Preliminary Results on the Genotyping of Philippine Swamp and Riverine Buffaloes Using the Affymetrix Axiom® Buffalo Genotyping Array

Preliminary results on the genotyping of Philippine swamp and riverine buffaloes using the Affymetrix Axiom® Buffalo Genotyping Array

Ester B. Flores1, Jesus Rommel V. Herrera1, Laila M. Labonite*1, Julius van der Werf2 and Cedric Gondro2

1Philippine Carabao Center, Nueva Ecija, Philippines

2University of New England School of Environmental and Rural Science, Armidale, New South Wales, Australia

The Philippine Carabao Center (PCC) has put into place a genetic evaluation of dairy and swamp buffaloes through the use of estimated breeding values (EBVs). The availability of Affymetrix Axiom® Buffalo Genotyping Array allows further refining of the genetic evaluation through possible establishment of genomic breeding values (GEBVs). As an initial effort in the establishment of GEBVs, this study aims to genotype the Philippine swamp and riverine buffaloes using the Affymetrix Axiom® Buffalo Genotyping Array. Genomic DNA of 960 buffalo samples were extracted and purified according to Affymetrix requirement. Genotyping of the purified samples was done using the 90,000 buffalo SNP array. Analysis of the results was performed through the Affymetrix Genotyping Console™ Software and Affymetrix SNPolisher™ package available online. A total of 917 samples or 95.5% of the samples submitted passed the sample QC threshold and proceeded to the genotyping process. Further, the average cluster call rate and the average sample reproducibility were 99.5% and 99.9%, respectively. Of the 90,000 SNPs in the array, 74.53% were polymorphic high-resolution, 1.10% were no minor homozygous and 0.01% were hemizygous. Further, the riverine buffalo has higher polymorphic high-resolution percentage than the swamp buffalo, while for the percentage of no minor homozygous, the swamp buffalo is relatively higher than riverine. The principal component analysis also showed the population stratification of seven buffalo populations. These data will be used for genome wide association studies for milk and milk component traits, genomic selection and diversity studies.