Linkage Disequilibrium: Conifer Genomics Module 10


Nicholas Wheeler, Oregon State University; David Harry, Oregon State University; Heather L. Merk, The Ohio State University

This is the tenth module in a series of 17 developed by the Conifer Translational Genomics Network (CTGN) and Pine Reference Sequence (PineRefSeq). This module by CTGN explores the foundations of linkage disequilibrium (LD) and provides tree-specific examples.


This module focuses on linkage disequilibrium or LD. An understanding of LD will pave the way for the introduction of association genetics and genomic selection. LD is at the root of virtually all marker informed breeding applications. Most outcrossing plants, including the vast majority of coniferous and flowering trees, have genomes that are largely in linkage equilibrium at the population level. QTL mapping works because specific crosses create short-lived LD as a function of genetic linkage unspoiled by generations of recombination (crossing over). Strong LD is largely a function of tight linkage. As we shall see, there are other factors at play; alleles in different genes at great distances from one another on a linkage group, or even on different linkage groups, may persist in LD for some time. The study of LD has revealed a great deal about genome organization and evolution.

Module Screen Shot and Link


Module 10 — Linkage Disequilibrium

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References Cited

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  • Gibson, G., and S. Muse. 2009. A primer of genome science. Sinauer Associates, Sunderland, MA.
  • Grattapaglia, D. 2007. Marker–assisted selection in Eucalyptus. p. 251-281. In. E. P. Guimaraes, J. Ruane, B. D. Scherf, A. Sonnino, and J. D. Dargie (ed.) Marker assisted selection: Current status and future perspectives in crops, livestock, forestry and fish. Food and Agriculture Organization of the United Nations (FAO), Rome, Italy.
  • Grattapaglia, D. and M. Kirst. 2008. Eucalyptus applied genomics: from gene sequences to breeding tools. New Phytologist 179: 911-929. (Available online at: (verified 1 June 2011).
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Cite This Learning Module

Author Contributions

  • Nicholas Wheeler and David Harry developed the learning module content.
  • Heather Merk developed the webpage.

Funding Statement

Support for the Conifer Translational Genomics Network project and the development of the teaching modules hosted here was provided by the USDA/NRI CSREES CAP Award # 2007-55300-18603, the USDA/NIFA AFRI Applied Plant Genomics Coordinated Agricultural Project Award #2009-85606-05680 and the USDA Forest Service. Development of this page was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.


Linkage_Disequilibrium.pdf (2.08 MB)

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