Location: Genetics and Animal Breeding
Project Number: 3040-31000-099-000-D
Project Type: In-House Appropriated
Start Date: Nov 21, 2017
End Date: Oct 31, 2022
Objective 1: Utilize next-generation sequencing technologies to improve the contiguity of the swine genome assembly and better characterize genomic variation in pigs. Subobjective 1.A: Utilize segregation analysis to improve the porcine genome assembly. Subobjective 1.B: Develop more comprehensive gene models for the swine genome. Subobjective 1.C: Develop an electronic warehouse of genomic variants that can be utilized by the swine genomics research community. Objective 2: Develop genotyping products for commercial swine producers to increase the efficiency of swine production. Subobjective 2.A: Identify predictive genetic markers for traits associated with production efficiency in commercial swine populations. Subobjective 2.B: Develop strategies for inclusion of predictive markers in selection programs.
The principal goals of this project are to enhance our understanding of the biological processes important to swine production and provide the U.S. swine industry with genetic tools that will ensure that it remains the global leader in providing safe, nutritious, and economic pork products. The swine industry has been faced with significant challenges, many of which revolve around the production and performance of feeder pigs. The environment in which females are housed is continually evolving, and the increasing cost of feed has resulted in continuous shifts in the utilization of feed stuffs. Each new challenge requires an assessment of potential solutions. Genetic selection can be used to address many production issues. If DNA variants associated with changes in phenotype can be identified, then marker assisted selection can be implemented to expedite genetic progress. Predictive genetic markers need to be transferred to commercial entities that will rapidly evaluate and adopt them. The increasing improvements to the porcine genome, better annotations of genes from model organisms, and enhanced bioinformatics technologies provide researchers with the necessary tools to identify functional genetic variants. Objective 1 focuses on improving the porcine genome assembly and detecting polymorphisms from data generated by next-generation sequencing. Objective 2 will strive to effectively transfer the results of the research from Objective 1 to producers. Development of marker panels along with economical genotyping platforms will be essential. Our research will focus on the evaluation of genetic markers based on their predicted effects on gene products to discover causal genetic variants of phenotypic variation. This will lead to the development of marker panels and economical genotyping platforms for industry applications.