An optimization approach to gene stacking

European Journal of Operational Research

Volumn 214, Issue 1, 2011, Pages 168-178

  Xu, Pan ^a   Wang, Lizhi ^a   Beavis, William D ^b  

^a Iowa State University   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

Gene stacking; Integer programming; Multi objective optimization; Pareto frontier

Indexed keywords

ALLELIC VARIANTS; COMPUTATIONAL EXPERIMENT; GENETIC DIVERSITY; INBRED LINE; INTEGER PROGRAMMING MODELS; MULTI OBJECTIVE; NP-HARD; OPTIMIZATION APPROACH; PARETO FRONTIER; PARETO FRONTIERS; PARETO OPTIMAL SOLUTIONS; STACKING SCHEME;

GENES; GENETIC PROGRAMMING; GROUND VEHICLE PARTS AND EQUIPMENT; MULTIOBJECTIVE OPTIMIZATION; PARETO PRINCIPLE;

INTEGER PROGRAMMING;

EID: 79957976419     PISSN: 03772217     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ejor.2011.04.012     Document Type: Article

References (39)

1. J.A. Anderson, S. Chao, and S. Liu Molecular breeding using a major QTL for Fusarium head blight resistance in wheat Crop Science 48 2008
2. W.D. Beavis, D. Grant, M. Albertsen, and R. Fincher Quantitative trait loci for plant height in four maize populations and their associations with qualitative genetic loci TAG Theoretical and Applied Genetics 83 2 1991 141 145
3. R.E. Bellman Dynamic Programming 1957 Princeton University Press Princeton, New Jersey
4. R. Bernardo, and A. Charcosset Usefulness of gene information in marker-assisted recurrent selection: A simulation appraisal Crop Science 46 2006 614 621
5. R. Bernardo, and J. Yu Prospects for genomewide selection for quantitative traits in maize Crop Science 47 2007 1082 1090 (Pubitemid 47309157)
6. J.R. Birge, and F.V. Louveaux Introduction to Stochastic Programming 1997 Springer New York
7. D.G. Bonnett, G.J. Rebetzke, and W. Spielmeyer Strategies for efficient implementation of molecular markers in wheat breeding Molecular Breeding 15 2005 75 85 (Pubitemid 40374285)
8. D.J. Cahill, D.H. Schmidt. Use of marker assisted selection in a product development breeding program. In: Proceedings of the 4th International Crop Science Congress, 2004.
9. A. Chinchuluun, and P.M. Pardalos A survey of recent developments in multiobjective optimization Annals of Operations Research 154 1 2007 29 50
10. A. Chinchuluun, P.M. Pardalos, A. Migdalas, and L. Pitsoulis Pareto Optimality,Game Theory and Equilibria 2008 Springer
11. V.C. Concibido, R.L. Denny, S.R. Boutin, R. Hautea, J.H. Orf, and N.D. Young Dna marker analysis of loci underlying resistance to soybean cyst nematode (heterodera glycines ichinohe) Crop Science 34 1994 240 246 (Pubitemid 2044345)
12. C. Darwin The Origin of Species 1872 John Murray London
13. J.C.M. Dekkers Prediction of response to marker-assisted and genomic selection using selection index theory Journal of Animal Breeding and Genetics 124 2007 331 341 (Pubitemid 350231125)
14. V. Deolalikar, P ≠ NP. Technical report, HP Research Labs, 2010.
15. S.R. Eathington, T.M. Crosbie, M.D. Edwards, R.S. Reiter, and J.K. Bull Molecular markers in a commercial breeding program Crop Science 47 2007 154 163
16. J.B.S. Haldane The combination of linkage values and the calculation of distance between the loci of linked factors Journal of Genetics 9 1919 299 309
17. F.S. Hillier, and G.J. Lieberman Introduction to Operations Research 2005 McGraw-Hill New York
18. N.K. Howes, S.M. Woods, and T.F. Townley-Smith Simulations and practical problems of applying multiple marker assisted selection and doubled haploids to wheat breeding programs Euphytica 100 1998 225 230 (Pubitemid 28205290)
19. J. Jung, R. Fan, and L. Jin Combined linkage and association mapping of quantitative trait loci by multiple markers Genetics 170 2005 881 898 (Pubitemid 40980688)
20. P. Kall, and S.W. Wallace Stochastic Programming 1994 Wiley-Interscience New York
21. H. Kebede, P.K. Subudhi, D.T. Rosenow, and H.T. Nguyen Quantitative trait loci influencing drought tolerance in grain sorghum (Sorghum bicolor L. Moench) Theoretical and Applied Genetics 103 2001 266 276 (Pubitemid 32770179)
22. D.D. Kosambi The estimation of map distance from recombination values Annals of Eugenics 12 3 1944 172 175
23. H. Kuchel, G. Ye, R. Fox, and S. Jefferies Genetic and economic analysis of a targeted marker-assisted wheat breeding strategy Molecular Breeding 16 2005 67 78 (Pubitemid 41298034)
24. R. Lande, and R. Thompson Efficiency of marker-assisted selection in the improvement of quantitative traits Genetics 124 1990 743 756 (Pubitemid 20106345)
25. C. Lange, and J.C. Whittaker On prediction of genetic values in marker-assisted selection Genetics 159 2001 1375 1381 (Pubitemid 34033475)
26. T.F.C. Mackay, The genetic architecture of quantitative traits: lessons from Drosophila Current Opinion in Genetics & Development, vol. 14, 2004, pp. 253-257.
27. T.H. Mattheiss, and S.B. Land A tree breeding strategy based on multiple objective linear programming INTERFACES 14 1984 96 104 (Pubitemid 15600515)
28. K.G. Murty Operations Research: Deterministic Optimization Models 1995 Prentice-Hall Englewood Cliffs, NJ
29. P.M. Pardalos, Y. Siskos, and C. Zopounidis Advances in Multicriteria Analysis 1995 Kluwer Academic Publishers
30. D.W. Podlich, C.R. Winkler, and M. Cooper Mapping as you go: An effective approach to marker-assisted-selection of complex traits Crop Science 44 2004 1560 1571 (Pubitemid 39175497)
31. M.O. Pumphrey, R. Bernardo, and J.A. Anderson Validating the Fhb1 QTL for Fusarium head blight resistance in near-isogenic wheat lines developed from breeding populations Crop Science 47 2007 200 206 (Pubitemid 46327853)
32. M.L. Puterman Markov Decision Processes 1994 John Wiley & Sons, Inc.; New York
33. A. Robertson Inbreeding in artificial selection programmes Genetical Research 2 1961 189 194
34. B. Servin, O.C. Martin, M. Mézard, and F. Hospital Toward a theory of marker-assisted gene pyramiding Genetics 168 2004 513 523 (Pubitemid 39346613)
35. S.D. Tanksley, and J. Hewitt Use of molecular markers in breeding for soluble solids content in tomatoa re-examination Theoretical and Applied Genetics 75 1988 811 823
36. J. Wang, S.C. Chapman, D.G. Bonnett, G.J. Rebetzke, and J. Crouch Application of population genetic theory and simulation models to efficiently pyramid multiple genes via marker-assisted selection Crop Science 47 2007 582 588
37. J.C. Whittaker Marker assisted selection and introgression for mapping quantitative trait loci in line crosses using flanking markers Heredity 69 2001 315 324
38. R. Wu, C. Ma, and G. Casella Joint linkage and linkage disequilibrium mapping of quantitative trait loci in natural populations Genetics 160 2002 779 792 (Pubitemid 34194546)
39. C. Zopounidis, and P.M. Pardalos Handbook of Multicriteria Analysis 2010 Springer