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An optimization approach to gene stacking

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  • Xu, Pan
  • Wang, Lizhi
  • Beavis, William D.

Abstract

We present a multi-objective integer programming model for the gene stacking problem, which is to bring desirable alleles found in multiple inbred lines to a single target genotype. Pareto optimal solutions from the model provide strategic stacking schemes to maximize the likelihood of successfully creating the target genotypes and to minimize the number of generations associated with a stacking strategy. A consideration of genetic diversity is also incorporated in the models to preserve all desirable allelic variants in the target population. Although the gene stacking problem is proved to be NP-hard, we have been able to obtain Pareto frontiers for smaller sized instances within one minute using the state-of-the-art commercial computer solvers in our computational experiments.

Suggested Citation

  • Xu, Pan & Wang, Lizhi & Beavis, William D., 2011. "An optimization approach to gene stacking," European Journal of Operational Research, Elsevier, vol. 214(1), pages 168-178, October.
  • Handle: RePEc:eee:ejores:v:214:y:2011:i:1:p:168-178
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    References listed on IDEAS

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    1. Altannar Chinchuluun & Panos Pardalos, 2007. "A survey of recent developments in multiobjective optimization," Annals of Operations Research, Springer, vol. 154(1), pages 29-50, October.
    2. T. H. Mattheiss & Samuel B. Land, 1984. "A Tree Breeding Strategy Based on Multiple Objective Linear Programming," Interfaces, INFORMS, vol. 14(5), pages 96-104, October.
    3. Richard Bellman, 1957. "On a Dynamic Programming Approach to the Caterer Problem--I," Management Science, INFORMS, vol. 3(3), pages 270-278, April.
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    Cited by:

    1. Billionnet, Alain, 2013. "Mathematical optimization ideas for biodiversity conservation," European Journal of Operational Research, Elsevier, vol. 231(3), pages 514-534.
    2. Joseph Byrum & Bill Beavis & Craig Davis & Greg Doonan & Tracy Doubler & Von Kaster & Ron Mowers & Sam Parry, 2017. "Genetic Gain Performance Metric Accelerates Agricultural Productivity," Interfaces, INFORMS, vol. 47(5), pages 442-453, October.

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