Design of a Buffalo SNP Panel

There is a considerable interest to enhance dairy production for buffalos in Asia and rest of the world. The importance of buffalo in helping provide economic security for developing economies by meeting growing demands for protein-based nutrition cannot be overstated. To exploit the inherent potential of dairy buffalo, we initiated development of genome-based resources that can be used to identify important selective variation in these species and develop DNA-based tools for genetic improvement. SNP discovery was performed using three methods: 1) k-mer hash error correction of Illumina reads during the genome assembly process of more than 100X sequence read depth generated from a Mediterranean, female water buffalo, 2) alignment of sequence contigs and Illumina paired end reads from 86 other animals representing 8 breeds and 2 subspecies of buffalo, and 3) alignment to the bovine genome with a consensus sequence derived representing the buffalo sequence. The expected sequence yield generated from this sampling should exceed 470X depth of genome coverage, and is composed of deep coverage (more than 12X) from 3 animals and 5X paired end coverage from 83 animals. This strategy of sequencing also allows for detection of copy number variation between animals. The results of this SNP discovery will be used to identify selective sweeps, establish a baseline for shared and unique diversity, and serve as a resource for high density SNP assay development.  A total of 16,675,440 SNP were discovered using strategy 3, and after filtering 5,800,477 SNP remained. A total of 90,000 SNP were then selected for the high density SNP assay. Preliminary results from genotypes of 1,063 samples indicated that 67,330 (75%) SNP varied in the population assayed. An additional 9229 (10%) SNP were monomorphic in the samples genotyped. The remaining SNP failed for a variety of reasons.