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

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

  • Farhad Bordbar, Chinese Academy of Agricultural Sciences
  • ,
  • Just Jensen
  • Bo Zhu, Chinese Academy of Agricultural Sciences
  • ,
  • Zezhao Wang, Chinese Academy of Agricultural Sciences
  • ,
  • Lei Xu, Chinese Academy of Agricultural Sciences
  • ,
  • Tianpeng Chang, Chinese Academy of Agricultural Sciences
  • ,
  • Ling Xu, Chinese Academy of Agricultural Sciences
  • ,
  • Min Du, Washington State University
  • ,
  • Lupei Zhang, Chinese Academy of Agricultural Sciences
  • ,
  • Huijiang Gao, Chinese Academy of Agricultural Sciences
  • ,
  • Lingyang Xu, Chinese Academy of Agricultural Sciences
  • ,
  • Junya Li, Chinese Academy of Agricultural Sciences

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.

OriginalsprogEngelsk
Artikelnummere0223671
TidsskriftPLOS ONE
Vol/bind14
Nummer10
ISSN1932-6203
DOI
StatusUdgivet - okt. 2019

Se relationer på Aarhus Universitet Citationsformater

ID: 169352688