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

Authors: WALSH, JESSE - Oak Ridge Institute For Science And Education (ORISE); WOODHOUSE, MARGARET - Iowa State University; Andorf, Carson; Sen, Taner

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/24/2019
Publication Date: 1/3/2020
Citation: Walsh, J.R., Woodhouse, M.R., Andorf, C.M., Sen, T.Z. 2020. Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize. Biomed Central (BMC) Plant Biology. 20. https://doi.org/10.1186/s12870-019-2218-8.
DOI: https://doi.org/10.1186/s12870-019-2218-8

Interpretive Summary: Maize genomes were duplicated approximately 5 to 12 million years ago. In this study, we identify and compare gene expression, protein abundance, and gene function between regions that were duplicated. Our study found distinct differences between duplicated regions, and this information would be helpful for breeders because similar genes that control agronomic traits may have different functions that may need to be studied further or identifying these duplicated genes can provide a larger set of candidate genes to target for breeding.

Technical Abstract: Maize 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. Here 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. Our 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.