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

11 Citations (Scopus)

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 1 2018

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inbred lines
Zea mays
fractionation
Genome
genome
corn
Genes
genes
Duplicate Genes
genome assembly
duplicate genes
phenotypic variation

Keywords

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

PubMed: MeSH publication types

  • Journal Article

Cite this

The limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines. / Brohammer, Alex B.; Kono, Thomas; Springer, Nathan M; McGaugh, Suzanne E; Hirsch, Candice N.

In: Plant Journal, Vol. 93, No. 1, 01.01.2018, p. 131-141.

Research output: Contribution to journalArticle

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