Testing candidate gene effects on milk production traits in dairy cattle under various parameterizations and modes of inheritance

Abstract

The major objectives of this study were 1) to assess the statistical properties of models commonly used for the estimation of single nucleotide polymorphism (SNP) effects under the assumption of various modes of inheritance and various parameterizations of SNP genotypes using simulated data, and 2) to compare effects of the selected polymorphisms located within butyrophilin (BTN1A1), diacylglycerol acyltransferase 1 (DGAT1), leptin (LEP), and leptin receptor (LEPR) candidate genes on milk production traits using data from 2 dairy cattle breeds (190 Jersey cows and 475 Polish Holstein-Friesian cows). Simulation results showed that type I error and power were not dependent on the assumed parameterization, but differences were observed regarding confidence intervals of estimated SNP effects. In the presence of epistasis, correct confidence intervals for all (epistatic and nonepistatic) SNP and all modes of inheritance were provided only by the parameterization proposed by C. H. Kao and Z. B. Zeng in 2002. However, if no dominance effect was included in the model, confidence intervals for SNP effects were correct for all parameterizations. Results based on real data showed that for both breeds the additive effects of polymorphisms were generally similar, except for LEPR, which had a different allele associated with increased fat content in Holstein-Friesians than in Jerseys. In both breeds, DGAT1 had the largest additive effect of the polymorphisms considered, but its effect on most milk traits was more pronounced in Jerseys than in Holstein-Friesians. Evidence of epistasis was found between LEPR and DGAT1, as well as between LEPR and BTN1A1, but only for milk content traits and only in the Holstein-Friesian breed. There was also more evidence for dominance in the Holstein-Friesian breed than in the Jersey breed.

The effect of DGAT1 polymorphism on milk production traits in dairycows depending on environmental temperature

“…In the association analysis carried out without air temperature taken into account, the DGAT1:K232 allele significantly decreased milk and protein yields and increased fat yield and fat and protein contents (data not shown). These results are consistent with the findings of many previous studies performed in several dairy cattle populations (e.g., 6,8,13). To the best of the authors' knowledge, the influence of weather conditions on DGAT1 effects on milk yield and composition has not been investigated to date, although Duchemin et al (14) found significant K232A genotype by season interactions for some fatty acid contents in milk.…”

“…In our previous study, the effect of this polymorphism on fat and protein contents in milk showed changes over time, being low in the first stage of lactation, and increased as lactation progressed (9). The significant impact of lactation stage on K232A Other reports suggest that the effect of DGAT1 may also depend on breed (8,13,16) and parity (15,16). Now it seems that the impact of K232A on milk yield traits in hot seasons may be decreased.…”

Effect of DGAT1 polymorphisms on the estimated breeding values of Czech Simmental sires

“…When different effects depending on the breed are found, e.g. Suchocki et al (2010) noted a stronger effect in Jersey than in Holstein, the gene polymorphisms should be evaluated regarding the breed. In the paper, we have analyzed the dual-purpose Czech Simmental cattle, as in most cases the dairy breeds, predominantly Holstein, are in the spotlight.…”

Modelling effects of candidate genes on complex traits as variables over time

“…The credibility of this finding is enhanced by the fact that it was confirmed in two independent data sets of Jersey and HF breeds. In Jerseys, for example, the impact of this polymorphism on fat yield was observed to be less pronounced than in HFs, and the results for milk and protein yields seemed to be inconsistent across studies (Spelman et al 2002;Suchocki et al 2010a). Many investigations proved that the lysineencoding Lys232 allele was associated with an increase in fat and protein percentages as well as in fat yield, whereas the alanine-encoding 232Ala variant increased milk and protein yields (Grisart et al 2002;Spelman et al 2002;Thaller et al 2003;Sanders et al 2006;Gautier et al 2007;N€ aslund et al 2008).…”

“…In Jerseys, for example, the impact of this polymorphism on fat yield was observed to be less pronounced than in HFs, and the results for milk and protein yields seemed to be inconsistent across studies (Spelman et al 2002;Suchocki et al 2010a). In our previous analysis, using cumulative 305-day lactation yields and a data set from the Polish HF population (similar to the current dataset) and from the Jersey population, we did not detect an effect of BTN1A1 on most analysed traits (Szyda & Komisarek 2007;Suchocki et al 2010a). Variation in the magnitudes of DGAT1 effects might result from the genetic background, which may differ between breeds and can change over generations in response to selection.…”