Genotype by Birth or Rearing Type Interaction in Merino Sheep

Abstract

This thesis aimed to investigate genotype by environment (birth or rearing type) interaction (GEI) in Merino sheep for growth traits using univariate and bivariate mixed models and also random regression model analysis with phenotype data and using genome wide association study with genome data. The impact of accounting for sire by birth and rearing type interaction in sheep breeding programs was investigated. In the first research chapter, univariate and bivariate mixed models were used for the analysis of birth weight (BWT), weaning weight (WWT), post weaning weight (PWWT), scan fat (PFAT) and eye muscle depth (PEMD) with and without inclusion of sire by birth type (BT) or rearing type (RT) interactions. Models fitted sire by BT or RT to estimate its contribution to phenotypic variation and to estimate breeding values for expression of traits both in single and twin BT or RT environments. Univariate analysis showed a significant sire x BT interaction accounting for 1.59% and 2.49% of the phenotypic variation for BWT and WWT, respectively, and no significant effect for PWWT, PFAT and PEMD. Sire x RT interaction effects were much smaller and only significant for PEMD. The genetic correlation between breeding values for growth in single and twin BT varied from 0.47 to 0.99. In the next research chapter, univariate and bivariate random regression models (RRM) were fitted to repeated measurements of body weight of Merino lambs from 75 to 300 days of age to explore genetic differences in growth paths between single and twin lambs. A sire by birth type and sire by rearing type interaction contributed around 2-6% to variation in body weight at 200 until 300 days of age, while before 225 days of age the contribution was almost zero. Genotype expression differed in different birth types and in different rearing types particularly in earlier life of lambs for birth type and in late age for rearing type with birth type having a larger effect than rearing type, with the genetic correlation between weight in different BT varying over the trajectory from 0.75-0.97. In the third research chapter, a genome wide association study was applied to investigate the association of genetic markers with birth weight (BWT) and the interaction of significant marker effects with birth type (BT) in Merino lambs. Eleven and fifteen genome-wide significant SNPs for birth weight were detected for birth weight in singles and twins, respectively, with 11 of those overlapping, and 17 genome-wide significant SNPs were found when using all data. OAR6_41936490.1 and OAR6_41877997.1 were the most significant SNPs for single and twin birth weight, respectively. Among 17 significant SNPs detected by GWAS there were 9 that had a significant SNP by BT interaction, indicating that gene by BT interaction contributed to BWT variation. In the final research chapter, the impact of accounting for sire by birth type interaction on percentage of incorrect animals and sires selected was investigated by comparison with using a bivariate "expected" model for birth weight (BWT), weaning weight (WWT) and post weaning weight (PWWT) in Merino lambs. Correlation of EBV of lambs or sires and genetic gain between 4 EBVs from 3 proposed models (for BWT, WWT and PWWT) were investigated. The impact of accounting for sire by birth type interaction on the percentage of animals and sires incorrectly selected was small but this percentage was about 10% compared with the best model. The impact of accounting for sire by birth type interaction was also small when considering loss in genetic gain, but the loss was below 4% compared to the best model. In conclusion, although the existence of genotype by birth type interaction for growth traits in Merino sheep was small, but its impact on incorrect animals and sires can be ignored in breeding program.