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Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array

SIMPLE SUMMARY: Evaluating population genetic background and genomic selection signatures can provide important insights into the uniqueness and the genetic relationship among breeds. In this study, we analyzed the genetic diversity, population structure, and phylogenetic relationships between Huaxi...

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Autores principales: Ma, Jun, Gao, Xue, Li, Junya, Gao, Huijiang, Wang, Zezhao, Zhang, Lupei, Xu, Lingyang, Gao, Han, Li, Hongwei, Wang, Yahui, Zhu, Bo, Cai, Wentao, Wang, Congyong, Chen, Yan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8698132/
https://www.ncbi.nlm.nih.gov/pubmed/34944246
http://dx.doi.org/10.3390/ani11123469
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author Ma, Jun
Gao, Xue
Li, Junya
Gao, Huijiang
Wang, Zezhao
Zhang, Lupei
Xu, Lingyang
Gao, Han
Li, Hongwei
Wang, Yahui
Zhu, Bo
Cai, Wentao
Wang, Congyong
Chen, Yan
author_facet Ma, Jun
Gao, Xue
Li, Junya
Gao, Huijiang
Wang, Zezhao
Zhang, Lupei
Xu, Lingyang
Gao, Han
Li, Hongwei
Wang, Yahui
Zhu, Bo
Cai, Wentao
Wang, Congyong
Chen, Yan
author_sort Ma, Jun
collection PubMed
description SIMPLE SUMMARY: Evaluating population genetic background and genomic selection signatures can provide important insights into the uniqueness and the genetic relationship among breeds. In this study, we analyzed the genetic diversity, population structure, and phylogenetic relationships between Huaxi cattle and its ancestors. The results showed that Huaxi cattle has formed its own unique genetic structure features, which could be clearly distinguished from its ancestors and similar populations. Moreover, some genes associated with important economic traits, including growth and development, reproduction, milk quality, and immune response, were identified by scanning potentially selected genomic regions, which may play an essential role in the excellent environmental adaptability and growth performance of Huaxi cattle. Our study will contribute to the genetic evaluation and rational breeding strategy, and give an extensive reference for understanding the genetic basis of economically important traits in Huaxi cattle. ABSTRACT: Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.
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spelling pubmed-86981322021-12-24 Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array Ma, Jun Gao, Xue Li, Junya Gao, Huijiang Wang, Zezhao Zhang, Lupei Xu, Lingyang Gao, Han Li, Hongwei Wang, Yahui Zhu, Bo Cai, Wentao Wang, Congyong Chen, Yan Animals (Basel) Article SIMPLE SUMMARY: Evaluating population genetic background and genomic selection signatures can provide important insights into the uniqueness and the genetic relationship among breeds. In this study, we analyzed the genetic diversity, population structure, and phylogenetic relationships between Huaxi cattle and its ancestors. The results showed that Huaxi cattle has formed its own unique genetic structure features, which could be clearly distinguished from its ancestors and similar populations. Moreover, some genes associated with important economic traits, including growth and development, reproduction, milk quality, and immune response, were identified by scanning potentially selected genomic regions, which may play an essential role in the excellent environmental adaptability and growth performance of Huaxi cattle. Our study will contribute to the genetic evaluation and rational breeding strategy, and give an extensive reference for understanding the genetic basis of economically important traits in Huaxi cattle. ABSTRACT: Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle. MDPI 2021-12-06 /pmc/articles/PMC8698132/ /pubmed/34944246 http://dx.doi.org/10.3390/ani11123469 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ma, Jun
Gao, Xue
Li, Junya
Gao, Huijiang
Wang, Zezhao
Zhang, Lupei
Xu, Lingyang
Gao, Han
Li, Hongwei
Wang, Yahui
Zhu, Bo
Cai, Wentao
Wang, Congyong
Chen, Yan
Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array
title Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array
title_full Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array
title_fullStr Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array
title_full_unstemmed Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array
title_short Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array
title_sort assessing the genetic background and selection signatures of huaxi cattle using high-density snp array
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8698132/
https://www.ncbi.nlm.nih.gov/pubmed/34944246
http://dx.doi.org/10.3390/ani11123469
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