Nonparametric analysis of the impact of inbreeding on production in Jersey cows

Under dominance, the relationship between a quantitative trait and the inbreeding coefficient (F) is expected to be linear. Epistasis involving dominance effects or selection against inbred individuals can produce nonlinear patterns in the form of inbreeding depression. The form of the relationship between F and yield traits was explored via local regression (LOESS). First-lactation milk, fat, and protein records from 59,778 Jersey cows with at least 6 generations of known pedigree were used. The F ranged from 0.6 to 34% and median F was 6.3%. The LOESS regressions of predicted residuals from an animal model (empirical best linear unbiased predictions, EBLUP) on F were calculated for each trait; the EBLUP model included fixed herd-year-season, age at calving and DIM effects, and random additive genetic effects. The relationship between EBLUP residuals and inbreeding was complex and nonlinear. Yields were unaffected for F 20% for fat and protein yield. For SCS, both parametric and LOESS fits were consistent with the absence of sizable dominance effects. Effects of inbreeding on performance seemed to be more complex than suggested by previous studies based on linear regression. Results should be interpreted with caution because the data were scarce at high levels of F.