Published on Nov. 15, 2016

De novo assembly and comparison of whole genome consensus sequences for nine breeds of beef cattle

With the recent rise in re-sequencing efforts fueled by next-generation short read sequencing technologies, we have lost sight of the overarching goal of trying to understand what functions a genetic variant has at the molecular level, which is one of the main reasons we started sequencing genomes to begin with. Instead, immense focus has been placed on identifying SNPs that are associated with important phenotypes. These association studies have undoubtedly allowed forward progression of the industry through genetics through providing variants that can be assayed and selected for or against. However, the main limitation of these studies is they very rarely identify causal mutations, instead a SNP linked to the causal mutation is identified. To further enhance the genetic merit of beef cattle in the United States and improve efficiency and profitability of beef production, we need to elucidate and understand the panoply of genetic variation that exists across our most productive beef cattle breeds. The utilization of this knowledge will further genetic progress in animal health and production by improving the detection of causal variants underlying economically important phenotypes. Further, the assembly  of whole genome sequences to commence the discovery of these variants will provide a novel resource to the bovine genomic community, which is currently restricted by the inadequacy of whole genome reference sequences with which to compare re-sequenced animals. These efforts are guaranteed to greatly expand our current knowledge of genetic variation and improve association studies to assist in determining causal variants and providing more valuable and accurate genomic predictions for beef cattle breeders.