Identification of Single Nucleotide Polymorphism from Indian <i>Bubalus bubalis</i> through Targeted Sequence Capture

Abstract

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.

Uncovering genomic diversity and trait annotations in Garole sheep for improvement

“…Annotation of these SNPs revealed their distribution across various genomic regions, with a notable proportion located within transcript regions. The observed transition-to-transversion (Ts/Tv) ratio of 2.43 per sample on average indicated a higher frequency of G>A and C>T substitutions, consistent with previous findings in related species (Patel et al, 2017) [15] . Among the annotated SNPs, 760 were associated with 175 candidate genes implicated in production traits, particularly milk composition and yield.…”

“…Retained SNPs obtained of Garole were annotated using SnpEff v4.4 (Cingolani et al, 2012) [15] . Then, the annotated SNPs presented within the genes were screened on literature and also in animal QTL (Quantitative Trait Loci) database v 2019 (www.animalgenome.org) for identifying candidate genes associated with production traits.…”

Genome-wide characterisation of regions under intense selection based on runs of homozygosity in Charolais cattle

“…The FAF2 gene was identified in BTA7 (39.41 -39.47 Mb). Based on Patel et al (2017), this gene is associated with some reproductive function in cattle. Gene NLRP3 involved in the innate immune system was also observed on BTA7 (42.18 -42.23) (Mallikarjunappa et al, 2018).…”

Molecular portrait of squamous cell carcinoma of the bovine horn evaluated by high-throughput targeted exome sequencing: a preliminary report

“…Overall, 30,916,291 bases (30.9 Mb) were specifically included in design. The probe design and details are mentioned in our previous studies [ 15 , 16 ]. The probes were used to enrich targets by using Roche NimbleGen SeqCap EZ Libraries capture as per manufacturer’s protocol.…”