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 journalArticle

13 Scopus citations

Abstract

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
Volume93
Issue number1
DOIs
StatePublished - Jan 2018

Keywords

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

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