ArticleFrontiers in plant science2018
ADAM-Plant: A Software for Stochastic Simulations of Plant Breeding From Molecular to Phenotypic Level and From Simple Selection to Complex Speed Breeding Programs.
Article in Frontiers in plant science, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Conventional and Molecular Breeding Tools for Accelerating Genetic Gain in Faba Bean (Frontiers in plant science · 2021Pooled it
- Using deep learning models as a genetic architecture for the simulation of breeding schemes.G3 (Bethesda, Md.) · 2026Article
- Prioritization of deleterious mutations informs genomic prediction and increases the rate of gain in common bean (Phaseolus vulgaris L.), a simulation study.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Bridging tradition and innovation: a review of computer simulations in plant breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Strategies to improve on selection based on estimated breeding values.Genetics, selection, evolution : GSE · 2026Article
- Optimization of breeding program design through stochastic simulation with evolutionary algorithms.G3 (Bethesda, Md.) · 2025Article
- 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.Frontiers in genetics · 2025Article
- Evaluating genomic selection and speed breeding for Fusarium head blight resistance in wheat using stochastic simulations.Molecular breeding : new strategies in plant improvement · 2025Article
- The pipelines of deep learning-based plant image processing.Quantitative plant biology · 2025Review
- PyBrOpS: a Python package for breeding program simulation and optimization for multi-objective breeding.G3 (Bethesda, Md.) · 2024Article
- A framework for simulating genotype-by-environment interaction using multiplicative models.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Genetic Gain and Inbreeding in Different Simulated Genomic Selection Schemes for Grain Yield and Oil Content in Safflower.Plants (Basel, Switzerland) · 2024Article
- Stochastic simulation to optimize rice breeding at IRRI.Frontiers in plant science · 2024Article
- FieldSimR: an R package for simulating plot data in multi-environment field trials.Frontiers in plant science · 2024Article
- Realized Genetic Gain in Rice: Achievements from Breeding Programs.Rice (New York, N.Y.) · 2023Review
- Optimization of breeding program design through stochastic simulation with kernel regression.G3 (Bethesda, Md.) · 2023Article
- A simulation study comparing advanced marker-assisted selection with genomic selection in tree breeding programs.G3 (Bethesda, Md.) · 2023Article
- Population size in QTL detection using quantile regression in genome-wide association studies.Scientific reports · 2023Article
- Blib is a multi-module simulation platform for genetics studies and intelligent breeding.Communications biology · 2022Article
- genomicSimulation: fast R functions for stochastic simulation of breeding programs.G3 (Bethesda, Md.) · 2022Article
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6 authors.
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Abstract
Making decisions on plant breeding programs require plant breeders to be able to test different breeding strategies by taking into account all the crucial factors affecting crop genetic improvement. Due to the complexity of the decisions, computer simulation serves as an important tool for researchers and plant breeders. This paper describes ADAM-plant, which is a computer software that models breeding schemes for self-pollinated and cross-pollinated crop plants using stochastic simulation. The program simulates a population of plants and traces the genetic changes in the population under different breeding scenarios. It takes into account different population structures, genomic models, selection (strategies and units) and crossing strategies. It also covers important features e.g., allowing users to perform genomic selection (GS) and speed breeding, simulate genotype-by-environment interactions using multiple trait approach, simulate parallel breeding cycles and consider plot sizes. In addition, the software can be used to simulate datasets produced from very complex breeding program in order to test new statistical methodology to analyze such data. As an example, three wheat-breeding strategies were simulated in the current study: (1) phenotypic selection, (2) GS, and (3) speed breeding with genomic information. The results indicate that the genetic gain can be doubled by GS compared to phenotypic selection and genetic gain can be further increased considerably by speed breeding. In conclusion, ADAM-plant is an important tool for comparing strategies for plant breeding and for estimating the effects of allocation of different resources to the breeding program. In the current study, it was used to compare different methodologies for utilizing genomic information in cereal breeding programs for selection of best-fit breeding strategy as per available resources.
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