Preliminary genome-wide association study for wet-dry phenotype in smallholder ovine populations in South Africa

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.

Keywords: conception rate, Dorper, heritability, Namaqua Afrikaner, reproduction, South African Mutton Merino