Applications of High-Throughput Sequencing for Fertility, Demography, and Genome Improvement

Abstract Text: New sequencing technologies have allowed researchers to tackle new problems and revisit old ones. At the University of Missouri we are using Illumina sequencing to identify loss-of-function mutations in 150 influential artificial insemination sires. We are sequencing each bull to high coverage (~30X) to accurately call homozygous and heterozygous genotypes within individual animals. Using this information we can identify variants that are predicted to have deleterious effects on gene products or are never observed as homozygotes. Many of these will be embryonic lethals which are reducing fertility rates in beef cattle.  We are also using whole-genome sequences to infer the effective population sizes of cattle over time. This will allow us to identify the changes that have altered the genomes within and among breeds of cattle. Perhaps most importantly, we are using new sequencing technologies to improve the assembly for the cattle reference genome. In addition to existing Sanger data, the bovine genomics community is generating Illumina and PacBio data that will be used to close gaps and more accurately scaffold the reference genome sequence. Each sequencing technology has its own strengths and weaknesses. By combining different sequencing technologies we harness a technology’s strength and use complimentary technologies to overcome its weaknesses. We are also working to annotate regulatory elements throughout the bovine genome, as nearly three quarters of causal mutations for quantitative traits seem to lie within noncoding regulatory elements. These improvements will allow researchers to more easily identify important variants.

Keywords: sequencing, genome, assembly