Calculation of Inbreeding Coefficients using Incomplete Pedigrees and its Influence on Inbreeding Depression and Breeding Value for Milk Production in Hokkaido Holstein Populations of Japan.

Objectives of this study were to compare the inbreeding coefficients calculated using the regular algorithm (RA) and the algorithm proposed by VanRaden (VRA) with incomplete pedigrees and to investigate the inbreeding levels and the influence on inbreeding depression and breeding values for milk production in the Hokkaido Holstein population of Japan. Pedigree information used for calculation of inbreeding coefficients was obtained from the herdbook for registered Holsteins, dairy cattle milk records for nonregistered Holsteins, and INTERBULL evaluation files for bulls in foreign countries. These pedigree data consisted of 4,499,862 cows born between 1901 and 2000 and 130,301 bulls born between 1897 and 2000. An inbreeding coefficient for each animal was calculated using the recursive algorithm of the tabular method. Inbreeding coefficients were calculated using RA0 (RA algorithm assuming that all animals are related), RA50 (RA algorithm assuming that animals born before 1950 are unrelated), and VRA50 (VRA algorithm assuming that animals born before 1950 are unrelated). The data for estimation of inbreeding depression and breeding values comprised 1,620,939 cows and 4,810,604 records for 305-d lactation milk and fat yields, 1,239,977 cows and 3,372,368 records for protein yield, and 1,523,859 cows and 4,379,907 records for SNF yield. An animal model with inbreeding coefficients calculated using RA0 and VRA50 included a linear regression on inbreeding to estimate inbreeding depression as fixed effects. To reflect the reduced variance of Mendelian sampling, the ratio of error variance to additive genetic variance was corrected with inbreeding coefficients of sires and/or dams. Average numbers of generations for cows and bulls born in 2000 were 11.6 and 11.8 when the pedigree information is available, and 8.3 and 8.4 when animals born before 1950 are unrelated, respectively. Mean inbreeding coefficients for cows and bulls born in 2000 calculated with RA50 were 4.01% and 5.11%, respectively, and they increased to 4.18% and 5.15% with VRA50. These small increases occurred due to the fact that number of animals with unknown parents was small. The CPU time required for calculation of inbreeding coefficients was less with RA50 or VRA50 than with RA0. Mean inbreeding levels calculated using VRA50 were 0.26%, 0.56%, 1.23%, 1.89%, and 5.14% for cows and 0.31%, 0.43%, 0.77%, 1.97%, and 5.15% for bulls born in 1960, 1970, 1980, 1990, and 2000, respectively. The average increases in inbreeding per year were 0.07%, 0.06%, and 0.22% for cows and 0.03%, 0.12%, and 0.45% for bulls born in the 1971-1980, 1981-1990, and 1991-2000, respectively. Estimates of inbreeding depression were -24.8 kg for milk, -0.9 kg for fat, -0.7 kg for protein, and -2.1 kg for SNF. Correlation between breeding values corrected using inbreeding coefficients calculated with RA0 and VRA50 was 0.999 or more for all traits. However, the average breeding value corrected using inbreeding coefficients with VRA50 was slightly lower than the one with RA0. The results of this study suggest that inbreeding coefficients with VRA50 could be used to understand approximately the outline of inbreeding levels in the Hokkaido Holstein population and to apply to not only genetic evaluation but also selection and mating programs considering inbreeding depression.