Molecular, phylogenetic and comparative genomic analysis of the cytokinin oxidase/dehydrogenase gene family in the Poaceae

Sabine Mameaux, James Cockram, Thomas Thiel, Burkhard Steuernagel, Nils Stein, Stefan Taudien, Peter Jack, Peter Werner, John C Gray, Andy J Greenland, Wayne Powell

Research output: Contribution to journalArticleResearchpeer-review

24 Citations (Scopus)

Abstract

The genomes of cereals such as wheat (Triticum aestivum) and barley (Hordeum vulgare) are large and therefore problematic for the map-based cloning of agronomicaly important traits. However, comparative approaches within the Poaceae permit transfer of molecular knowledge between species, despite their divergence from a common ancestor sixty million years ago. The finding that null variants of the rice gene cytokinin oxidase/dehydrogenase 2 (OsCKX2) result in large yield increases provides an opportunity to explore whether similar gains could be achieved in other Poaceae members. Here, phylogenetic, molecular and comparative analyses of CKX families in the sequenced grass species rice, brachypodium, sorghum, maize and foxtail millet, as well as members identified from the transcriptomes/genomes of wheat and barley, are presented. Phylogenetic analyses define four Poaceae CKX clades. Comparative analyses showed that CKX phylogenetic groupings can largely be explained by a combination of local gene duplication, and the whole-genome duplication event that predates their speciation. Full-length OsCKX2 homologues in barley (HvCKX2.1, HvCKX2.2) and wheat (TaCKX2.3, TaCKX2.4, TaCKX2.5) are characterized, with comparative analysis at the DNA, protein and genetic/physical map levels suggesting that true CKX2 orthologs have been identified. Furthermore, our analysis shows CKX2 genes in barley and wheat have undergone a Triticeae-specific gene-duplication event. Finally, by identifying ten of the eleven CKX genes predicted to be present in barley by comparative analyses, we show that next-generation sequencing approaches can efficiently determine the gene space of large-genome crops. Together, this work provides the foundation for future functional investigation of CKX family members within the Poaceae.

Original languageEnglish
Pages (from-to)67-82
Number of pages16
JournalPlant Biotechnology Journal
Volume10
Issue number1
DOIs
Publication statusPrint publication - Jan 2012
Externally publishedYes

Fingerprint

Hordeum
Poaceae
Triticum
Genome
Genes
Gene Duplication
Setaria Plant
Brachypodium
Sorghum
Prednisolone
Transcriptome
Zea mays
cytokinin oxidase
Organism Cloning
DNA
Proteins

Bibliographical note

© 2011 National Institute of Agricultural Botany (NIAB). Plant Biotechnology Journal © 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

Keywords

  • Chromosomes, Artificial, Bacterial/genetics
  • Expressed Sequence Tags
  • Gene Expression Regulation, Plant
  • Genes, Plant/genetics
  • Genomics/methods
  • Hordeum/enzymology
  • Molecular Sequence Data
  • Multigene Family/genetics
  • Oxidoreductases/genetics
  • Phylogeny
  • Physical Chromosome Mapping
  • Plant Proteins/genetics
  • Poaceae/enzymology
  • Seeds/enzymology
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid
  • Transcriptome/genetics
  • Triticum/enzymology

Cite this

Mameaux, Sabine ; Cockram, James ; Thiel, Thomas ; Steuernagel, Burkhard ; Stein, Nils ; Taudien, Stefan ; Jack, Peter ; Werner, Peter ; Gray, John C ; Greenland, Andy J ; Powell, Wayne. / Molecular, phylogenetic and comparative genomic analysis of the cytokinin oxidase/dehydrogenase gene family in the Poaceae. In: Plant Biotechnology Journal. 2012 ; Vol. 10, No. 1. pp. 67-82.
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Mameaux, S, Cockram, J, Thiel, T, Steuernagel, B, Stein, N, Taudien, S, Jack, P, Werner, P, Gray, JC, Greenland, AJ & Powell, W 2012, 'Molecular, phylogenetic and comparative genomic analysis of the cytokinin oxidase/dehydrogenase gene family in the Poaceae', Plant Biotechnology Journal, vol. 10, no. 1, pp. 67-82. https://doi.org/10.1111/j.1467-7652.2011.00645.x

Molecular, phylogenetic and comparative genomic analysis of the cytokinin oxidase/dehydrogenase gene family in the Poaceae. / Mameaux, Sabine; Cockram, James; Thiel, Thomas; Steuernagel, Burkhard; Stein, Nils; Taudien, Stefan; Jack, Peter; Werner, Peter; Gray, John C; Greenland, Andy J; Powell, Wayne.

In: Plant Biotechnology Journal, Vol. 10, No. 1, 01.2012, p. 67-82.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Mameaux, Sabine

AU - Cockram, James

AU - Thiel, Thomas

AU - Steuernagel, Burkhard

AU - Stein, Nils

AU - Taudien, Stefan

AU - Jack, Peter

AU - Werner, Peter

AU - Gray, John C

AU - Greenland, Andy J

AU - Powell, Wayne

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KW - Plant Proteins/genetics

KW - Poaceae/enzymology

KW - Seeds/enzymology

KW - Sequence Analysis, DNA

KW - Sequence Homology, Nucleic Acid

KW - Transcriptome/genetics

KW - Triticum/enzymology

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