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ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » Research » Research Project #443341

Research Project: Validate Causative Mutations in Agriculturally-Important Vertebrates

Location: Plant Genetics Research

Project Number: 5070-31320-001-000-D
Project Type: In-House Appropriated

Start Date: Nov 30, 2022
End Date: Nov 29, 2027

Objective 1. Using gene editing techniques, systematically alter the DNA sequence predicted to cause beneficial changes in pig production and to test these changes in vitro and, where warranted, in vivo. Sub-objective 1.A. Establish porcine cell lines that will be important for phenotyping various agriculture traits while identifying candidate gene loci to evaluate effects of variants on these cell lines. Sub-objective 1.B. Characterize the range of phenomena of known variants identified by porcine QTL data, differentially expressed gene analysis, and known variants from other species in gene edited cells. Sub-objective 1.C. Produce genetically modified pigs to validate in vivo effects of improved alleles. Objective 2. Test the effects of sequence modifications for on- and off-target effects. Sub-objective 2.A. Explore the application of Cas9 inhibitors or new editing systems to reduce off-site cleavage events. Sub-objective 2.B. Modification of guide RNA to diminish unintended cleavage events. Objective 3. Develop efficient methods for gene modification of poultry. Sub-objective 3.A. Establish methods for producing genetically modified poultry. Sub-objective 3.B. Identify candidate genes that are associated with beneficial changes in poultry production and test genetic modification(s) in vitro to characterize variant effects on cellular phenotypes. Sub-objective 3.C. Produce genetically modified poultry to validate in vivo effects of improved alleles.

By using gene editing techniques, we will systematically alter DNA sequences predicted to cause beneficial changes in pig and poultry production and test these changes in vitro and in vivo where warranted. In addition, we will comprehensively test effects of sequence modifications for on- and off-target effects. Gene editing and other technologies will be used to systematically alter DNA sequence in ways that were predicted to improve traits to (1) determine whether the sequence variation is causal for the change in the trait, and (2) determine any other changes in traits that might simultaneously occur through pleiotropy effects. The research will focus on both pigs and poultry, and the goal will be to develop pigs and poultry with improved traits of interest, without having deleterious effects on animal production. Simultaneously, we will work toward understanding relationships between genes and various physiological functions within both pigs and poultry. Finally, we will refine editing methods for poultry production to increase efficiency of this process. Together, the information gleaned from this project will facilitate genetic gain, improve animal welfare, increase sustainability, and directly improve production efficiency of swine and poultry and will likely be valuable to humans and other livestock species.