Reliability of breeding values for feed intake and feed efficiency traits in dairy cattle: when dry matter intake recordings are sparse under different scenarios
Negussie, E.; Mehtiö, T.; Mäntysaari, P.; Løvendahl, P.; Mäntysaari, E.A.; Lidauer, M.H.
Journal of Dairy Science 102(8): 7248-7262
ISSN/ISBN: 1525-3198 PMID: 31155258 DOI: 10.3168/jds.2018-16020
Currently, routine recordings of dry matter intake (DMI) in commercial herds are practically nonexistent. Recording DMI from commercial herds is a prerequisite for the inclusion of feed efficiency (FE) traits in dairy cattle breeding goals. To develop future on-farm phenotyping strategies, recording strategies that are low cost and less demanding logistically and that give relatively accurate estimates of the animal's genetic merit are therefore needed. The objectives of this study were (1) to estimate genetic parameters for daily DMI and FE traits and use the estimated parameters to simulate daily DMI phenotypes under different DMI recording scenarios (SCN) and (2) to use the simulated data to estimate for different scenarios the associated reliability of estimated breeding value and accuracies of genomic prediction for varying sizes of reference populations. Five on-farm daily DMI recording scenarios were simulated: once weekly (SCN1), once monthly (SCN2), every 2 mo (SCN3), every 3 mo (SCN4), and every 4 mo (SCN5). To estimate reliability of estimated breeding values, DMI and FE observations and true breeding values were simulated based on variance components estimated for daily observations of Nordic Red cows. To emulate realistic on-farm recording, 5 data set replicates, each with 36,037 DMI and FE records, were simulated for real pedigree and data structure of 789 Holstein cows. Observations for the 5 DMI recording scenarios were generated by discarding data in a step-wise manner from the full simulated data per the scenario's definitions. For each of these scenarios, reliabilities were calculated as correlation between the true and estimated breeding values. Variance components and genetic parameters were estimated for daily DMI, residual feed intake (RFI), and energy conversion efficiency (ECE) fitting the random regression model. Data for variance components were from 227 primiparous Nordic Red dairy cows covering 8 to 280 d in milk. Lactation-wise heritability for DMI, RFI, and ECE was 0.33, 0.12, and 0.32, respectively, and daily heritability estimates during lactation ranged from 0.18 to 0.45, 0.08 to 0.32, and 0.08 to 0.45 for DMI, RFI, and ECE, respectively. Genetic correlations for DMI between different stages of lactation ranged from -0.50 to 0.99. The comparison of different on-farm DMI recording scenarios indicated that adopting a less-frequent recording scenario (SCN3) gave a similar level of accuracy as SCN1 when 17 more daughters are recorded per sire over the 46 needed for SCN1. Such a strategy is less demanding logistically and is low cost because fewer observations need to be collected per animal. The accuracy of genomic predictions associated with the 5 recording scenarios indicated that setting up a relatively larger reference population and adopting a less-frequent DMI sampling scenario (e.g., SCN3) is promising. When the same reference population size was considered, the genomic prediction accuracy of SCN3 was only 5.0 to 7.0 percentage points lower than that for the most expensive DMI recording strategy (SCN1). We concluded that DMI recording strategies that are sparse in terms of records per cow but with slightly more cows recorded per sire are advantageous both in genomic selection and in traditional progeny testing schemes when accuracy, logistics, and cost implications are considered.