Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

Hu, Mingyue; Jiang, Hao; Lai, Weining; Shi, Lulu; Yi, Wenfeng; Sun, Hao; Chen, Chengzhen; Yuan, Bao; Yan, Shouqing; Zhang, Jia-Bao

doi:10.3390/ani13101717

Cited by 3 publications

(1 citation statement)

References 78 publications

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“…Based on the maximum 5% of F ST values and maximum and minimum 5% of π ratio, genes under selection in both the SG group and HGG group were identified. In KOBAS (version 3.0) (Hu et al., 2023), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to conduct functional enrichment analysis to understand the biological processes and pathways involving the selected genes. The p ‐value cut‐off of .05 was considered to be significantly enriched.…”

Section: Methodsmentioning

confidence: 99%

Genomic evidence for climatic adaptation in Fejervarya multistriata

Lei,

Yan,

Jin

et al. 2023

Diversity and Distributions

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AimGenetic diversity driven by natural selection contributes to population divergence in amphibians, thus facilitating local adaptation to climate change. Understanding the mechanisms of genetic adaptation is one of the important issues in evolutionary biology. This study set out to reveal drivers responsible for intraspecific divergence in Fejervarya multistriata and further investigate the potential involvement of selected genes in responding to climate challenges.LocationChina.MethodTo identify adaptive traits associated with climate change, we conducted genome RAD‐seq of 300 F. multistriata individuals from 15 locations across a bio‐geographical range with gradual climatic variation in China.ResultsThe results indicate a substantial genetic diversity among populations of F. multistriata and highlight specific genes and pathways that likely contribute to intraspecific divergence. The demographic history of F. multistriata can be traced back to the last interglacial period, during which elevated temperatures may have led to a significant decline in effective population size. The analysis of genome‐climate association identified five candidate genes (BMP2K, NRAP, ZW10, MYH1 and PLB1) potentially involved in local climate adaptation.Main ConclusionsOur findings have shed light on the genetic mechanisms of local adaptation to climate change in F. multistriata, thereby aiding in determining the possible fate of populations under future climate change.

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Section: Methodsmentioning

confidence: 99%

Genomic evidence for climatic adaptation in Fejervarya multistriata

Lei,

Yan,

Jin

et al. 2023

Diversity and Distributions

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Unraveling inbreeding patterns and selection signals in Alpine Grey cattle

Gomez Proto,

Mancin,

Sartori

et al. 2024

animal

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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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Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

Cited by 3 publications

References 78 publications

Genomic evidence for climatic adaptation in Fejervarya multistriata

Genomic evidence for climatic adaptation in Fejervarya multistriata

Unraveling inbreeding patterns and selection signals in Alpine Grey cattle

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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