Gleaning Functional and Conservation Information From Water Buffalo Variant Data

Buffalo genome variants are currently available from a comparison against the bos taurus genome and a preliminary Buffalo genome draft. Because single nucleotide variants (SNVs) data have been mapped against the bos taurus genome, it is possible to annotate SNVs to genes and predict potential functional consequences using existing annotation software such as SIFT and Variant Effect Predictor. Determining the functional annotation of SNVs in the buffalo would be helpful in starting to define where potentially functional variants, underlying QTL, and gene associations occur in the genome. Besides characterizing functional changes of variants, it is also possible to look for conserved variants that segregate in both the buffalo and the cow. The discovered SNVs were filtered for being polymorphic in at least one breed and having at depth of coverage of at least 10x, resulting in 21,584,133 SNVs to be used for analysis. Finding ancestral alleles could be helpful in understanding where genetic variation has been maintained despite evolutionary divergence. Studying functional annotation and ancestral conservation of variants could help to better understand how swamp and river buffalo, and breeds within each of these subspecies, vary from each other at both the molecular and, possibly, phenotypic levels.