Identification of muscle-specific candidate genes in Simmental beef cattle using imputed next generation sequencing


Autoři: Farhad Bordbar aff001;  Just Jensen aff002;  Bo Zhu aff001;  Zezhao Wang aff001;  Lei Xu aff001;  Tianpeng Chang aff001;  Ling Xu aff001;  Min Du aff003;  Lupei Zhang aff001;  Huijiang Gao aff001;  Lingyang Xu aff001;  Junya Li aff001
Působiště autorů: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China aff001;  Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark aff002;  Department of Animal Sciences, Washington Center for Muscle Biology, Washington State University, Pullman, Washington, United States of America aff003
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: 10.1371/journal.pone.0223671

Souhrn

Genome-wide association studies (GWAS) have commonly been used to identify candidate genes that control economically important traits in livestock. Our objective was to detect potential candidate genes associated mainly with muscle development traits related to dimension of hindquarter in cattle. A next generation sequencing (NGS) dataset to imputed to 12 million single nucleotide polymorphisms (SNPs) (from 1252 Simmental beef cattle) were used to search for genes affecting hindquarter traits using a linear, mixed model approach. We also used haplotype and linkage disequilibrium blocks to further support our identifications. We identified 202 significant SNPs in the bovine BTA4 chromosome region associated with width of hind leg, based on a stringent statistical threshold (p = 0.05/ effective number of SNPs identified). After exploring the region around these SNPs, we found candidate genes that were potentially related to the associated markers. More importantly, we identified a region of approximately 280 Kb on the BTA4 chromosome that harbored several muscle specific candidate genes, genes to be in a potential region for muscle development. However, we also found candidate gene SLC13A1 on BTA4, which seems to be associated with bone disorders (such as chondrodysplasia) in Simmental beef cattle.

Klíčová slova:

Cattle – Genome-wide association studies – Legs – Livestock – Meat – Next-generation sequencing – Skeletal muscles – Beef


Zdroje

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