ADAM is a stochastic simulation program for modelling selective breeding programs in animals and plants. It simulates populations over time and traces genetic change under alternative breeding strategies and operational workflows. A key strength of ADAM is its capability to simulate complex traits (mimicking important biological aspects of plant and animal genetics) and to combine many interacting steps in real breeding pipelines.
Main advantages of ADAM
- Stochastic simulation: ADAM uses stochastic simulation, which is a precise way to model complex breeding programs.
- Broad scenario evaluation: It enables evaluation of a wide range of breeding program designs and assumptions.
- Modern breeding methods: It supports modelling of methods such as marker- and gene-assisted selection, selective genotyping, multiple ovulation and embryo transfer (MOET), and sexed semen.
- Testing new technologies: It allows new technologies and techniques to be explored and benchmarked in different breeding scenarios.
- Modular design: ADAM has a modular structure, making it easier to extend with new methods and strategies.
Additional advantages of ADAM-Multi
- Breeding optimization and model validation: ADAM was developed to support breeding-program optimization in both animals and plants, and to generate data for validation of statistical models used in genetic evaluations.
- Multi-breed simulation: ADAM-Multi supports simulation of breeding programs involving multiple breeds and crossbreeding settings, enabling comparisons of strategies across breed structures and populations.
- Polyploid and multiallelic QTL simulation: Unlike many simulation tools that assume bi-allelic quantitative trait loci (QTL), ADAM-Multi includes an updated simulation model that can represent multiple alleles at QTL and supports species with different ploidy levels (important for crops such as potato).
- Non-additive genetic architectures: ADAM-Multi can simulate additive, dominance, and epistatic genotypic effects, enabling more realistic exploration of genetic architectures beyond purely additive assumptions.
- Compatibility with standard assumptions: If a bi-allelic QTL assumption is desired, the ADAM-Multi model reduces to the same assumptions used in common simulation programs and standard quantitative genetics textbooks.
- Plant-focused demonstration (potato example): The ADAM-Multi paper demonstrates these extensions in small-scale potato breeding studies, showing (1) dense bi-allelic markers can still predict breeding values effectively in well-structured populations even when underlying QTL are multi-allelic, and (2) explicitly including non-additive effects in the prediction model did not improve the rate of genetic gain in the studied scenarios.
Software versions and availability
ADAM (animals only) - classic version
- This is the original animal-breeding simulator and remains usable at the Center for Quantitative Genetics and Genomics (QGG).
- Note: We do not provide a standalone “download-and-run anywhere” version. External users typically need an account via collaboration to run ADAM in the QGG computing environment.
ADAM-Multi - current version for animals and plants
- ADAM-Multi is the actively developed successor and can simulate both plant and animal breeding programs. It includes extensions for multiple breeds, species with different ploidy levels, and more general genotypic effect models (e.g., allowing multiple alleles at quantitative trait loci).
ADAM-Plant - literature only
- The earlier plant-focused extension is documented in the ADAM-Plant paper (link below); current development is represented by ADAM-Multi.
Practical notes / limitations
ADAM is often used together with DMU packages for predicting breeding values; these tools may require a licence in commercial settings.
The program is written in Fortran and is typically used on Unix/Linux systems. It requires parameter and input-file setup before execution; installation can be challenging for new users.
Based on user experience, it can take time (often several weeks to a few months) for new users to become comfortable with the assumptions, modelling choices, and preparation of input files needed to run their own scenarios.
Access and support
For access, documentation/examples, and guidance on running ADAM in the QGG environment, please contact the current maintainer:
Thinh Tuan Chu
Literature
Pedersen, L. D., Sørensen, A. C., Henryon, M., Ansari-Mahyari, S., & Berg, P. (2009). ADAM: A computer program to simulate selective-breeding schemes for animals. Livestock Science, 121(2–3), 343–344. https://doi.org/10.1016/j.livsci.2008.06.028
Liu, H., Tessema, B. B., Jensen, J., Cericola, F., Andersen, J. R., & Sørensen, A. C. (2019). ADAM-Plant: A software for stochastic simulations of plant breeding. Frontiers in Plant Science, 9, 1926. https://doi.org/10.3389/fpls.2018.01926
Chu, T. T., & Jensen, J. (2025). ADAM-Multi: software to simulate complex breeding programs for animals and plants. Frontiers in Genetics, 16, 1513615. https://doi.org/10.3389/fgene.2025.1513615
