Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

James C. Schnable, Nathan M. Springer, Michael Freeling

Research output: Contribution to journalArticlepeer-review

501 Scopus citations


Ancient tetraploidies are found throughout the eukaryotes. After duplication, one copy of each duplicate gene pair tends to be lost (fractionate). For all studied tetraploidies, the loss of duplicated genes, known as homeologs, homoeologs, ohnologs, or syntenic paralogs, is uneven between duplicate regions. In maize, a species that experienced a tetraploidy 5-12 million years ago, we show that in addition to uneven ancient gene loss, the two complete genomes contained within maize are differentiated by ongoing fractionation among diverse inbreds as well as by a pattern of overexpression of genes from the genome that has experienced less gene loss. These expression differences are consistent over a range of experiments quantifying RNA abundance in different tissues. We propose that the universal bias in gene loss between the genomes of this ancient tetraploid, and perhaps all tetraploids, is the result of selection against loss of the gene responsible for the majority of total expression for a duplicate gene pair. Although the tetraploidy of maize is ancient, biased gene loss and expression continue today and explain, at least in part, the remarkable genetic diversity found among modern maize cultivars.

Original languageEnglish (US)
Pages (from-to)4069-4074
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number10
StatePublished - Mar 8 2011
Externally publishedYes


  • Genome evolution
  • Paleopolyploidy
  • Synteny


Dive into the research topics of 'Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss'. Together they form a unique fingerprint.

Cite this