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Gene fractionation and function in the ancient subgenomes of maize

Simon Renny-Byfield, Eli Rodgers-Melnick, Jeffrey Ross-Ibarra
doi: https://doi.org/10.1101/095547
Simon Renny-Byfield
1Department of Plant Sciences, University of California, Davis, CA 95616, USA,
2DuPont Pioneer, Johnston, IA 50131, USA,
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  • For correspondence: sbyfield@ucdavis.edu rossibarra@ucdavis.edu
Eli Rodgers-Melnick
2DuPont Pioneer, Johnston, IA 50131, USA,
3Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA,,
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Jeffrey Ross-Ibarra
1Department of Plant Sciences, University of California, Davis, CA 95616, USA,
4Center for Population Biology and Genome Center, University of California, Davis, CA 95616,USA.
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  • For correspondence: sbyfield@ucdavis.edu rossibarra@ucdavis.edu
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Abstract

The maize genome experienced an ancient whole genome duplication approximately 10 million years ago and the duplicate subgenomes have since experienced reciprocal gene loss (fractionation) such that many genes have returned to single-copy status. This process has not affected the subgenomes equally; reduced gene expression in one of the subgenomes mitigates the consequences of mutations and gene deletions and is thought to drive higher rates of fractionation. Here we take advantage of published genome-wide SNP and phenotype association data to show that, in accordance with predictions of this model, paralogs with greater expression contribute more to phenotypic variation compared to their lowly expressed counterparts. Furthermore, paralogous genes in the least-fractionated subgenome account for a greater degree of phenotypic diversity than those resident on the more-fractionated subgenome. We also show that the two subgenomes of maize are distinct in epigenetic characteristics. Intriguingly, analysis of singleton genes reveals that these differences persist even after fractionation is complete.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 20, 2016.
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Gene fractionation and function in the ancient subgenomes of maize
Simon Renny-Byfield, Eli Rodgers-Melnick, Jeffrey Ross-Ibarra
bioRxiv 095547; doi: https://doi.org/10.1101/095547
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Gene fractionation and function in the ancient subgenomes of maize
Simon Renny-Byfield, Eli Rodgers-Melnick, Jeffrey Ross-Ibarra
bioRxiv 095547; doi: https://doi.org/10.1101/095547

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