Project Number: 1245-31000-104-00
Project Type: Appropriated

Start Date: Jul 24, 2012
End Date: Jul 23, 2017

Objective:
The long-term objective of this project is to enhance selection in target ruminant populations by integrating traditional, quantitative-based selection methods with DNA marker-based tools. To successfully meet this objective and better understand the underlying gene networks affecting phenotypic variation, basic research to characterize both genome structure and activity must be done as a complementary effort. Objective 1: Develop biological resources and computational tools to enhance characterization of ruminant genomes. De novo reference genome assemblies will be developed for Zebu cattle (Bos indicus), goat (Capra hircus), and water buffalo (Bos bubalis). In addition, improvements will be made to the existing reference assembly for Bos taurus cattle. These reference genome resources are essential for discovery of single nucleotide polymorphisms (SNP) and copy number variation (CNV) polymorphisms commonly segregating in target populations. Objective 2: Utilize genotypic data to enhance genetic improvement of food animals across a spectrum of ruminant production systems. Objective 3: Characterize functional genetic variation for improved fertility and environmental sustainability of ruminants.

Approach:
Completion of our objectives is expected, in the short term, to improve methods of genome-wide selection in the U.S. dairy industry as well as initiate 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 resequencing and comparative genome alignment and annotation, quantitative genetics, and gene expression analyses, 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 Genome and HapMap projects and genotypic data derived from the official USDA genome enhanced genetic evaluations for NA dairy cattle.