pedSimulate-package: Pedigree, genetic merit, phenotype, and genotype simulation

In pedSimulate: Pedigree, Genetic Merit, Phenotype, and Genotype Simulation

Pedigree, genetic merit, phenotype, and genotype simulation

Description

An R package for simulating a pedigree with genetic merits and phenotypes, starting from a base population (generation 0) or an existing pedigree. The pedigree depth and design can be chosen by the values provided to the arguments of the simulation function. Genotypes can be simulated for a given pedigree, or an appended pedigree to an existing pedigree with genotypes. Marker effects to be chosen by the researcher.

Details

Starting from a base population with a user-defined size and equal number of males and females, next generations are simulated for the user-defined litter size and number of generations. No selection (natural or artificial) and non-random mating is applied to this population. Alternatively, the simulation can be started from an existing pedigree. Natural (mortality) and artificial selection are applied to the next generations. Different generation overlap, selection intensities and selection patterns can be applied to males and females. Selected males and females are ordered similarly/differently to simulate various random, assortative or disassortative mating scenarios. Performance and genetic merit of individuals are simulated using the basic rules of quantitative genetics. The performance (P) of an individual is influenced by genetic (A) and environmental (E) effects. Thus, P = A + E, and Var(P) = Var(A) + Var(E). The additive genetic merit (A) of an individual is the average of its parents' additive genetic merits (PA = (A_sire + A_dam)/2) plus the Mendelian Sampling term due to the sampling of alleles passed from the parent to the offspring. The Mendelian Sampling variance is half of Var(A) in the base population. Because there is no provided information for environmental effects, the environment effect is assigned to individuals from a normal distribution of random numbers (E ~ N(0, IVar(E))). The package also provides functions to identify halfsib, fullsib and parent-progeny matings in the pedigree. For a given pedigree, genotypes can be simulated. Marker effects can be chosen by the researcher and added to the simulated phenotypes. In that case, genetic effects and variance used to simulate phenotypes change to residual polygenic effects and variance (genetic effects and variance not explained by the markers).

Author(s)

Mohammad Ali Nilforooshan [e-mail]

References

Mrode, R. A. 2005. Linear Models for the Prediction of Animal Breeding Values, 2nd ed. Cambridge, MA: CABI Publishing. <ISBN:9780851989969, 0851989969>

Nilforooshan, M. A. 2022. pedSimulate – An R package for simulating pedigree, genetic merit, phenotype, and genotype data. R. Bras. Zootec., 51:e20210131. <doi:10.37496/rbz5120210131>

pedSimulate documentation built on Sept. 26, 2023, 9:06 a.m.