Alternative strategies for genetic analyses of milk flow in dairy cattle

Invited review: Recursive models in animal breeding: Interpretation, limitations, and extensions

Structural equation models allow causal effects between 2 or more variables to be considered and can postulate unidirectional (recursive models; RM) or bidirectional (simultaneous models) causality between variables. This review evaluated the properties of RM in animal breeding and how to interpret the genetic parameters and the corresponding estimated breeding values. In many cases, RM and mixed multitrait models (MTM) are statistically equivalent, although subject to the assumption of variance-covariance matrices and restrictions imposed for achieving model identification. Inference under RM requires imposing some restrictions on the (co)variance matrix or on the location parameters. The estimates of the variance components and the breeding values can be transformed from RM to MTM, although the biological interpretation differs. In the MTM, the breeding values predict the full influence of the additive genetic effects on the traits and should be used for breeding purposes. In contrast, the RM breeding values express the additive genetic effect while holding the causal traits constant. The differences between the additive genetic effect in RM and MTM can be used to identify the genomic regions that affect the additive genetic variation of traits directly or causally mediated for another trait or traits. Furthermore, we presented some extensions of the RM that are useful for modeling quantitative traits with alternative assumptions. The equivalence of RM and MTM can be used to infer causal effects on sequentially expressed traits by manipulating the residual (co)variance matrix under the MTM. Further, RM can be implemented to analyze causality between traits that might differ among subgroups or within the parametric space of the independent traits. In addition, RM can be expanded to create models that introduce some degree of regularization in the recursive structure that aims to estimate a large number of recursive parameters. Finally, RM can be used in some cases for operational reasons, although there is no causality between traits.

Genetic Parameters Estimation of Milking Traits in Polish Holstein-Friesians Based on Automatic Milking System Data

The automatic milking system (AMS) provides a large amount of information characterizing the course of each milking cow, which is not available in the conventional system. The aim of our study was to estimate heritability and genetic correlations for milk yield (MY), milking frequency (MF), and speed (MS) for 1713 Polish Holstein-Friesian primiparous cows milked in barns with an AMS. Daily heritability indicators estimated using second-order Legendre polynomials and Random Regression Models showed high variation during lactation, ranging 0.131-0.345 for MY, 0.153-0.322 for MF, and 0.336-0.493 for MS. The rates of genetic correlation between traits ranged: 0.561-0.929 for MY-MF, (-0.255)-0.090 for MF-MS, (-0.174)-0.020 for MY-MS. It is possible to carry out effective selection for milking speed, which provides an opportunity to increase the number of cows per milking robot, and thus increase the profitability of production in the herd. The results proved that selection for milk yield and daily milking frequency is also feasible. The research showed a high, positive genetic correlation between milking frequency and milk yield, which allows us to conclude that preferring breeding cows with a natural tendency to frequent visits to the milking robot should indirectly improve the genetic basis of milking.

Genetic parameters for longitudinal behavior and health indicator traits generated in automatic milking systems

Abstract. Genetic (co)variance components were estimated for alternative functional traits generated by automatic milking systems (AMSs), and reflecting dairy cow behavior and health. Data recording spanned a period of 30 days and included 70 700 observations (visits to the AMS) from 922 Holstein cows kept in three German farms. The three selected farms used the same type of AMS and specific selection gates allowing “natural cow behavior on a voluntary basis”. AMS traits used as behavior indicator traits were AMS visits per cow and day as binary traits, with a threshold for equal to or greater than three visits (VIS3) and equal to or greater than four visits (VIS4), knocking off the milking device with a threshold of at least one udder quarter, also as a binary trait (KO), milking duration of each AMS visit in minutes (DUR), average milk flow in kg min−1 (AMF), and the interval between two consecutive milkings (INT). Electrical conductivity (EC) of milk from each udder quarter and in total was used as a health indicator trait. For genetic analyses, in univariate and bivariate models, linear and generalized linear mixed models (GLMMs) with a logit link function were applied to Gaussian distributed and binary traits, respectively. The heritability was 0.08 ± 0.03 for VIS3, 0.05 ± 0.05 for VIS4, 0.03 ± 0.03 for KO, 0.19 ± 0.07 for DUR, 0.25 ± 0.07 for AMF, and 0.07 ± 0.03 for INT. Heritabilities for EC varied between 0.37 ± 0.08 and 0.46 ± 0.09, depending on the udder quarter. On the genetic scale, an increased number of AMS visits (VIS3 and VIS4) were associated with an increase of KO (rg= 0.24 and rg= 0.55, respectively). From a genetic perspective, high-milk-yielding cows visited the AMS more often (rg= 0.49 for VIS3 and rg= 0.80 for VIS4), had a faster AMF (rg= 0.40), and shorter INT (rg= −0.51). When considering these traits as behavior indicator traits, selection of cows with desired temperament simultaneously increases milk yield. An increase of automatically and objectively recorded AMS traits with moderate heritabilities justifies modifications of dairy cattle breeding goals towards higher emphasis on behavioral traits, especially when developing specific robot indices. Nevertheless, ongoing research in this regard with a larger data is suggested in order to validate the results from the present pilot study.