Location: Genetics and Animal Breeding
Project Number: 3040-31000-104-021-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Jul 1, 2024
End Date: Jun 30, 2027
Objective:
The objective of the proposal is to create a pangenome representation of the pig genome, to replace the single-animal reference assembly used by the community since 2016. Recent advances in sequencing technology support much higher quality/accuracy genome assemblies and the ARS investigators are leaders in the field of generating the sequence data and drafting genome assemblies. A total of 72 haplotype-resolved assemblies will be created in the proposal from the most highly-used commercial pig breeds in the U.S., supporting creation of a pangenome representation by our collaborators. This pangenome will be used in place of the prior reference for defining genetic variation between individual animals in order to identify superior genetics and enhance breeding programs.
Approach:
We will use our expertise in generating haplotype-resolved assemblies from two samples provided by MSU; Landrace x Yorkshire and Duroc x Hampshire crosses that represent the most common animals used in U.S. swine production. The assemblies will be created using a pedigree structure where sequence from the parents of the crosses is used to resolve the parental haplotypes. We will use SciNet resources and various software on Ceres and Atlas HPC to assemble these genomes. The use of male individuals will provide the first complete sex chromosome assemblies for commercial swine.
