AdamPlant: A Tool to Simulate Selective-Breeding Schemes for Farmed Crops

AdamPlant is a computer program that models selective-breeding schemes for plants using stochastic simulation. AdamPlant is a powerful and flexible software, which can simulate a variety of population structures, genetic models, ploidy levels, reproductive systems, selection strategies and crossing designs. AdamPlant simulates breeding schemes in the following steps: (1) generate base plants by sampling chromosome haplotypes from a founder population or by importing stored haplotypes; (2) select genetic model from infinitesimal model or genomic model (finite-locus model); (3) determine the number of traits and recording strategy, assign QTL effects and/or polygenic effects for the trait and generate phenotypes; (4) perform truncation or optimum contribution selection based on phenotype, best linear unbiased prediction (BLUP) or genomic BLUP for specified selection unit e.g. single plant or family; and (5) generate offspring by crossing design for parental lines, selfing or double haploid technology. Results that are obtained include the true and estimated breeding values for all individuals or families at each time step, overall and trait-wise genetic gain, generation interval, accuracy of the prediction of breeding values, within-/between-family variance and realized plot- and variety- heritabilities. Inbreeding is also calculated based on either pedigree information or the identity-by-descent markers that are used to trace each base plant’s contribution. AdamPlant can be used to evaluate realistic complex breeding schemes where two or more competing interchange breeding material. Adam is written in FORTRAN 95, and is under continuous development at Center for Quantitative Genetics and Genomics (QGG), Department of Molecular Biology and Genetics, Aarhus University.