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Genomic Control of Retinal Cell Number: Challenges, Protocol, and Results

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Book cover Systems Genetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1488))

Abstract

This chapter considers some of the challenges in obtaining accurate and consistent estimates of neuronal population size in the mouse retina, in order to identify the genetic control of cell number through QTL mapping and candidate gene analysis. We first discuss a variety of best practices for analyzing large numbers of recombinant inbred strains of mice over the course of a year in order to amass a satisfactory dataset for QTL mapping. We then consider the relative merits of using average cell density versus estimated total cell number as the target trait to be assessed, and why estimates of heritability may differ for these two traits when studying the retina in whole-mount preparations. Using our dataset on cell number for 12 different retinal cell types across the AXB/BXA recombinant inbred strain set as an example, we briefly review the QTL identified and their relationship to one another. Finally, we discuss our strategies for parsing QTL in order to identify prospective candidate genes, and how those candidates may in turn be dissected to identify causal regulatory or coding variants. By identifying the genetic determinants of nerve cell number in this fashion, we can then explore their roles in modulating developmental processes that underlie the formation of the retinal architecture.

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Author information

Authors and Affiliations

  1. Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106-5060, USA

    Patrick W. Keeley, Irene E. Whitney & Benjamin E. Reese

  2. Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106-9625, USA

    Patrick W. Keeley & Irene E. Whitney

  3. Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA

    Irene E. Whitney & Benjamin E. Reese

  4. Department of Psychological and Brain Sciences, University of California, Santa Barbara, CA, 93106-9660, USA

    Benjamin E. Reese

Authors
  1. Patrick W. Keeley
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  2. Irene E. Whitney
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  3. Benjamin E. Reese
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Correspondence to Benjamin E. Reese .

Editor information

Editors and Affiliations

  1. Department of Infection Genetics, Helmholtz Centre for Infection Research & University of Veterinary Medicine Hannover, Braunschweig, Niedersachsen, Germany

    Klaus Schughart

  2. Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA

    Robert W. Williams

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Keeley, P.W., Whitney, I.E., Reese, B.E. (2017). Genomic Control of Retinal Cell Number: Challenges, Protocol, and Results. In: Schughart, K., Williams, R. (eds) Systems Genetics. Methods in Molecular Biology, vol 1488. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6427-7_17

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  • DOI: https://doi.org/10.1007/978-1-4939-6427-7_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6425-3

  • Online ISBN: 978-1-4939-6427-7

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