Chapter 3. Methods and Software for Genetic Mapping

  1. Prof. Dr. Khalid Meksem2,
  2. Prof. Dr. Günter Kahl3
  1. James C. Nelson

Published Online: 28 APR 2005

DOI: 10.1002/3527603514.ch3

Book Title

The Handbook of Plant Genome Mapping: Genetic and Physical Mapping

The Handbook of Plant Genome Mapping: Genetic and Physical Mapping

Additional Information

How to Cite

Nelson, J. C. (2005) Methods and Software for Genetic Mapping, in The Handbook of Plant Genome Mapping: Genetic and Physical Mapping (eds K. Meksem and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. doi: 10.1002/3527603514.ch3

Editor Information

  1. 2

    Dept. Plant, Soil, Agriculture Southern Illinois University, Carbondale, IL 629, USA

  2. 3

    Plant Molecular Biology Biocentre and GenXPro Johann Wolfgang Goethe University Marie-Curie-Strasse 9 60439 Frankfurt am Main, Germany

Author Information

  1. Department of Plant Pathology, Kansas State University, Manhattan, KS 66506-5502, USA

Publication History

  1. Published Online: 28 APR 2005
  2. Published Print: 26 JAN 2005

ISBN Information

Print ISBN: 9783527311163

Online ISBN: 9783527603510

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Keywords:

  • plant genome mapping;
  • genetic mapping;
  • methods and software;
  • locus grouping;
  • locus ordering;
  • multilocus distance estimation;
  • variant and mixed cross designs;
  • methods and tools for QTL mapping in plants;
  • single-marker association;
  • interval mapping (SIM);
  • multiple-trait (MT) QTL mapping;
  • multiple-cross (MC) QTL mapping;
  • future directions in mapping

Summary

This chapter contains sections titled:

  • Introduction

    • Methods and Tools for Genetic Linkage Mapping in Plants

      • Statement of the Problem

    • Locus Grouping

    • Locus Ordering

    • Multilocus Distance Estimation

    • Using Variant and Mixed Cross Designs

      • Outbreeding Species

      • Autopolyploid Species

      • Combining Datasets

    • Linkage-mapping Software Availability, Interfaces, and Features

  • Methods and Tools for QTL Mapping in Plants

    • Statement of the Problem

    • Single-marker Association

      • Metric Traits

      • Categorical Traits

    • Interval Mapping: Simple (SIM)

      • ML Methods

      • Least-squares (Regression) and Nonparametric Methods

    • Interval Mapping: Composite (CIM)

    • Significance Testing

    • Interval Mapping: Multiple-QTL Model Building

      • Stepwise and Exhaustive-search Methods for Building Multiple-QTL Models

      • Markov Chain Monte Carlo (MCMC) Methods

      • Genetic Algorithms

    • Multiple-trait (MT) QTL Mapping

    • Multiple-cross (MC) QTL Mapping

    • Computational Optimization Methods

  • Future Directions in Mapping Methods and Tools

    • Future of Linkage and QTL Mapping

    • Adequacy of Software Tools for Plant Mapping

      • Software Merit Criteria

      • Analytical Scope

      • Ease of Learning and Use

      • Accessibility and Extensibility

    • A Development Model for Public Genetic Mapping Software

  • References

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