Preliminary genome-wide association study for wet-dry phenotype in smallholder ovine populations in South Africa
| dc.contributor.author | Molotsi, A. H. | en_ZA |
| dc.contributor.author | Taylor, J. F. | en_ZA |
| dc.contributor.author | Cloete, S. W. P. (Schalk Willem Petrus van der Merwe) | en_ZA |
| dc.contributor.author | Muchadeyi, F. | en_ZA |
| dc.contributor.author | Decker, J. E. | en_ZA |
| dc.contributor.author | Sandenbergh, L. | en_ZA |
| dc.contributor.author | Dzama, K. | en_ZA |
| dc.date.accessioned | 2018-12-04T07:41:57Z | |
| dc.date.available | 2018-12-04T07:41:57Z | |
| dc.date.issued | 2017-04-10 | |
| dc.description | CITATION: Molotsi, A. H., et al. 2017. Preliminary genome-wide association study for wet-dry phenotype in smallholder ovine populations in South Africa. South African Journal of Animal Science, 47(3):327-331, doi:10.4314/sajas.v47i3.9. | en_ZA |
| dc.description | The original publication is available at http://www.sasas.co.za | en_ZA |
| dc.description.abstract | 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. | en_ZA |
| dc.description.uri | http://www.sasas.co.za/preliminary-genome-wide-association-study-wet-dry-phenotype-smallholder-ovine-populations-south | |
| dc.description.version | Publisher's version | en_ZA |
| dc.format.extent | 5 pages : illustrations | en_ZA |
| dc.identifier.citation | Molotsi, A. H., et al. 2017. Preliminary genome-wide association study for wet-dry phenotype in smallholder ovine populations in South Africa. South African Journal of Animal Science, 47(3):327-331, doi:10.4314/sajas.v47i3.9 | en_ZA |
| dc.identifier.issn | 2221-4062 (online) | |
| dc.identifier.issn | 0375-1589 (print) | |
| dc.identifier.other | doi:10.4314/sajas.v47i3.9 | |
| dc.identifier.uri | http://hdl.handle.net/10019.1/104769 | |
| dc.language.iso | en_ZA | en_ZA |
| dc.publisher | South African Society for Animal Science | en_ZA |
| dc.rights.holder | Authors retain copyright | en_ZA |
| dc.subject | Sheep -- South Africa -- Reproduction | en_ZA |
| dc.subject | Sheep -- Breeding | en_ZA |
| dc.subject | Single nucleotide polymorphisms (SNPs) | en_ZA |
| dc.subject | Binomial reproductive trait in sheep | en_ZA |
| dc.title | Preliminary genome-wide association study for wet-dry phenotype in smallholder ovine populations in South Africa | en_ZA |
| dc.type | Article | en_ZA |