Molecular Breeding

, Volume 28, Issue 4, pp 421–436 | Cite as

The role and basics of computer simulation in support of critical decisions in plant breeding

Review

Abstract

A number of crucial decisions face the plant breeder before any field activities directed to crop genetic improvement are actually initiated, primarily related to choice of parents and breeding strategy options. Because of the impact, the complexity of these decisions, and the cost of implementing multiple options, computer simulation can be an important resource for the modern breeder. To maximize utility, the simulation tool must be based on effective models of the genome, the breeding process, and other ‘processes’ involved in genetic recombination, identification, and production of new cultivars. Additionally, the statistical methodology employed has ramifications for predicting performance and breeding outcome. The objective of this work is to highlight the role of computer simulation in the planning phases of crop genetic improvement, the basics of model building, statistical considerations, and key issues to be addressed. Examples of publicly available simulation software for plant breeding scenarios are described (features, functionalities, and assumptions) and new directions for improved/expanded approaches and tools are discussed.

Keywords

Computer simulation Genome model Model building Choice of parents Breeding strategy Breeding method 

Abbreviations

BLUP

Best linear unbiased prediction

DH

Doubled haploid

GCA

General combining ability

GEI

Genotype-by-environment interaction

GS

Genomic selection

GWS

Genome-wide selection

LASSO

Least absolute shrinkage and selection operator

LD

Linkage disequilibrium

LE

Linkage equilibrium

LS

Least squares

MAS

Marker-assisted selection

NAM

Maize nested association mapping population

QTL

Quantitative trait locus or loci

RIL

Recombinant inbred line

Notes

Acknowledgments

This research was supported in part by a grant from Monsanto Company, St. Louis, MO, USA; X. Sun and T. Peng were also supported in their graduate studies as Monsanto Fellows in Plant Breeding through a gift of Monsanto Company to the University of Illinois. Many thanks to Drs. Andres Gordillo, Hans Peter Maurer, Nick Lauter, Nick Tinker, Jiankang Wang, and Edie Paul for valued input on their respective software programs. We also extend our appreciation to Drs. Jason Bull, Andrew Davis, G.R. Johnson, and John W. Dudley for their helpful review and valuable commentary on the manuscript. In addition, we wish to thank two anonymous reviewers whose comments helped to improve the manuscript.

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Department of Crop Sciences, Illinois Plant Breeding CenterUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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