Dataset Information

Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data.

ABSTRACT: Bohai Black cattle are one of the well-known cattle breeds with black coat color in China, which are cultivated for beef. However, no study has conducted a comprehensive analysis of genomic diversity and selective pressures in Bohai Black cattle. Here, we performed a comprehensive analysis of genomic variation in 10 Bohai Black cattle (five newly sequenced and five published) and the published whole-genome sequencing (WGS) data of 50 cattle representing five "core" cattle populations. The population structure analysis revealed that Bohai Black cattle harbored the ancestry with European taurine, Northeast Asian taurine, and Chinese indicine. The Bohai Black cattle demonstrated relatively high genomic diversity from the other cattle breeds, as indicated by the nucleotide diversity (pi), the expected heterozygosity (HE) and the observed heterozygosity (HO), the linkage disequilibrium (LD) decay, and runs of homozygosity (ROH). We identified 65 genes containing more than five non-synonymous SNPs (nsSNPs), and an enrichment analysis revealed the "ECM-receptor interaction" pathways associated with meat quality in Bohai Black cattle. Five methods (CLR, θπ, FST, θπ ratio, and XP-EHH) were used to find several pathways and genes carried selection signatures in Bohai Black cattle, including black coat color (MC1R), muscle development (ITGA9, ENAH, CAPG, ABI2, and ISLR), fat deposition (TBC1D1, CYB5R4, TUSC3, and EPS8), reproduction traits (SPIRE2, KHDRBS2, and FANCA), and immune system response (CD84, SLAMF1, SLAMF6, and CDK10). Taken together, our results provide a valuable resource for characterizing the uniqueness of Bohai Black cattle.

SUBMITTER: Ma X

PROVIDER: S-EPMC8909316 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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Publications

Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data.

Ma Xiaohui X Cheng Haijian H Liu Yangkai Y Sun Luyang L Chen Ningbo N Jiang Fugui F You Wei W Yang Zhangang Z Zhang Baoheng B Song Enliang E Lei Chuzhao C

Animals : an open access journal from MDPI 20220307 5

Bohai Black cattle are one of the well-known cattle breeds with black coat color in China, which are cultivated for beef. However, no study has conducted a comprehensive analysis of genomic diversity and selective pressures in Bohai Black cattle. Here, we performed a comprehensive analysis of genomic variation in 10 Bohai Black cattle (five newly sequenced and five published) and the published whole-genome sequencing (WGS) data of 50 cattle representing five "core" cattle populations. The popula ...[more]

PMID: 35268233

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Dataset Information

Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data.

Publications

Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data.

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