Project Number: 8042-31000-112-000-D
Project Type: In-House Appropriated
Start Date: Jul 24, 2022
End Date: Jul 23, 2027
Objective 1: Develop biological resources and computational tools to enhance the representation and annotation characterization of dairy breed-specific bovine and other genomes. Sub-objective 1.A: Improve dairy breed-specific bovine and other genome assemblies for pangenome representation. Sub-objective 1.B: SNP and CNV mapping in cattle and other ruminants. Sub-objective 1.C: Evaluate digestive tract function and identify gastrointestinal microorganism effects on nutrient digestibility, milk production capacity, nutrient use efficiency, and health in dairy cattle. Objective 2: Apply novel tools to utilize genotypic and phenotypic data to enhance genetic improvement in ruminant production systems. Sub-objective 2.A: Continue work on community-based breeding programs and develop imputation pipeline and data in goats. Sub-objective 2.B: Characterize and localize within and across breed measures of dominance as observed in inbreeding depression and heterosis. Objective 3: Characterize functional genetic and epigenetic variations for improved fertility, growth, health, production, reproduction, and environmental sustainability of ruminants. Sub-objective 3.A: Epigenome-wide Association Study based on DNA methylation. Sub-objective 3.B: FarmGTEx for goats.
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. 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 Genomes, HapMap, 1000 Bull Genomes, FAANG, Bovien Pangenome, and FarmGTEx projects, and genotypic data derived from the Council on Dairy Cattle Breeding (CDCB) genome-enhanced genetic evaluations for North American dairy cattle.