Browsing by Author "Sandenbergh, L."

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    The adaption of the South Africa sheep industry to new trends in animal breeding and genetics : a review
    (South African Society for Animal Science, 2014-10-11) Cloete, S. W. P. (Schalk Willem Petrus van der Merwe); Olivier, J. J.; Sandenbergh, L.; Snyman, M. A.
    The history of sheep breeding research in South Africa can be divided roughly into four eras, namely the research and development phase, the commencement of recording and evaluation, the expansion of recording schemes, and, most recently, the adaptation of schemes to international benchmarks. The most recent era has presented scientists with the greatest challenges, namely the inclusion of genomic breeding values in routine sheep recording and of disease-resistance traits during routine evaluation. The establishment of reference populations for the major South African sheep breeds to estimate genomic breeding values is an immediate challenge. This process may be facilitated by a number of genetic resource flocks that are phenotyped for traits that are not routinely recorded in the national evaluation. A limited number of these animals are also genotyped. There is strong evidence that resistance of sheep to external and internal parasites is heritable, and may be improved by purposeful selection. Efforts should be concentrated on the inclusion of disease resistance traits in national analyses where appropriate. However, seen against the background that South African investment in research is appreciably less than in developed countries, lack of funding and high-capacity manpower may impede rapid progress. There thus seem to be many challenges for future generations of sheep breeding scientists.
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    Evaluation of the OvineSNP50 chip for use in four South African sheep breeds : short communication
    (South African Society for Animal Science, 2016) Sandenbergh, L.; Cloete, S. W. P. (Schalk Willem Petrus van der Merwe); Roodt-Wilding, R.; Snyman, M. A.; Bester-Van Der Merwe, A. E.
    Relatively rapid and cost-effective genotyping using the OvineSNP50 chip holds great promise for the South African sheep industry and research partners. However, SNP ascertainment bias may influence inferences from the genotyping results of South African sheep breeds. Therefore, samples from Dorper, Namaqua Afrikaner (NA), South African Merino (SA Merino) and South African Mutton Merino (SAMM) were genotyped to determine the utility of the OvineSNP50 chip for these important South African sheep breeds. After quality control measures had been implemented, 85 SA Merino, 20 Dorper, 20 NA and 19 SAMM samples remained, with an average call rate of 99.72%. A total of 49 517 (91.30%) SNPs on the chip met quality control measures and were included in downstream analyses. The NA had the fewest polymorphic loci, 69.20%, while the SAMM, Dorper and SA Merino had between 81.16% and 86.85% polymorphic loci. Most loci of the SA Merino, Dorper and SAMM had a MAF greater than or equal to 0.3. In contrast, the NA exhibited a large number of rare alleles (MAF < 0.1) and a uniform distribution of other loci across the MAF range (0.1 < MAF ≤ 0.5). The NA exhibited the least genetic diversity and had the greatest inbreeding coefficient among the four breeds. The results of the Dorper, SA Merino, and SAMM compare favourably with those of international breeds and thus demonstrate the utility of the OvineSNP50 chip for these breeds. Effects of SNP ascertainment bias, however, could be seen in the number of non-polymorphic loci and MAF distribution of the three commercial breeds in comparison with those of the NA. The implementation of methods to reduce the effect of SNP ascertainment bias and to ensure unbiased interpretation of genotype results should therefore be considered for future studies using OvineSNP50 chip genotype results.
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    Preliminary genome-wide association study for wet-dry phenotype in smallholder ovine populations in South Africa
    (South African Society for Animal Science, 2017-04-10) Molotsi, A. H.; Taylor, J. F.; Cloete, S. W. P. (Schalk Willem Petrus van der Merwe); Muchadeyi, F.; Decker, J. E.; Sandenbergh, L.; Dzama, K.
    The aim of this study was to identify single nucleotide polymorphisms (SNPs) associated with genomic region underlying variation in the binomial reproductive trait ‘wet-dry’ in sheep. The wet-dry phenotype was used to represent the reproductive status of the ewes, divided into two categories, dry (ewes that did not lamb or that lost a lamb) and wet (ewes that had lambed and had at least one suckling lamb). Wet-dry records were obtained from smallholder farmers (n = 176) and Nortier Research Farm (n = 131) for the 2014 breeding season. Ages of the ewes ranged from 1 year to 6+ years. Data from 307 individuals were analysed, of which 172 Dorpers and 4 White Dorpers were from smallholder sheep flocks and 48 Dorpers, 46 Namaqua Afrikaners, 26 South African Mutton Merinos, 4 South African Mutton Merino x Dorper and 7 Dorper x South African Mutton Merino crossbreds were from the research farm. A logistic regression model was fitted to adjust the data for the fixed effects of farm, breed, and age of the ewe and weight at mating as a covariate. Linkage disequilibrium (LD) and inbreeding coefficient were estimated using PLINK. Association analysis was performed using the genome-wide efficient mixed-model association package (GEMMA) to determine whether any significant SNPs were associated with the wet-dry reproductive trait. The wet-dry phenotype differed significantly between the smallholder (0.63 ± 0.04) and research farm flocks (0.79 ± 0.04). Genome-wide LD across all populations was r2 = 0.36. Dorpers from the smallholder flock exhibited rapid LD decay versus the resource ovine populations. Inbreeding levels were also lower for the smallholder flock (4 ± 0.003%) versus the research flock (13 ± 0.008%). No significant SNPs were identified after correction for false discovery rate. The heritability estimate for wet-dry using SNP information was 0.24. This estimate concurs with the literature and indicates the possibility of using genomic selection to improve reproduction in smallholder sheep flocks.