1a. Objectives (from AD-416)
ARS and the Cooperator are interested in investigating the commercial application of whole genome selection in Jersey cattle. This investigation is essential for gauging if genome enhanced predictions of genetic merit are as or more reliable than current statistical-based methods of estimating genetic merit; ultimately allowing the Cooperator to accelerate selection for genetic improvement and intensify outputs in current production scenarios. Our Project Plan has two objectives: 1) collect DNA samples and generate ~50,000 SNP marker genotypes from each of more than 700 elite animals in the Jersey herdbook; and 2) analyze this data through the whole genome selection analysis pipeline to generate genome enhanced predictions of genetic merit. The Cooperator has the funding and access to important animals of the breed through its membership and partnership with members of the National Association of Animal Breeders. ARS has the expertise and facilities to process these samples across the BovineSNP50 genotyping assay and generate SNP marker genotypes for analysis of whole genome selection.
1b. Approach (from AD-416)
The project will be managed jointly between ARS and the Cooperator. The Cooperator will evaluate its animal registry and lead collection of DNA from appropriate animals for genotyping. ARS will generate and analyze the SNP marker genotypes using BovineSNP50 data. These resources will provide the data needed to generate genome enhanced predictions of genetic merit for the Jersey breed; thus aiding selection of superior animals by the Coopeerator for its member and partners practicing selection for genetic improvement. ARS will analyze, store, and distribute genotypic information (as agreed upon with the Cooperator) that will be used for whole genome selection studies. Both ARS and the Cooperator will jointly work together to collect and curate DNA samples. Also, as needed, both parties will educate breeders and members in the process of whole genome selection. All of these activities will be considered true collaborations and thus, by definition, each party will be considered to have provided a true intellectual contribution consistent with authorship.
3. Progress Report
ARS scientists have met the objectives and Jersey cattle are now a part of the “official” genetic evaluations based on genetic predictions using genome-wide marker data. ARS scientists have now extended analysis of this data to refine the map positions of regions of the genome that are potentially lethal for embryo/fetus development when present in 2 copies (homozygous). Next-generation sequencing libraries have been prepared from elite sires carrying this haplotype affecting fertility on Chr 15 to look for specific causative variants or reduced haplotypes. Monitoring activities associated with this project include email correspondence, face-to face meetings and conference calls. This research supports an objective of its related in-house project to use genotypic data and resulting bovine haplotype map to enhance genetic improvement in dairy cattle through development and implementation of whole genome selection and enhanced parentage verification approaches (obj. #2) and to characterize conserved genome elements and identify functional genetic variation (obj #3).