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A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies

View ORCID ProfileJose A. Valdes Franco, View ORCID ProfileJoseph L. Gage, View ORCID ProfilePeter J. Bradbury, View ORCID ProfileLynn C. Johnson, View ORCID ProfileZachary R. Miller, View ORCID ProfileEdward S. Buckler, View ORCID ProfileM. Cinta Romay
doi: https://doi.org/10.1101/2020.08.31.268425
Jose A. Valdes Franco
1Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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  • For correspondence: jav246@cornell.edu
Joseph L. Gage
2Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
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  • ORCID record for Joseph L. Gage
  • For correspondence: jav246@cornell.edu
Peter J. Bradbury
3United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA
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Lynn C. Johnson
2Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
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  • ORCID record for Lynn C. Johnson
Zachary R. Miller
2Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
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Edward S. Buckler
1Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
2Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
3United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA
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M. Cinta Romay
2Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
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  • ORCID record for M. Cinta Romay
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Abstract

As a result of millions of years of transposon activity, multiple rounds of ancient polyploidization, and large populations that preserve diversity, maize has an extremely structurally diverse genome, evidenced by high-quality genome assemblies that capture substantial levels of both tropical and temperate diversity. We generated a pangenome representation (the Practical Haplotype Graph, PHG) of these assemblies in a database, representing the pangenome haplotype diversity and providing an initial estimate of structural diversity. We leveraged the pangenome to accurately impute haplotypes and genotypes of taxa using various kinds of sequence data, ranging from WGS to extremely-low coverage GBS. We imputed the genotypes of the recombinant inbred lines of the NAM population with over 99% mean accuracy, while unrelated germplasm attained a mean imputation accuracy of 92 or 95% when using GBS or WGS data, respectively. Most of the imputation errors occur in haplotypes within European or tropical germplasm, which have yet to be represented in the maize PHG database. Also, the PHG stores the imputation data in a 30,000-fold more space-efficient manner than a standard genotype file, which is a key improvement when dealing with large scale data.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Dating of second genome duplication. VG reference corrected.

  • https://www.maizegenetics.net/post/the-first-maize-phg-database-now-available

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
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Posted September 28, 2020.
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A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies
Jose A. Valdes Franco, Joseph L. Gage, Peter J. Bradbury, Lynn C. Johnson, Zachary R. Miller, Edward S. Buckler, M. Cinta Romay
bioRxiv 2020.08.31.268425; doi: https://doi.org/10.1101/2020.08.31.268425
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A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies
Jose A. Valdes Franco, Joseph L. Gage, Peter J. Bradbury, Lynn C. Johnson, Zachary R. Miller, Edward S. Buckler, M. Cinta Romay
bioRxiv 2020.08.31.268425; doi: https://doi.org/10.1101/2020.08.31.268425

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