Dominance effects estimation of TLR4 and CACNA2D1 genes for health and production traits using logistic regression

Knowledge of nonadditive variance and genetic effects can be helpful in explaining the total genetic variation formost of the traits. The objective of this study was to estimate dominance effects of several single-nucleotide polymorphism (SNP) genotypes for the production traits and clinical mastitis residual (CMR), in Holstein dairy cattle in a case-control study. Records of 305 days lactation were obtained for production traits and CMR. Animals were selected based on extreme values for CMR from mixed model analyses. Samples were genotyped for four SNP-single genotypes and their associations with production traits (breeding values for protein and fat yield, and protein and fat percentage) were estimated by applying logistic regression analyses. Calculation of contrast between both homozygous and heterozygous genotypes permitted to estimate dominance effects, which ranged from -0.49 to 0.35 standard deviation units for the production traits and clinical mastitis (CM), respectively. Results showed that the dominance effects may be important in contribution of total genetic effects for production traits and CM. Therefore, evaluation of animals based on additive variance alone and disregarding nonadditive effects may lead to failure in selection programmes and exactly estimating the genetic variation. The method that we used would help breeders in accurately estimation of genotypic values in a new genomic selection scenario including dominance effects.