Objective:
Technology will be developed for improving genomic selection of dairy cattle. The Cooperator has capacity to conduct high throughput DNA sequencing, and to assist ARS efforts in whole genome haplotype reconstruction and haplotype tracking.

Approach:
Whole genome sequencing of four of the highest impact Holstein bulls in North America will be used to identify single nucleotide polymorphisms (SNPs), copy number variants (CNV), insertions and deletions (indels) and haplotypes affecting traits of economic importance to the dairy industry. The Cooperator will take the lead role in generating at least 30x genome coverage through paired-end sequencing using Illumina technology. Complete haplotype reconstructions will be performed for each bull using a combination of sequence information from first order relatives among the bulls chosen for sequencing and high throughput SNP genotyping from high density SNP assays of progeny tested sons in the CDDR collection. ARS will provide SNP genotype information and long insert mate pair sequences as needed to aid haplotype reconstruction. Haplotypes originating from the four bulls will be identified in the current bull and cow populations using high throughput genotyping, and chromosome segments (CS) that change in frequency due to artificial selection will be determined. Identification of such CS will enable more accurate genomic selection for economically important traits. Within these CS, candidate polymorphisms responsible for traits under selection originating from the four bulls can then identified for even greater precision in genomic selection. Cooperator will perform high throughput DNA sequencing, SNP detection, haplotype reconstruction and tracking through multi-generation pedigrees. ARS will perform high throughput DNA sequencing, SNP detection, mate pair library construction, and detection of signature of selection as part of this research.