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Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures

Understanding the genetic diversity in Xiangxi cattle may facilitate our efforts toward further breeding programs. Here we compared 23 Xiangxi cattle with 78 published genomes of 6 worldwide representative breeds to characterize the genomic variations of Xiangxi cattle. Based on clustering models in...

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Autores principales: Luo, Xiaoyu, Li, Jianbo, Xiao, Chentong, Sun, Luyang, Xiang, Weixuan, Chen, Ningbo, Lei, Chuzhao, Lei, Hong, Long, Yun, Long, Ting, Suolang, Quji, Yi, Kangle
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9196905/
https://www.ncbi.nlm.nih.gov/pubmed/35711927
http://dx.doi.org/10.3389/fgene.2022.816379
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author Luo, Xiaoyu
Li, Jianbo
Xiao, Chentong
Sun, Luyang
Xiang, Weixuan
Chen, Ningbo
Lei, Chuzhao
Lei, Hong
Long, Yun
Long, Ting
Suolang, Quji
Yi, Kangle
author_facet Luo, Xiaoyu
Li, Jianbo
Xiao, Chentong
Sun, Luyang
Xiang, Weixuan
Chen, Ningbo
Lei, Chuzhao
Lei, Hong
Long, Yun
Long, Ting
Suolang, Quji
Yi, Kangle
author_sort Luo, Xiaoyu
collection PubMed
description Understanding the genetic diversity in Xiangxi cattle may facilitate our efforts toward further breeding programs. Here we compared 23 Xiangxi cattle with 78 published genomes of 6 worldwide representative breeds to characterize the genomic variations of Xiangxi cattle. Based on clustering models in population structure analysis, we displayed that Xiangxi cattle had a mutual genome ancestor with Chinese indicine, Indian indicine, and East Asian taurine. Population genetic diversity was analyzed by four methods (nucleotide diversity, inbreeding coefficient, linkage disequilibrium decay and runs of homozygosity), and we found that Xiangxi cattle had higher genomic diversity and weaker artificial selection than commercial breed cattle. Using four testing methods (θπ, CLR, F (ST), and XP-EHH), we explored positive selection regions harboring genes in Xiangxi cattle, which were related to reproduction, growth, meat quality, heat tolerance, and immune response. Our findings revealed the extent of sequence variation in Xiangxi cattle at the genome-wide level. All of our fruitful results can bring about a valuable genomic resource for genetic studies and breed protection in the future.
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spelling pubmed-91969052022-06-15 Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures Luo, Xiaoyu Li, Jianbo Xiao, Chentong Sun, Luyang Xiang, Weixuan Chen, Ningbo Lei, Chuzhao Lei, Hong Long, Yun Long, Ting Suolang, Quji Yi, Kangle Front Genet Genetics Understanding the genetic diversity in Xiangxi cattle may facilitate our efforts toward further breeding programs. Here we compared 23 Xiangxi cattle with 78 published genomes of 6 worldwide representative breeds to characterize the genomic variations of Xiangxi cattle. Based on clustering models in population structure analysis, we displayed that Xiangxi cattle had a mutual genome ancestor with Chinese indicine, Indian indicine, and East Asian taurine. Population genetic diversity was analyzed by four methods (nucleotide diversity, inbreeding coefficient, linkage disequilibrium decay and runs of homozygosity), and we found that Xiangxi cattle had higher genomic diversity and weaker artificial selection than commercial breed cattle. Using four testing methods (θπ, CLR, F (ST), and XP-EHH), we explored positive selection regions harboring genes in Xiangxi cattle, which were related to reproduction, growth, meat quality, heat tolerance, and immune response. Our findings revealed the extent of sequence variation in Xiangxi cattle at the genome-wide level. All of our fruitful results can bring about a valuable genomic resource for genetic studies and breed protection in the future. Frontiers Media S.A. 2022-05-27 /pmc/articles/PMC9196905/ /pubmed/35711927 http://dx.doi.org/10.3389/fgene.2022.816379 Text en Copyright © 2022 Luo, Li, Xiao, Sun, Xiang, Chen, Lei, Lei, Long, Long, Suolang and Yi. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Luo, Xiaoyu
Li, Jianbo
Xiao, Chentong
Sun, Luyang
Xiang, Weixuan
Chen, Ningbo
Lei, Chuzhao
Lei, Hong
Long, Yun
Long, Ting
Suolang, Quji
Yi, Kangle
Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures
title Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures
title_full Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures
title_fullStr Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures
title_full_unstemmed Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures
title_short Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures
title_sort whole-genome resequencing of xiangxi cattle identifies genomic diversity and selection signatures
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9196905/
https://www.ncbi.nlm.nih.gov/pubmed/35711927
http://dx.doi.org/10.3389/fgene.2022.816379
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