Monitoring of genetic diversity in the Japanese Black cattle population by the use of pedigree information

The gene pool of the Japanese Black cattle has been completely closed to foreign breeds during the last 100 years. Genetic diversity of the Japanese Black cattle from 1960 to 2000 was monitored with three estimates of effective number of ancestors. Founder genome equivalent (N_ge) accounts for all the causes of reduction of diversity. Effective number of founders (N_ef) and non‐founders (N_enf) explain reduced diversity because of unequal genetic contributions of founders and random genetic drift in non‐founders, respectively. Further examination using gene dropping simulation was conducted to obtain information on survival of founder alleles. Unique founder alleles were dropped down along the actual pedigree with Monte Carlo procedure following Mendelian segregation rules, and generated genotypes of all the current live animals (612 959 heads). Pedigree records consisted of 2 075 188 animals was used for these analysis. The estimates of three effective numbers (N_ef, N_ge, and N_enf) decreased from 418.6 to 50.3, 86.6 to 7.3, and 109.2 to 8.5, respectively, during the period 1960–2000. The increasing differences between two kinds of genetic diversity indices derived from N_ge and N_ef showed that large part of the reduced diversity from 1980 was attributed to genetic drift caused by the intensive use of particular limited number of sires. In gene dropping analysis, probabilities of extinction of founder alleles were derived from their distributions of frequency in the current animals. Several founders showed low probabilities of allele extinction, irrespective of their relatively low genetic contributions. This suggests that these founders have lineages through which their alleles are surely transmitted to the current breed. The use of these founders as a strategy for recovering the genetic diversity was discussed.