4.7 Article

Identification of Candidate Genes Regulating Carcass Depth and Hind Leg Circumference in Simmental Beef Cattle Using Illumina Bovine Beadchip and Next-Generation Sequencing Analyses

Journal

ANIMALS
Volume 12, Issue 9, Pages -

Publisher

MDPI
DOI: 10.3390/ani12091103

Keywords

genome-wide association study; carcass depth; hind leg circumference; next-generation sequencing; Simmental beef cattle

Funding

  1. Agricultural Science and Technology Innovation Program in the Chinese Academy of Agricultural Sciences [ASTIP-IAS03, CAAS-ZDRW202102]
  2. China Agriculture Research System of MOF and MARA
  3. National Beef Cattle Industrial Technology System [CARS-37]
  4. Science and Technology Project of Inner Mongolia Autonomous Region [2020GG0210, KJXM2020002-01]

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Genome-wide association studies were used to identify SNPs and candidate genes related to carcass depth and hind leg circumference in Simmental beef cattle. Several potential SNPs and candidate genes, including CDKAL1 and E2F3, were identified, which can help breeders understand and improve meat yield.
Genome-wide association studies are a robust means of identifying candidate genes that regulate economically important traits in farm animals. The aim of this study is to identify single-nucleotide polymorphisms (SNPs) and candidate genes potentially related to carcass depth and hind leg circumference in Simmental beef cattle. We performed Illumina Bovine HD Bead-chip (similar to 670 k SNPs) and next-generation sequencing (similar to 12 million imputed SNPs) analyses of data from 1252 beef cattle, to which we applied a linear mixed model. Using a statistical threshold (p = 0.05/number of SNPs identified) and adopting a false discovery rate (FDR), we identified many putative SNPs on different bovine chromosomes. We identified 12 candidate genes potentially annotated with the markers identified, including CDKAL1 and E2F3, related to myogenesis and skeletal muscle development. The identification of such genes in Simmental beef cattle will help breeders to understand and improve related traits, such as meat yield.

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