Efficient multipoint mapping: Making use of dominant repulsion-phase markers

D. I. Mester, Y. I. Ronin, Y. Hu, J. Peng, E. Nevo, A. B. Korol

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)1102-1112
Number of pages11
JournalTheoretical And Applied Genetics
Volume107
Issue number6
DOIs
StatePublished - 1 Oct 2003

Keywords

  • Bootstrap
  • Dominant marker
  • Multilocus ordering
  • Repulsion phase
  • Synchronized optimization algorithm

ASJC Scopus subject areas

  • Genetics
  • Agronomy and Crop Science
  • Biotechnology

Fingerprint

Dive into the research topics of 'Efficient multipoint mapping: Making use of dominant repulsion-phase markers'. Together they form a unique fingerprint.

Cite this