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- W2885593292 abstract "Afrikaner, Drakensberger, and Nguni are theSouth African (SA) landraces that played major roles in the social,cultural and economic history of SA. These breeds are valuablegenetic resources for beef production and limited information isavailable for these breeds at the genome level. The aim of thisstudy was to perform SNP discovery in these three breeds usingwhole genome sequencing. Ninety cattle representing the threebreeds were used to identify more about 17.6 M putative variantsincluding SNPs and Indels. DNA was extracted from blood and hairsamples, quantified and prepared at 50ng/?l concentration forsequencing at the Agricultural Research Council BiotechnologyPlatform using an Illumina HiSeq 2000. The fastq files were used tocall the variants using the Genome Analysis Tool Kit. A total of4,369,879 (16% of the total SNPs) were identified as novel.Annotation of these variants classified them into functionalcategories. Within the coding regions, 43% of the SNPs werenonsynonymous substitutions that encode for alternate amino acids.Functional enrichment analysis of novel SNPs identified significantnumber of genes (p < 0.001) that were located within 5% of 1,481100kb windows. Gene ontology terms identified genes such as MLANAand SYT10 that have been associated with coat colour and sense ofsmell in mouse, respectively, and the ADAMS3 gene has beenassociated with fertility in cattle. Furthermore, whole genomescreening detected 688 candidate selective sweeps (ZHp Z-scores ?-4) across all three breeds, of which 223 regions were assigned asbeing putative selective sweeps (ZHp scores ? -5). We alsoidentified 96 regions with extremely low ZHp Z-scores (? -6) inAfrikaner and Nguni. Several genes such as KIT and MITF that havebeen associated with skin pigmentation in cattle, and CACNA1C,which has been associated biopolar disorder in human wereidentified in these regions. Breed-specific SNPs (2,272,667) wereidentified across the breeds and only 186 of these SNPs wereidentified as putative breed-specific SNPs. These SNPs were furthertested for their ability to assign individuals to a breed and needfurther validation. This study provides the first analysis ofsequence data to discover SNPs in indigenous SA cattle breeds.These results provide insight into the genetic composition of thebreeds and offer the potential for further applications in theirgenetic improvement." @default.
- W2885593292 created "2018-08-22" @default.
- W2885593292 creator A5040625107 @default.
- W2885593292 date "2018-01-01" @default.
- W2885593292 modified "2023-09-27" @default.
- W2885593292 title "Genome-wide marker discovery in three South African indigenous cattle breeds (Afrikaner Drakensberger and Nguni) using next generation sequencing" @default.
- W2885593292 hasPublicationYear "2018" @default.
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