Low and high-density SNP genotyping assays are available for performing genome-wide analyses in cattle ( Matukumalli et al., 2009). These developments have also enabled the simultaneous estimation of SNP allele frequencies in a diverse range of reference populations ( Van Tassell et al., 2008). The development of next generation sequencing (NGS) technologies has enabled rapid and cost-effective generation of sequence data for SNP discovery in cattle ( Le Roex et al., 2012 Mullen et al., 2012). ![]() The information will play an important role in our efforts to understand the genetic history of our cattle and in designing appropriate breed improvement programmes. This study provides the first analysis of sequence data to discover SNPs in indigenous South African cattle breeds. Genes such as KIT and MITF that have been associated with skin pigmentation in cattle and CACNA1C, which has been associated with biopolar disorder in human, were identified in these regions. We also identified 96 regions with extremely low ZH p Z-scores (≤-6) in Afrikaner and Nguni. Further analysis of the variants detected 688 candidate selective sweeps (ZH p Z-scores ≤ -4) across all three breeds, of which 223 regions were assigned as being putative selective sweeps (ZH p scores ≤-5). Gene ontology terms identified genes such as MLANA, SYT10, and CDC42EP5 that have been associated with coat color in mouse, and ADAMS3, DNAJC3, and PAG5 genes have been associated with fertility in cattle. The study of distribution of SNP across the genome identified regions showing notable differences in the densities of SNPs among the breeds and highlighted many regions of functional significance. Within the coding regions, about 30% of the SNPs were non-synonymous substitutions that encode for alternate amino acids. Annotation of the identified variants classified them into functional categories. A total of 1,678,360 were identified as novel using Run 6 of 1000 Bull Genomes Project. The fastq files were used to call the variants using the Genome Analysis Tool Kit. DNA was extracted from blood and hair samples, quantified and prepared at 50 ng/μl concentration for sequencing at the Agricultural Research Council Biotechnology Platform using an Illumina HiSeq 2500. The objective of this study was to perform SNP discovery in three South African indigenous breeds (Afrikaner, Drakensberger, and Nguni) using whole genome sequencing. ![]() However, the majority of validated SNPs for which allele frequencies have been estimated are limited primarily to European breeds. Single nucleotide polymorphism arrays have created new possibilities for performing genome-wide studies to detect genomic regions harboring sequence variants that affect complex traits.
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