Use of segregation analysis to reduce genotyping costs

Abstract

An iterative approach to genotyping operations is described, in which one or more individuals and/or loci are genotyped in each cycle. Segregation analysis after each genotyping provides updated genotype probabilities for all individuals/loci remaining ungenotyped. Individuals/loci to be genotyped in each cycle are chosen on a criterion that includes one or more of: genotype probability index, numerator relationship, parental status, estimated breeding value. The approach was tested on a simulated population with a single locus segregating. After genotyping about 10, 20 and 80% of the population, the resulting information contained about 50, 60 and 100% of the utility (average genotype probability index) of full genotyping.