Building Ultra-High-Density Linkage Maps Based on Efficient Filtering of Trustable Markers

Genetics
Y I RoninA B Korol

Abstract

The study is focused on addressing the problem of building genetic maps in the presence of ∼103-104 of markers per chromosome. We consider a spectrum of situations with intrachromosomal heterogeneity of recombination rate, different level of genotyping errors, and missing data. In the ideal scenario of the absence of errors and missing data, the majority of markers should appear as groups of cosegregating markers ("twins") representing no challenge for map construction. The central aspect of the proposed approach is to take into account the structure of the marker space, where each twin group (TG) and singleton markers are represented as points of this space. The confounding effect of genotyping errors and missing data leads to reduction of TG size, but upon a low level of these effects surviving TGs can still be used as a source of reliable skeletal markers. Increase in the level of confounding effects results in a considerable decrease in the number or even disappearance of usable TGs and, correspondingly, of skeletal markers. Here, we show that the paucity of informative markers can be compensated by detecting kernels of markers in the marker space using a clustering procedure, and demonstrate the utility of this approach fo...Continue Reading

References

Jun 1, 1966·Proceedings of the National Academy of Sciences of the United States of America·M Feldman
Nov 19, 2004·Computational Biology and Chemistry·D I MesterA B Korol
May 10, 2008·PLoS Genetics·Laurent Duret, Peter F Arndt
Apr 2, 2010·Genome Research·Niclas BackströmHans Ellegren
Jun 7, 2012·G3 : Genes - Genomes - Genetics·Y RoninA Korol
Apr 23, 2013·Molecular Ecology·Marius RoestiDaniel Berner
May 15, 2013·G3 : Genes - Genomes - Genetics·Cyrille SaintenacEduard Akhunov
Sep 21, 2013·Genome Biology·Eva BauerChris-Carolin Schön
Oct 1, 2013·Bioinformatics·Pasi RastasPetri Auvinen
Jul 30, 2014·Frontiers in Genetics·Martin Mascher, Nils Stein
Mar 17, 2015·Proceedings of the National Academy of Sciences of the United States of America·Eli Rodgers-MelnickEdward S Buckler
Feb 7, 2016·Seminars in Cell & Developmental Biology·Mridula Nambiar, Gerald R Smith
May 20, 2016·G3 : Genes - Genomes - Genetics·Hsin Y TsaiRoss D Houston
Jul 6, 2016·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Chunhui LiTianyu Wang

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Citations

Jun 29, 2018·The Plant Journal : for Cell and Molecular Biology·Katherine W JordanEduard D Akhunov
Sep 29, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Andrii FatiukhaTamar Krugman
Feb 13, 2021·International Journal of Molecular Sciences·Andrii FatiukhaTamar Krugman

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