Genometric Analysis Simulation Program (GASP)

Components

Individual Components

• Single locus component


• Polygenic component


• Common sibship environment component


• Covariate component (random effect)


• Trait specific environment component

Component Descriptions

• Single locus component. Each single locus can be used either as a marker locus or as a locus that contributes to a trait. Each locus is parameterized in terms of the following: locus name, number of alleles, recombination fraction between that locus and the previous locus, allele name and frequency (one for each allele), genotype name (one for each genotype corresponding to allele 11, 12, 13, ..., 1n, 22, 23, ..., nn), genotypic value (one for each genotype), and a genotype specific "variance" (the same for each genotype). The genotype specific variance indicates whether the locus is qualitative or quantitative. A genotype specific variance of 0 indicates a locus with a "qualitative" effect, typically used as a marker locus. A genotypic variance of 1 indicates a locus with a "quantitative" effect.



• Polygenic component. The polygenic component for parents is generated using a random deviate from a normal distribution N(0,1). The polygenic component for children is based on the parents' breeding value (mid-parental value) and a random deviate from a normal distribution N(0,1).



• Common sibship environment component. The common sibship environment component assigns a single random deviate drawn from a normal distribution N(0,1) to all members of a common full sibship.



• Covariate component (random effect). The covariate component is based on a single random deviate drawn from a normal distribution N(0,1).



• Trait specific environment component. A random environment component must be included with any single locus component in the specification of a trait, although different components can be paired with different single locus components. The random environment component is based on a single deviate from a normal distribution N(0,1), and is used to specify the proportion of variation not due to the other specified components.