Between-founder heterogeneity in inbreeding depression for production in Jersey cows

Severity of inbreeding depression depends on the hidden (i.e., recessive) genetic load carried by a population. If the load is distributed unevenly among founder genomes, or founder-lines were exposed to variable amounts of selection, descendants from different founders may be differentially affected by inbreeding. Between-founder heterogeneity in inbreeding depression for production traits and somatic cell score in milk (SCS) was studied using records from 59,788 Jersey cows. Inbreeding coefficients (F) were partitioned into components due to four founders, plus a remainder. A two-stage statistical analysis was performed. First, empirical best linear unbiased predictions (EBLUP) of residuals for milk, fat and protein yield, and for SCS, were computed using linear models including fixed effects of herd-year-season, age at calving and days in milk, and random additive genetic effects of individual cows. Second, models with total and partial inbreeding coefficients as predictor variables were fitted to EBLUP residuals, for each trait. Tests of differences between slopes indicated that regressions of milk, fat and protein yield on partial inbreeding coefficients were heterogeneous; SCS did not exhibit inbreeding depression. Hence, alleles contributing to inbreeding depression for production in this Jersey population seem to be associated with specific founders. This indicates that a homogeneous effect of inbreeding on production may be an incorrect statistical specification in genetic evaluation models that attempt to account for inbreeding depression. Furthermore, the observed variability between effects of partial inbreeding due to different founders implies that inbreeding effects on yield traits may be due to alleles with major effects. (c) 2006 Elsevier B.V. All rights reserved.