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Table 3 Difference (Diff) between expected phenotypes of cows with low and high inbreeding, for significant traits and total inbreeding measures

From: Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein–Friesian dairy cattle

Trait \(\varvec{F}_{{\varvec{PED}}}\) \(\varvec{F}_{{\varvec{ROH}}}\) \(\varvec{F}_{{\varvec{GRM}}}\)
Low High Diff Low High Diff Low High Diff
MY 8175 7977 198 8227 7926 301 8232 7917 315
FY 345.4 337.4 8.0 347.0 335.9 11.1 346.7 336.2 10.5
PY 285.8 279.2 6.6 287.5 277.5 10.0 287.5 277.4 10.1
CI 393.0 395.4 − 2.4 392.2 396.2 − 4.0 392.2 396.2 − 4.0
IFL 39.6 40.3 − 0.7 38.9 41.1 − 2.2 38.7 41.4 − 2.7
CR 64.5 62.9 1.6 64.8 62.6 2.2 64.9 62.5 2.4
SCS400 1579 1583 − 4 1578 1585 − 7 1578 1585 − 7
  1. MY: 305-day milk yield (kg); FY: 305-day fat yield (kg); PY: 305-day protein yield (kg); CI: calving interval (days); IFL: interval first to last insemination (days); CR: conception rate (%); SCS400: somatic cell score day 151 to 400 (1000 + 100*[log2 of cells/mL])
  2. \(F_{PED}\): pedigree inbreeding based on all generations; \(F_{ROH}\): inbreeding based on all regions of homozygosity; \(F_{GRM}\): inbreeding based on the genomic relationship matrix computed with allele frequencies of 0.5
  3. Low and high inbreeding were defined as the 5% and 95% percentile, respectively. Low and high inbreeding equalled 2.8% and 8.0% for \(F_{PED}\), 8.5% and 16.9% for \(F_{ROH}\) and 25.9% and 32.4% for \(F_{GRM}\)