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

TY - JOUR

T1 - ADAM-Plant

T2 - A Software for Stochastic Simulations of Plant Breeding From Molecular to Phenotypic Level and From Simple Selection to Complex Speed Breeding Programs

AU - Liu, Huiming

AU - Tessema, Biructawit Bekele

AU - Jensen, Just

AU - Cericola, Fabio

AU - Andersen, Jeppe Reitan

AU - Sørensen, Anders Christian

PY - 2019/1

Y1 - 2019/1

N2 - 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.

AB - 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.

KW - Breeding program

KW - Genomic selection

KW - Plant breeding

KW - Stochastic simulation

KW - Wheat

U2 - 10.3389/fpls.2018.01926

DO - 10.3389/fpls.2018.01926

M3 - Journal article

C2 - 30687343

SN - 1664-462X

VL - 9

SP - 1926

JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

M1 - 1926

ER -