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The Maize Pan-Genome

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The Maize Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

The pan-genome of a species is comprised of genes/sequences that are present in all individuals in the species (core genome) and genes/sequences that are present in only a subset of individuals within the species (dispensable genome). In maize, the study of the pan-genome began in the 1940s through cytogenetic experiments and has seen an increased focus in research over the last decade largely driven by advances in genome sequencing technologies. It is estimated there are at least 1.5x as many genes in the pan-genome (greater than 60,000 genes) as there are in any individual’s genome (~40,000 genes), with even more variation outside the gene space being observed. This variation has been associated with phenotypic variation and is hypothesized to be an important contributor to the high levels of heterosis often observed in maize hybrids. Due to the high level of variation and the existing genetic and genomic resources, maize has become a model species for plant pan-genomics studies. This chapter will review the mechanisms that can create genome content variation, tools that are available to study the pan-genome, the history of maize pan-genome research ranging from the early cytogenetic studies to today’s genomics-based approaches, and the functional consequences of this variation.

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Acknowledgements

This work was funded in part by the National Science Foundation (Grant IOS-1546727) and ABB was supported by the DuPont Pioneer Bill Kuhn Honorary Fellowship and the University of Minnesota MnDRIVE Global Food Ventures Graduate Fellowship.

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Authors and Affiliations

  1. Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, 55108, MN, USA

    Alex B. Brohammer, Thomas J. Y. Kono & Candice N. Hirsch

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Correspondence to Candice N. Hirsch .

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  1. Department of Genetics, University of Georgia, Athens, GA, USA

    Jeffrey Bennetzen

  2. USDA-ARS, Columbia, MO, USA

    Sherry Flint-Garcia

  3. Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA

    Candice Hirsch

  4. Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy

    Roberto Tuberosa

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Brohammer, A.B., Kono, T.J.Y., Hirsch, C.N. (2018). The Maize Pan-Genome. In: Bennetzen, J., Flint-Garcia, S., Hirsch, C., Tuberosa, R. (eds) The Maize Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-97427-9_2

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