ADAM-multi: software to simulate complex breeding programs for animals and plants with different ploidy levels and generalized genotypic effect models to account for multiple alleles

Stochastic simulation software, ADAM, has been developed for the purpose of breeding optimization in animals and plants, and for validation of statistical models used in genetic evaluations. Just like other common simulation programs, ADAM assumed the bi-allelic state of quantitative trait locus (QTL). While the bi-allelic state of marker loci is due to the common choice of genotyping technology of single nucleotide polymorphism (SNP) chip, the assumption may not hold for the linked QTL. In the version of ADAM-Multi, we employ a novel simulation model capable of simulating additive, dominance, and epistatic genotypic effects for species with different levels of ploidy, providing with a more realistic assumption of multiple allelism for QTL variants. When assuming bi-allelic QTL, our proposed model becomes identical to the model assumption in common simulation programs, and in genetic textbooks. Along with the description of the updated simulation model in ADAM-Multi, this paper shows two small-scale studies that investigate the effects of multi-allelic versus bi-allelic assumptions in simulation and the use of different prediction models in a single-population breeding program for potatoes. We found that genomic models using dense bi-allelic markers could effectively predicted breeding values of individuals in a well-structure population despite the presence of multi-allelic QTL. Additionally, the small-scale study indicated that including non-additive genetic effects in the prediction model for selection did not lead to an improvement in the rate of genetic gains of the breeding program.