Sampling genotype configurations in a large complex pedigree

Many genetic problems can be solved by Monte Carlo method. This often requires sampling genotype configurations over pedigree. Current available samplers are inefficient for large animal pedigrees. A new sampler suitable for large complex pedigrees has been developed and evaluated. The sampler uses simple and iterative peeling algorithms alternately. The sampler was compared to two other samplers on hypothetical pedigree of 79 individuals and recessive disease. The behaviour of the sampler was evaluated in four experimental designs on real bovine pedigree of 907,903 animals. The application of the sampler was also exemplified in identical by descent study.