Project Number: 8042-31000-001-00-D
Project Type: In-House Appropriated
Start Date: Jul 24, 2017
End Date: Jul 23, 2022
Objective 1: Develop biological resources and computational tools to enhance characterization of breed-specific bovine and other genomes. De novo reference genome assemblies will be developed for dairy cattle breeds (Holstein and Jersey). In addition, improvements will be made to the existing, but suboptimal, reference assemblies for Bos taurus cattle, Zebu cattle (Bos indicus), and American bison (Bison bison). These reference genome resources are essential for discovery of single nucleotide polymorphisms (SNP) and copy number variation (CNV) polymorphisms segregating in target populations. Genome characterization will be done by state-of-the-art platforms using short- and long-read sequencing of selected animals. Candidate animals will be derived from those populations targeted for genome-based genetic improvement to enable development of novel tools for proper parent and breed composition identification. To complement these studies, epigenomic and metagenomic surveys will be explored to better define DNA methylation and ruminant microbiome, which in turn will improve overall annotation of genes, genetic variation, epigenetic variation and other sequence motifs affecting phenotype expression. Objective 2: Utilize genotypic data to enhance genetic improvement in ruminant production systems. This objective has two components. The first component identifies signatures of selection and evaluates the potential to develop community-based breeding programs based on population structure and management system limitations in goats. The second component requires the optimization and application of statistical methodologies to develop cheap low-density SNP panels that can be used to guide genetic improvement of production traits while maintaining variants enriched by natural selection during adaptation of local breeds to marginal production environments. Objective 3: Characterize functional genetic variation for improved fertility, growth, and environmental sustainability of ruminants. The third objective involves detection of genetic variation affecting fertility, growth and environmental sustainability during early embryonic development or adaptation to climate or disease using whole genome or exome resequencing. The resultant sequence information will be integrated with other database resources that provide basic information about gene expression activity and motif patterns to guide selection of positional candidate genes for further study and validation of functional annotation in ruminants. Sub-objectives for objectives 1,2 and 3 are listed in post plan under related documents.
Completion of our objectives is expected, in the short term, to improve genome-wide selection in the U.S. dairy industry as well as facilitate new genome-enhanced breeding strategies to bring economic and genetic stability to various ruminant value chains in developing nations. Ultimately, longer term objectives to identify and understand how causative genetic variation affects livestock biology will require a combination of genome sequencing and comparative genomics, quantitative genetics, epigenomics and metagenomics, all of which are components of this project plan and areas of expertise in our group. Efforts to characterize genome activity and structural conservation/variation are an extension of our current research program in applied genomics. This project plan completely leverages the resources derived from the Bovine and Caprine Genomes, HapMap, 1000 Bull Genomes, ADAPTmap, and FAANG projects, and genotypic data derived from the Council on Dairy Cattle Breeding (CDCB) genome-enhanced genetic evaluations for North American dairy cattle and African Goat Improvement Network under the Feed the Future Initiative.