Genomic-based genetic parameters for daily milk yield and various lactation persistency traits in American Holstein cattle

Abstract

Genomic-based genetic parameters for daily milk yield and lactation persistency were estimated for the first 3 lactations in American Holstein cattle. Data included 5,235,411 daily milk yield records on automatic milking systems and milking parlors from 11,788 genotyped cows that calved from 2012 to 2019. A total of 62,029 SNPs remained after quality control. Single-trait random regression models were used to estimate variance and covariance components based on Bayesian inference. The systematic effects in the model included calving year, calving season, milking system, and calving age as linear and quadratic covariates. Random effects included additive genetic, permanent environment, and residual effects modeled with parametric (i.e., Wood, Wilmink, and Ali and Schaeffer) and non-parametric functions (i.e., Legendre orthogonal polynomials and B-splines). The same number of coefficients was considered for all fixed and random regressions in each analysis. Twenty-six models were compared for each lactation and models were selected based on goodness of fit and parsimony, estimates of variance components, heritabilities, correlations, credibility and interpretation of the results, and computational demand and time. Consequently, the model using fourth-order Legendre orthogonal polynomials and 10 classes of heterogeneous residual variance was considered the optimal model. The daily heritability estimates across DIM ranged from 0.12 to 0.22 for milk yield in parity 1 (MY1), 0.11 to 0.19 for milk yield in parity 2 (MY2), and from 0.03 to 0.15 for milk yield in parity 3 (MY3). For lactation persistency, the heritability estimates ranged from 0.05 to 0.18 for MY1, from 0.06 to 0.20 for MY2, and from 0.05 to 0.16 for MY3. Overall, the heritability estimate values were of low to moderate magnitude. In general, null to moderate genetic correlations were observed between lactation persistency and 305-d milk yield, indicating weak association between lactation persistency and milk yield, which is desirable (but should not be neglected). Ten measures of lactation persistency were evaluated using genomic breeding values. The third lactation persistency measurement (derived by subtracting the area under the curve of lactation in the final third from the area under the curve in the initial third of lactation) is recommended as the selection criterion, as these measures showed a moderate heritability (0.18 for MY1, 0.20 for MY2, and 0.15 for MY3) and a low to moderate genetic correlation (0.38 for MY1, 0.23 for MY2, and 0.20 for MY3) with 305-d milk yield. In summary, this study provides genetic parameter estimates for longitudinal daily milk yield and various lactation persistency traits in American Holstein cattle. These estimates will be useful to optimize lactation persistency in high-producing dairy cows through selection as they suggest null or weak association between LP and milk yield, and therefore, enhance the profitability of the dairy industry through extended lactations.