Abstract
The paper is devoted to the problem of multipoint gene ordering with a particular focus on "dominance" complication that acts differently in conditions of coupling-phase and repulsion-phase markers. To solve the problem we split the dataset into two complementary subsets each containing shared codominant markers and dominant markers in the coupling-phase only. Multilocus ordering in the proposed algorithm is based on pairwise recombination frequencies and using the well-known travelling salesman problem (TSP) formalization. To obtain accurate results, we developed a multiphase algorithm that includes synchronized-marker ordering of two subsets assisted by re-sampling-based map verification, combining the resulting maps into an integrated map followed by verification of the integrated map. A new synchronized Evolution-Strategy discrete optimization algorithm was developed here for the proposed multilocus ordering approach in which common codominant markers facilitate stabilization of the marker order of the two complementary maps. High performance of the employed algorithm allows systematic treatment for the problem of verification of the obtained multilocus orders, based on computing-intensive bootstrap and jackknife technologies for detection and removing unreliable marker scores. The efficiency of the proposed algorithm was demonstrated on simulated and real data.
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Acknowledgements
This study was supported by the Israeli Ministry of Absorption, the United States-Israel Binational Science Foundation (grant 4556), the German-Israeli Cooperation Project (DIP project funded by the BMBF and supported by the BMBFs International Bureau at the DLR), and the Ancell-Teicher Research Foundation for Molecular Genetics and Evolution. We thank the JoinMap software developers for the possibility to use the package for comparative testing with our new algorithm. The useful comments and suggestions of anonymous referees and J. Snape are acknowledged with thanks.
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Mester, D.I., Ronin, Y.I., Hu, Y. et al. Efficient multipoint mapping: making use of dominant repulsion-phase markers. Theor Appl Genet 107, 1102–1112 (2003). https://doi.org/10.1007/s00122-003-1305-1
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DOI: https://doi.org/10.1007/s00122-003-1305-1