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Population Structure and Selection Signal Analysis of Nanyang Cattle Based on Whole-Genome Sequencing Data

With a rich breeding history, Nanyang cattle (NY cattle) have undergone extensive natural and artificial selection, resulting in distinctive traits such as high fertility, excellent meat quality, and disease resistance. This makes them an ideal model for studying the mechanisms of environmental adap...

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Published in:Genes 2024-03, Vol.15 (3), p.351
Main Authors: Zhang, Yan, Wei, Zhitong, Zhang, Man, Wang, Shiwei, Gao, Tengyun, Huang, Hetian, Zhang, Tianliu, Cai, Hanfang, Liu, Xian, Fu, Tong, Liang, Dong
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container_end_page
container_issue 3
container_start_page 351
container_title Genes
container_volume 15
creator Zhang, Yan
Wei, Zhitong
Zhang, Man
Wang, Shiwei
Gao, Tengyun
Huang, Hetian
Zhang, Tianliu
Cai, Hanfang
Liu, Xian
Fu, Tong
Liang, Dong
description With a rich breeding history, Nanyang cattle (NY cattle) have undergone extensive natural and artificial selection, resulting in distinctive traits such as high fertility, excellent meat quality, and disease resistance. This makes them an ideal model for studying the mechanisms of environmental adaptability. To assess the population structure and genetic diversity of NY cattle, we performed whole-genome resequencing on 30 individuals. These data were then compared with published whole-genome resequencing data from 432 cattle globally. The results indicate that the genetic structure of NY cattle is significantly different from European commercial breeds and is more similar to North-Central Chinese breeds. Furthermore, among all breeds, NY cattle exhibit the highest genetic diversity and the lowest population inbreeding levels. A genome-wide selection signal analysis of NY cattle and European commercial breeds using Fst, θπ-ratio, and θπ methods revealed significant selection signals in genes associated with reproductive performance and immunity. Our functional annotation analysis suggests that these genes may be responsible for reproduction ( , , and ), immune response ( , , and ), and olfaction ( ). We provide a comprehensive overview of sequence variations in the NY cattle genome, revealing insights into the population structure and genetic diversity of NY cattle. Additionally, we identify candidate genes associated with important economic traits, offering valuable references for future conservation and breeding efforts of NY cattle.
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subjects Adaptability
Agricultural production
Animal genetics
Animals
Beef cattle
Biological diversity
Cattle
Cattle - genetics
Disease resistance
DNA sequencing
Fertility
Genes
Genetic diversity
Genetic structure
Genome - genetics
Genomes
Genomics
HSF1 protein
Humans
Immune response
Inbreeding
Meat quality
Nucleotide sequence
Nucleotide sequencing
Olfaction
Pax5 protein
Phenotype
Phylogenetics
Population genetics
Population structure
Quality control
Sequence Analysis, DNA
Software
Whole genome sequencing
Whole Genome Sequencing - methods
title Population Structure and Selection Signal Analysis of Nanyang Cattle Based on Whole-Genome Sequencing Data
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