The practical application of group genotyping theory in porcine herds

Abstract

This paper describes the practical implementation of a group genotyping strategy designed to increase the amount of information available from genotyping selected groups of individuals. Macrossan and Kinghorn (2005) developed a predictive index to help select the most informative group of animals to genotype under the conditions met in practice, being existing known genotypes and/or phenotypes, and pedigree information. That study details an experiment carried out in simulated pedigreed populations, modelled on a beef cattle herd of 500 breeding females, given 'full segregation analysis information'. This information is not available in practice, but is available in experimentally simulated populations. Full segregation analysis information results from privileged immediate knowledge of the genotypes of a group of individuals that are being considered for genotyping. This privileged information, together with truly known genotypes on other individuals, is used via segregation analysis to give a measure of the information value of genotypes. Using this information, the 'best' group to genotype can be identified, giving an upper limit to that which can be achieved in practice. During a stochastic search of a simulated population for this best group, evolutionary pressure was applied via the fitness function of average information content of genotypes across the population. Associated with this fitness increase were changes in the characteristics of the individuals selected in the 'best-so-far' group. Tracings of the evolutionary process in the simulated populations provided data upon which to model this evolutionary process. The resultant linear model simultaneously applies evolutionary pressure in opposite directions to increase individual animal relatedness to the herd (to increase the spread of information via segregation analysis) whilst decreasing within-group relatedness (to reduce redundancy of information). The model was shown to be potentially capable of increasing the amount of information available from group genotyping by 21% over a randomly chosen group of animals. The present study concerns the practical application of this predictive model in an industry porcine herd. The ability of the theoretical model to increase the amount of information available from group genotyping is tested in a comparison with two simple but sensible group selection strategies used in practice; herd sires only, or a combination of herd sires and dams.