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Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize

Authors
  • Walsh, Jesse R.1
  • Woodhouse, Margaret R.2, 3
  • Andorf, Carson M.1, 2
  • Sen, Taner Z.3, 2
  • 1 Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA , Ames (United States)
  • 2 Iowa State University, Ames, IA, 50011, USA , Ames (United States)
  • 3 Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA, 94710, USA , Albany (United States)
Type
Published Article
Journal
BMC Plant Biology
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Jan 03, 2020
Volume
20
Issue
1
Identifiers
DOI: 10.1186/s12870-019-2218-8
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundMaize experienced a whole-genome duplication event approximately 5 to 12 million years ago. Because this event occurred after speciation from sorghum, the pre-duplication subgenomes can be partially reconstructed by mapping syntenic regions to the sorghum chromosomes. During evolution, maize has had uneven gene loss between each ancient subgenome. Fractionation and divergence between these genomes continue today, constantly changing genetic make-up and phenotypes and influencing agronomic traits.ResultsHere we regenerate the subgenome reconstructions for the most recent maize reference genome assembly. Based on both expression and abundance data for homeologous gene pairs across multiple tissues, we observed functional divergence of genes across subgenomes. Although the genes in the larger maize subgenome are often expressing more highly than their homeologs in the smaller subgenome, we observed cases where homeolog expression dominance switches in different tissues. We demonstrate for the first time that protein abundances are higher in the larger subgenome, but they also show tissue-specific dominance, a pattern similar to RNA expression dominance. We also find that pollen expression is uniquely decoupled from protein abundance.ConclusionOur study shows that the larger subgenome has a greater range of functional assignments and that there is a relative lack of overlap between the subgenomes in terms of gene functions than would be suggested by similar patterns of gene expression and protein abundance. Our study also revealed that some reactions are catalyzed uniquely by the larger and smaller subgenomes. The tissue-specific, nonequivalent expression-level dominance pattern observed here implies a change in regulatory control which favors differentiated selective pressure on the retained duplicates leading to eventual change in gene functions.

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