Genome-wide single nucleotide polymorphism (SNP) identification in Red Sindhi cattle (Bos indicus) using whole-genome sequencing
DOI:
https://doi.org/10.5281/zenodo.22848102Keywords:
Red Sindhi cattle; Bos indicus; whole-genome sequencing; SNPs; genomic variation; genetic diversityAbstract
Red Sindhi cattle (Bos indicus) is an important indigenous breed with characteristics of adaptability, survival in tropical conditions, and disease resistance. Although they are agriculturally important, this breed has far less genomic information than taurine cattle. In the current study, the researchers sought to identify all single-nucleotide polymorphisms (SNPs) in the genome of Red Sindhi cattle using whole-genome sequencing (WGS) with next-generation sequencing (NGS). We performed paired-end whole-genome sequencing on genomic DNA from Red Sindhi cattle. The reads were sequenced and mapped to the Bos taurus reference genome (ARS-UCD1.2) using the BWA-MEM algorithm, and then the variants were called with the FreeBayes pipeline. We selected high-confidence variants based on stringent quality-filtering criteria. We finally obtained a filtered set of 5,932 high-confidence SNPs spread across the bovine genome. The average sequencing depth ranged from 30 to 32×, which is sufficient for reliable variant detection and genotype calling. Many of the remaining variants were heterozygous, indicating allelic variation in the samples analysed. Analysis of chromosome distribution showed an uneven distribution of SNPs across chromosomes, with chromosomes X and 14 having a relatively greater number of SNPs. This study provides a preliminary genome-wide SNP resource for Red Sindhi cattle and a foundation for future population genomics, comparative genomics, and functional annotation studies in indigenous indicine cattle breeds. Further large-scale studies with broader population sampling and more sophisticated population genomics analyses are needed to fully describe the breed's allelic variation.
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