Inferring purging from pedigree data

Abstract

The harmful effects of inbreeding can be reduced if deleterious recessive alleles were removed (purged) by selection against homozygotes in earlier generations. If only a few generations are involved, purging is due almost entirely to recessive alleles that reduce fitness to near zero. In this case the amount of purging and allele frequency change can be inferred approximately from pedigree data alone and are independent of the allele frequency. We examined pedigrees of 59,778 U.S. Jersey cows. Most of the pedigrees were for six generations, but a few went back slightly farther. Assuming recessive homozygotes have fitness 0, the reduction of total genetic load due to purging is estimated at 17%, but most of this is not expressed, being concealed by dominant alleles. Considering those alleles that are currently expressed due to inbreeding, the estimated amount of purging is such as to reduce the expressed load (inbreeding depression) in the current generation by 12.6%. That the reduction is not greater is due mainly to (1) generally low inbreeding levels because breeders in the past have tended to avoid consanguineous matings, and (2) there is essentially no information more than six generations back. The methods used here should be applicable to other populations for which there is pedigree information.