Genome-wide analysis emancipates genomic diversity and signature of selection in Altay white-headed cattle of Xinjiang, China

Wang, Yushu; Qi, Xingshan; Cheng, Haijian; Chen, Ningbo; Ahmed, Zulfiqar; Chen, Qiuming; Lei, Chuzhao; Yang, Xueyi

doi:10.3389/fgene.2023.1144249

Cited by 2 publications

(2 citation statements)

References 62 publications

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“…(3) permitting a maximum of 5 missing calls in a window. The number and length of ROHs were estimated for each breed, and the length of ROHs was categorized into three groups: 0.5-1 Mb, 1-2 Mb, and >2 Mb [26].…”

Section: Linkage Disequilibrium and Run Of Homozygositymentioning

confidence: 99%

Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation

Ayalew,

Wu,

Tarekegn

et al. 2023

Animals

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Over time, indigenous cattle breeds have developed disease resistance, heat tolerance, and adaptability to harsh environments. Deciphering the genetic mechanisms underlying adaptive traits is crucial for their improvement and sustainable utilization. For the first time, we performed whole-genome sequencing to unveil the genomic diversity, population structure, and selection signatures of Abigar cattle living in a tropical environment. The population structure analysis revealed that Abigar cattle exhibit high nucleotide diversity and heterozygosity, with low runs of homozygosity and linkage disequilibrium, suggesting a genetic landscape less constrained by inbreeding and enriched by diversity. Using nucleotide diversity (Pi) and population differentiation (FST) selection scan methods, we identified 83 shared genes that are likely associated with tropical adaption. The functional annotation analysis revealed that some of these genes are potentially linked to heat tolerance (HOXC13, DNAJC18, and RXFP2), immune response (IRAK3, MZB1, and STING1), and oxidative stress response (SLC23A1). Given the wider spreading impacts of climate change on cattle production, understanding the genetic mechanisms of adaptation of local breeds becomes crucial to better respond to climate and environmental changes. In this context, our finding establishes a foundation for further research into the mechanisms underpinning cattle adaptation to tropical environments.

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Section: Linkage Disequilibrium and Run Of Homozygositymentioning

confidence: 99%

Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation

Ayalew,

Wu,

Tarekegn

et al. 2023

Animals

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show abstract

“…SNPs with a minor allele frequency (MAF) of greater than 0.05 were considered in this analysis. The number and size of homozygosity (ROH) runs were estimated for each breed using the methods described in a previous study [ 78 ].…”

Section: Methodsmentioning

confidence: 99%

Whole Genome Scan Uncovers Candidate Genes Related to Milk Production Traits in Barka Cattle

Ayalew,

Wu,

Tarekegn

et al. 2024

IJMS

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In this study, our primary aim was to explore the genomic landscape of Barka cattle, a breed recognized for high milk production in a semi-arid environment, by focusing on genes with known roles in milk production traits. We employed genome-wide analysis and three selective sweep detection methods (ZFST, θπ ratio, and ZHp) to identify candidate genes associated with milk production and composition traits. Notably, ACAA1, P4HTM, and SLC4A4 were consistently identified by all methods. Functional annotation highlighted their roles in crucial biological processes such as fatty acid metabolism, mammary gland development, and milk protein synthesis. These findings contribute to understanding the genetic basis of milk production in Barka cattle, presenting opportunities for enhancing dairy cattle production in tropical climates. Further validation through genome-wide association studies and transcriptomic analyses is essential to fully exploit these candidate genes for selective breeding and genetic improvement in tropical dairy cattle.

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Genome-wide analysis emancipates genomic diversity and signature of selection in Altay white-headed cattle of Xinjiang, China

Cited by 2 publications

References 62 publications

Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation

Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation

Whole Genome Scan Uncovers Candidate Genes Related to Milk Production Traits in Barka Cattle

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