The limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines

Alex B. Brohammer, Thomas Kono, Nathan M Springer, Suzanne E McGaugh, Candice N Hirsch

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


Maize is a diverse paleotetraploid species with considerable presence/absence variation and copy number variation. One mechanism through which presence/absence variation can arise is differential fractionation. Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes during diploidization. Differential fractionation refers to non-shared gene loss events between individuals following a whole-genome duplication event. We investigated the prevalence of presence/absence variation resulting from differential fractionation in the syntenic portion of the genome using two whole-genome de novo assemblies of the inbred lines B73 and PH207. Between these two genomes, syntenic genes were highly conserved with less than 1% of syntenic genes being subject to differential fractionation. The few variably fractionated syntenic genes that were identified are unlikely to contribute to functional phenotypic variation, as there is a significant depletion of these genes in annotated gene sets. In further comparisons of 60 diverse inbred lines, non-syntenic genes were six times more likely to be variable than syntenic genes, suggesting that comparisons among additional genome assemblies are not likely to result in the discovery of large-scale presence/absence variation among syntenic genes.

Original languageEnglish (US)
Pages (from-to)131-141
Number of pages11
JournalPlant Journal
Issue number1
StatePublished - Jan 2018

Bibliographical note

Funding Information:
the University of Minnesota provided computational resources that contributed to this research. ABB was supported by the DuPont Pioneer Bill Kuhn Honorary Fellowship and the MnDRIVE Global Food Ventures Graduate Student Fellowship.

Publisher Copyright:
© 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd


  • Oryza sativa
  • Sorghum bicolor
  • Zea mays
  • comparative genomics
  • fractionation
  • presence/absence variation


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