Project Number: 1265-31000-098-09
Project Type: Reimbursable

Start Date: Apr 01, 2008
End Date: Dec 21, 2010

Objective:
We will generate a map of shared genetic variation between US and Pakistani dairy breeds and water buffalo based on 50,000 SNP marker genotypes and complete partial genome resequencing of Sahiwal and Dhanni cattle and 12X whole genome sequencing of Nili-Ravi buffalos to generate additional SNP resources for genotyping. This will be used to develop SNP assays and statistical analyses for whole genome association and genome selection studies of native dairy breeds and buffalo.

Approach:
Analysis will include comparative mapping of SNPs across bovine and water buffalo samples to characterize genic and intergenic polymorphisms maintained across species. Sequence information will be generated on an Illumina GA. For a modest cost, we expect to generate 24X coverage of 1% of the Bos indicus genome from pooled DNA samples. We also expect to generate a 12X coverage from random reads of the entire water buffalo genome using two different individuals from the Nili-Ravi breed. The 36 billion base pairs of information will be in the form of 35 bp tags that represent paired end reads of a known genomic DNA fragment size. This position information will be incorporated into the assembly of the water buffalo genome, and will provide necessary information to help discern between genetic diversity at a single locus and genome duplication events. Based on the number SNP discovered in objective 2, SNP assays (minimum 10,000 SNP) will be developed for each species. Approximately 500 assays for both Bos indicus and water buffalo will be delivered to Pakistan for processing. These data will be used to generate genome wide SNP data for whole genome association studies and investigations into whole genome selection.