Project Number: 5090-31000-026-07-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Jul 1, 2015
End Date: Dec 31, 2018
ARS will use Cooperator's "a posteriori" granddaughter design to identify important qualitative trait loci affecting productive traits in Holstein cattle. After these important trait loci have been identified, 30 Holstein bulls with more than 100 daughters will be selected for Illumina DNA sequencing. Sequence variants identified from the resulting DNA sequencing will be associated with the trait loci by concordance with predictions made by the "a posteriori" granddaughter design.
Cooperator will use a novel method of haplotype tracking with family information in order to identify genomic regions that are likely to influence productive traits. This method specifically targets bulls with high numbers of daughters in order to obtain statistically significant differences in measured phenotypes resulting from the carriers of the haplotypes. After the discovery of the haplotypes, 30 bulls that are predicted to carry the beneficial haplotype will be DNA sequenced using the Illumina HiSeq platform. The discovery of the haplotypes in each animal will allow for a targeted analysis of sequence data and will allow for statistical concordance to verify the causative variants in each sample. After candidate causative variants are discovered, 1,000 animals will be genotyped in Israel and the U.S. in order to confirm variant concordance with the beneficial phenotype on a population scale.