Identification of Single Nucleotide Polymorphism from Indian Bubalus bubalis through Targeted Sequence Capture

Bubalus bubalis (water buffalo) is an agro-economically important livestock species due to its multipurpose use in India and other Asian countries. The aim of this study was to identify single nucleotide polymorphisms (SNPs) from buffalo genome. Genomic DNA was isolated from 24 blood samples of three Indian buffalo breeds and subjected to targeted pyrosequencing, followed by variant calling and annotation. Target probes for enrichment were designed from exome and 5' and 3' untranslated regions of cattle genome. By targeted pyro-sequencing and variant calling from 3.92 Gb data, 923,964 high-quality SNPs were identified. Many SNPs were identified in regulatory regions, leading to conformational changes in factor-binding sites, which play a role in gene expression as in the case of LPL gene from low-milkproducing samples. Gene ontology (GO) enrichment and clustering, resulted in the enrichment of GO terms involved in milk production and transport, and fertility-related categories. Around 75% of SNPs were located on cattle quantitative trait loci, supporting trait-wise sample collection approach. Further, PCA analysis from the identified SNPs also supported sample selection strategy based on contrasting trait performance.