1a. Objectives (from AD-416):
To perform genetic evaluations, genomewide association studies, and bioinformatic analyses to identify genomic regions associated with daughter pregnancy rate, fertilization ability, and early embryonic development in dairy cattle. To entify putative causal relationships among traits. To determine optimal strategies for including genomic information in analyses.
1b. Approach (from AD-416):
ARS will provide expertise in genetic evaluations, genomewide association studies, and bioinformatic analyses to identify genomic regions associated with daughter pregnancy rate and early embryonic development in dairy cattle. This information will be used by both parties to jointly identify putative causal relationships among traits and determine optimal strategies for including genomic information in analyses. The Cooperator will provide phenotypic measurements of early embryonic development, genotypes for about 500 dairy bulls using a candidate gene SNP chip, and expertise in bioinformatics and functional biology. The Cooperator will apply for funding through the USDA-AFRI grant program.
3. Progress Report:
The project is related to in-house objective 2 (develop a more accurate genomic evaluation system with advanced, efficient methods to combine pedigrees, genotypes, and phenotypes for all animals). A manuscript describing the identification of novel single nucleotide polymorphisms (SNPs) in genes associated with cow fertility has been accepted for publication in the journal BMC Genomics, and a second paper focusing on genes associated with response to in vitro fertilization and embryonic development has been submitted to the journal, Biology of Reproduction. Additional data are being collected with colleagues at the University of Florida to validate previously identified SNPs in a large population of dairy cows in a commercial setting. Computing hardware and software were purchased in April 2013 to support the research effort. In May 2013, the principal investigator attended the Health Data Conference sponsored by the International Committee for Animal Recording in Aarhus, Denmark. The conference focused on logistics, challenges, and benefits of health data recording as related to food chain quality, management, and breeding.