of the work was to create, using the whole genome sequencing data, a list of genes associated with domestication, selection and adaptation in Russian cattle and sheep breeds, as well as to identify candidate genes and metabolic pathways for selection for cold adaptation. We used our original data on the search for signatures of selection in the genomes of Russian cattle (Yakut, Kholmogory, Buryat, Wagyu) and sheep (Baikal, Tuva) breeds. We used the HapFLK, DCMS, FST and PBS methods to identify DNA regions with signatures of selection. The number of candidate genes in potentially selective regions was 946 in cattle and 151 in sheep. We showed that the studied Russian cattle and sheep breeds have at least 10 genes in common, apparently involved in the processes of adaptation/selection, including adaptation to a cold climate, including the ASTN2, PM20D1, TMEM176A, and GLIS1 genes. Based on the intersection with the list of selected genes in at least two Arctic/Antarctic mammal species, 20 and 8 genes, have been identified in cattle and sheep, respectively, that are potentially involved in cold adaptation. Among them, the most promising for further research are the ASPH, NCKAP5L, ... Article in Journal/Newspaper Antarc* Antarctic Arctic Directory of Open Access Journals: DOAJ Articles Antarctic Arctic Kholmogory ENVELOPE(41.656,41.656,64.223,64.223) Tuva ENVELOPE(12.506,12.506,65.215,65.215) Vavilov Journal of Genetics and Breeding 27 5 463 470 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English Russian |
topic |
signatures of selection adaptation cold cattle sheep local breed russia whole genome sequencing Genetics QH426-470 |
spellingShingle |
signatures of selection adaptation cold cattle sheep local breed russia whole genome sequencing Genetics QH426-470 N. S. Yudin D. M. Larkin Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds |
topic_facet |
signatures of selection adaptation cold cattle sheep local breed russia whole genome sequencing Genetics QH426-470 |
description |
It is known that different species of animals, when living in the same environmental conditions, can form similar phenotypes. The study of the convergent evolution of several species under the influence of the same environmental factor makes it possible to identify common mechanisms of genetic adaptation. Local cattle and sheep breeds have been formed over thousands of years under the influence of domestication, as well as selection aimed at adaptation to the local environment and meeting human needs. Previously, we identified a number of candidate genes in genome regions potentially selected during domestication and adaptation to the climatic conditions of Russia, in local breeds of cattle and sheep using whole genome genotyping data. However, these data are of low resolution and do not reveal most nucleotide substitutions. The aim of the work was to create, using the whole genome sequencing data, a list of genes associated with domestication, selection and adaptation in Russian cattle and sheep breeds, as well as to identify candidate genes and metabolic pathways for selection for cold adaptation. We used our original data on the search for signatures of selection in the genomes of Russian cattle (Yakut, Kholmogory, Buryat, Wagyu) and sheep (Baikal, Tuva) breeds. We used the HapFLK, DCMS, FST and PBS methods to identify DNA regions with signatures of selection. The number of candidate genes in potentially selective regions was 946 in cattle and 151 in sheep. We showed that the studied Russian cattle and sheep breeds have at least 10 genes in common, apparently involved in the processes of adaptation/selection, including adaptation to a cold climate, including the ASTN2, PM20D1, TMEM176A, and GLIS1 genes. Based on the intersection with the list of selected genes in at least two Arctic/Antarctic mammal species, 20 and 8 genes, have been identified in cattle and sheep, respectively, that are potentially involved in cold adaptation. Among them, the most promising for further research are the ASPH, NCKAP5L, ... |
format |
Article in Journal/Newspaper |
author |
N. S. Yudin D. M. Larkin |
author_facet |
N. S. Yudin D. M. Larkin |
author_sort |
N. S. Yudin |
title |
Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds |
title_short |
Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds |
title_full |
Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds |
title_fullStr |
Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds |
title_full_unstemmed |
Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds |
title_sort |
candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of russian cattle and sheep breeds |
publisher |
Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
publishDate |
2023 |
url |
https://doi.org/10.18699/VJGB-23-56 https://doaj.org/article/80c370dc0a89462f9834eb76e20c16af |
long_lat |
ENVELOPE(41.656,41.656,64.223,64.223) ENVELOPE(12.506,12.506,65.215,65.215) |
geographic |
Antarctic Arctic Kholmogory Tuva |
geographic_facet |
Antarctic Arctic Kholmogory Tuva |
genre |
Antarc* Antarctic Arctic |
genre_facet |
Antarc* Antarctic Arctic |
op_source |
Вавиловский журнал генетики и селекции, Vol 27, Iss 5, Pp 463-470 (2023) |
op_relation |
https://vavilov.elpub.ru/jour/article/view/3865 https://doaj.org/toc/2500-3259 2500-3259 doi:10.18699/VJGB-23-56 https://doaj.org/article/80c370dc0a89462f9834eb76e20c16af |
op_doi |
https://doi.org/10.18699/VJGB-23-56 |
container_title |
Vavilov Journal of Genetics and Breeding |
container_volume |
27 |
container_issue |
5 |
container_start_page |
463 |
op_container_end_page |
470 |
_version_ |
1790594572871532544 |