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Linkage Disequilibrium Statistics and Block Visualization

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Plant Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2443))

Abstract

Linkage disequilibrium analysis enables researchers to interrogate the genome for patterns of coinheritance between genetic markers. Visualizing these patterns, and the characteristic haplotype “blocks” of linked variants can be challenging; however, advancements are being made through the development of bioinformatics software. Here, we introduce methods for producing linkage disequilibrium statistics using the widely applicable population genomics tool PLINK, before plotting linkage blocks generated in R and utilizing visualization software LDBlockShow to compare different measures of linkage and definitions of blocks.

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Author information

Authors and Affiliations

  1. School of Biological Sciences, University of Western Australia, Perth, WA, Australia

    Jacob Marsh

Authors
  1. Jacob Marsh
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Correspondence to Jacob Marsh .

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Editors and Affiliations

  1. School of Biological Sciences, University of Western Australia, Perth, WA, Australia

    David Edwards

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Marsh, J. (2022). Linkage Disequilibrium Statistics and Block Visualization. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 2443. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2067-0_25

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  • DOI: https://doi.org/10.1007/978-1-0716-2067-0_25

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2066-3

  • Online ISBN: 978-1-0716-2067-0

  • eBook Packages: Springer Protocols

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