A whole genome scan reveals distinct features of selection in Zhaotong cattle of Yunnan province

Lyu, Yang; Guan, Xiwen; Xu, Xinglong; Wang, Pengfei; Li, Qiaoxian; Panigrahi, Manjit; Zhang, Jicai; Chen, Ningbo; Huang, Bizhi; Lei, Chuzhao

doi:10.1111/age.13363

Cited by 4 publications

(1 citation statement)

References 95 publications

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“…Recently, WGS analysis of domestic cattle revealed that cattle worldwide can be divided into five continental groups: European taurine, Eurasian taurine, East Asian taurine, Chinese indicine, and Indian indicine (Chen et al, 2018). Many studies have employed WGS to analyze the unique adaptability of native Chinese cattle breeds (Chen et al, 2021;Lyu, Guan, et al, 2023;Lyu, Ren, et al, 2023;Shen et al, 2022) and identified a range of representative genes and signaling pathways. In the past, limited research has been performed on the genome diversity and population structure of the Anxi cattle breed's mtDNA and Y chromosomes.…”

Section: Introductionmentioning

confidence: 99%

Genomic characterization of dryland adaptation in endangered Anxi cattle in China

Lyu,

Yao,

Chen

et al. 2024

Animal Genetics

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Local species exhibit distinctive indigenous characteristics while showing unique productive and phenotypic traits. However, the advent of commercialization has posed a substantial threat to the survival of indigenous species. Anxi cattle, an endangered native breed in China, have evolved unique growth and reproductive characteristics in extreme desert and semidesert ecosystems. In this study, we conducted a genomic comparison of 10 Anxi cattle genomes with those of five other global populations/breeds to assess genetic diversity and identify candidate genomic regions in Anxi cattle. Population structure and genetic diversity analyses revealed that Anxi cattle are part of the East Asian cattle clade, exhibiting higher genetic diversity than commercial breeds. Through selective sweep analysis, we identified specific genetic variations linked to the environmental adaptability of Anxi cattle. Notably, we identified several candidate genes, including CERS3 involved in regulating skin permeability and antimicrobial functions, RBFOX2 associated with cardiac development, SLC16A7 participated in the regulation of pancreatic endocrine function, and SPATA3 related to reproduction. Our findings revealed the distinctive genomic features of Anxi cattle in dryland environments, provided invaluable insights for further research and breed preservation, and had important significance for enriching the domestic cattle breeding gene bank.

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Section: Introductionmentioning

confidence: 99%

Genomic characterization of dryland adaptation in endangered Anxi cattle in China

Lyu,

Yao,

Chen

et al. 2024

Animal Genetics

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Deciphering the Genetic Landscape: Insights Into the Genomic Signatures of Changle Goose

Chen,

Wu,

Zhu

et al. 2024

Evolutionary Applications

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The Changle goose (CLG), a Chinese indigenous breed, is celebrated for its adaptability, rapid growth, and premium meat quality. Despite its agricultural value, the exploration of its genomic attributes has been scant. Our study entailed whole‐genome resequencing of 303 geese across CLG and five other Chinese breeds, revealing distinct genetic diversity metrics. We discovered significant migration events from Xingguo gray goose to CLG and minor gene flow between them. We identified genomic regions through selective sweep analysis, correlating with CLG's unique traits. An elevated inbreeding coefficient in CLG, alongside reduced heterozygosity and rare single nucleotide polymorphisms (RSNPs), suggests a narrowed genetic diversity. Genomic regions related to reproduction, meat quality, and growth were identified, with the GATA3 gene showing strong selection signals for meat quality. A non‐synonymous mutation in the Sloc2a1 gene, which is associated with reproductive traits in the CLG, exhibited significant differences in allelic frequency. The roles of CD82, CDH8, and PRKAB1 in growth and development, alongside FABP4, FAF1, ESR1, and AKAP12 in reproduction, were highlighted. Additionally, Cdkal1 and Mfsd14a may influence meat quality. This comprehensive genetic analysis underpins the unique genetic makeup of CLG, providing a basis for its conservation and informed breeding strategies.

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Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data

Li,

Liu,

Ahmed

et al. 2024

Front. Genet.

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Introduction: To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands.Method: This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls. In addition, genes related to production traits were also searched by identifying Runs of Homozygosity (ROH) islands and important fragments from ancestors.Results: A total of 14,427,729 biallelic SNPs were discovered, with the majority located in intergenic and intron regions and a small percentage in exon regions, impacting protein function. Population genetic analyses including Principal Component Analysis (PCA), Neighbor-Joining (NJ) tree, and ADMIXTURE identified Angus, Holstein, and Mishima as the main ancestors of Crossbred beef cattle. In genetic diversity analysis, nucleotide diversity, linkage disequilibrium, and inbreeding coefficient analysis reveal that the genetic diversity of Crossbred beef cattle is at a moderate level, and a higher inbreeding coefficient indicates the need for careful breeding management. In addition, some genes related to economic traits are identified through the identification of Runs of Homozygosity (ROH) islands and important fragments from ancestors.Conclusion: This comprehensive genomic characterization supports the targeted improvement of economically important traits in Crossbred beef cattle, facilitating advanced breeding strategies.

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A whole genome scan reveals distinct features of selection in Zhaotong cattle of Yunnan province

Cited by 4 publications

References 95 publications

Genomic characterization of dryland adaptation in endangered Anxi cattle in China

Genomic characterization of dryland adaptation in endangered Anxi cattle in China

Deciphering the Genetic Landscape: Insights Into the Genomic Signatures of Changle Goose

Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data

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