Detection of Selection Signatures in some of the Water Buffaloes across the World

Abstract

In order to identify the selection signatures of the water buffalos across the world, the genomic information of 165 buffalos which belonged to 15 genetic groups of buffaloes was used. The genomic information was obtained from Dryad (doi:10.5061/dryad.h0cc7). The quality control and data filtration were performed using PLINK1.9 software. The genetic clustering and the population structure was examined using the GenABEL and Admixture1.23 software's, respectively. The results of principal component analysis showed that the examined populations could be classified into 4 separate categories. The results of population structure analysis confirmed the results of principal components analysis. The signatures of selection were searched with the help of iHS statistics using the ReHH software. Moreover, the unbiased F_ST (θ) estimator was calculated using the Plink1.9 software. The 25 and 24 genomic regions, which passed the unbiased F_ST and iHS statistics thresholds, were identified as selection cues, respectively. Selected regions were aligned on the bovine genome and 411 genes related to selected regions were identified. Of all the identified genes, 53 genes related to olfactory receptors (OR), 51 genes somehow involved in cell membrane structure and animal immunity against pathogens including initiate and regulate the immune response. The identified QTLs related to detected regions, were associated with milk production, milk somatic cells, fertility, ion disease, calving and growth. There is an acceptable consistent between the milk and fat production genes and the related identified QTLs.