ADAM-Plant: A Software for Stochastic Simulations of Plant Breeding From Molecular to Phenotypic Level and From Simple Selection to Complex Speed Breeding Programs

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.

Strategies Using Genomic Selection to Increase Genetic Gain in Breeding Programs for Wheat

“…In addition, the different actions taken at each breeding cycle stage reflected actual wheat-breeding programs. This was possible due to the use of the complex stochastic simulation program ADAM (Liu et al, 2019). The results of this study will contribute to the research on plant breeding as well as serve as a clear guideline for the plant breeding companies for implementation of genomic selection.…”

“…A stochastic simulation model was used to simulate a conventional wheat breeding strategy that run for 25 breeding cycles. Simulations were carried out using ADAM software (Liu et al, 2019). Two different wheat breeding strategies were simulated, (1) phenotypic selection and (2) genomic selection.…”

“…Stochastic simulation was used to quantify expected genetic gain in conventional wheat-breeding programs when incorporating genomic information in making selection decision. Stochastic simulation allow to model breeding schemes that mimics an actual breeding program on a very detailed level (Liu et al, 2019). For instance, stochastic simulation can be used to simulate an entire population of individual plants and it can accounts for the change in allele frequencies caused by selection.…”

MoBPSweb: A web-based framework to simulate and compare breeding programs

“…In recent years a variety of tools to simulate breeding programs ( Sargolzaei and Schenkel 2009 ; Faux et al 2016 ; Liu et al 2019 ; Pérez-Enciso et al 2020 ; Pook et al 2020 ) have been developed to aid breeders in their management decisions as they provide a controlled and repeatable environment to modify individual parameters of a breeding scheme and by that draw conclusions on their impact on the breeding objective. Potential selection goals usually include traits such as productivity, fitness, adaptation, and inbreeding.…”

Genotype by environment interactions in poultry breeding programs

“…Among these, ADAM, which has been intensively developed for more than 10 years, is a relatively comprehensive software for simulation of animal and plant breeding programs. Compared to other simulation programs, ADAM enables us to simulate numerous features for very complex breeding programs: polygenic (infinitesimal) model, genomic (finite locus) model, overlapping breeding cycles, different statistical models, storages of sperm and embryos, and different strategies for phenotyping, genotyping, selection, mating and family structures (Liu et al, 2019;. With the infinitesimal simulation models, stochastic simulation of a complex breeding program is relatively fast with ADAM (Liu et al, 2019;.…”