The development of genome-wide single nucleotide polymorphisms in blue wildebeest using the DArTseq platform.

Blue wildebeest (Connochaetes taurinus taurinus) are economically important antelope that are widely utilised in the South African wildlife industry. However, very few genomic resources are available for blue wildebeest that can assist in breeding management and facilitate research. This study aimed to develop a set of genome-wide single nucleotide polymorphism (SNP) markers for blue wildebeest. The DArTseq genotyping platform, commonly used in polyploid plant species, was selected for SNP discovery. A limited number of published articles have described the use of the DArTseq platform in animals and, therefore, this study also provided a unique opportunity to assess the performance of the DArTseq platform in an animal species. A total of 20,563 SNPs, each located within a 69 bp sequence, were generated. The developed SNP markers had a high average scoring reproducibility (>99%) and a low percentage missing data (~9.21%) compared to other reduced representation sequencing approaches that have been used in animal studies. Furthermore, the number of candidate SNPs per nucleotide position decreased towards the 3' end of sequence reads, and the ratio of transitions (Ts) to transversions (Tv) remained similar for each read position. These observations indicate that there was no read position bias, such as the identification of false SNPs due to low sequencing quality, towards the tail-end of sequencing reads. The DArTseq platform was also successful in identifying a large number of informative SNPs with desirable polymorphism parameters such as a high minor allele frequency (MAF). The Bos taurus genome was used for the in silico mapping of the marker sequences and a total of 6020 (29.28%) sequences were successfully mapped against the bovine genome. The marker sequences mapped to all of the bovine chromosomes establishing the genome-wide distribution of the SNPs. Moreover, the high observed Ts:Tv ratio (2.84:1) indicate that the DArTseq platform targeted gene-rich regions of the blue wildebeest genome. Finally, functional annotation of the marker sequences revealed a wide range of different putative functions indicating that these SNP markers can be useful in functional gene studies. The DArTseq platform, therefore, represents a high-throughput, robust and cost-effective genotyping platform, which may find adoption in several other African antelope and animal species.

Genetic diversity of Afrikaner cattle in southern Africa.

The Afrikaner is an indigenous South African breed of "Sanga" type beef cattle along with breeds such as the Drakensberger and Nguni. Six composite breeds have been developed from crosses with the Afrikaner. Additionally, Afrikaner has been the base from which exotic breeds were established in South Africa through backcrossing. The study examined genetic diversity of Afrikaner cattle by genotyping 1257 animals from 27 herds in different geographic areas of South Africa and Namibia using 11 microsatellite markers. Multiple-locus assignment, performed using the Bayesian clustering algorithm of STRUCTURE, revealed three underlying genotypic groups. These groups were not geographically localized. Across herds and markers, the proportion of unbiased heterozygosity ranged from 0.49 to 0.72 averaging 0.57; mean number of alleles per locus ranged from 3.18 to 7.09, averaging 4.81; and allelic richness ranged from 2.35 to 3.38, averaging 2.67. It is concluded that a low inbreeding level of 2.7% and a moderate to high degree of variation still persists within the Afrikaner cattle breed, despite the recent decline in numbers of animals.

The use of short tandem repeat polymorphisms for monitoring chimerism following bone marrow transplantation: a short report.

Following immunohaematopoietic stem cell transplantation, it is of importance to determine whether the new blood forming system is of recipient or donor origin and such phenotypic characterisation is called chimerism analysis. This is a dynamic process, which may be complete, mixed or split between compartments and in this way, plays an increasingly important role in predicting outcome for engraftment, rejection or residual disease predicating the need for pre-emptive immunotherapy. Based on recent workshop recommendations, peripheral blood cells have been used in the short tandem repeat (STR) assay to serially characterise the haematologic course and so evaluate the usefulness of this system. Forty-six patients from a single centre were followed serially for periods ranging between 3 and 60 months. The analysis was initially performed using the Applied Biosystems Profiler Plus Kit; currently, the Promega Powerplex 16 system is used. The overlap between the two assays has allowed for continuous comparison. The initial analysis was performed at 14 days post-transplant and repeated monthly. Stored DNA from the patient and donor was used to establish the pre-transplant profile. All post-transplant analyses were performed using peripheral blood. The results obtained were expressed as a percentage of the donor profile. To illustrate the ability of this technology, three representative profiles are described. In the first, stable engraftment is confirmed at 20 months with only donor pattern present. The second is intermediate, and while the patient is clinically disease free, there exists stable mixed chimerism at about 75% of donor cells. The third patient initially engrafted but the reappearance of recipient alleles presaged a haematological relapse; the latter is an indication for salvage with donor lymphocyte infusion and here this assay will be used to show the effectiveness of the intervention. These preliminary results show this to be a useful additional tool in monitoring post-transplant engraftment. As a basis for pro-active therapy, a larger study integrating the results of haematological and cytogenetic markers is planned.