title: Molecular, phylogenetic and comparative genomic analysis of the cytokinin oxidase/dehydrogenase gene family in the Poaceae.
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.
authors.affiliation: National Institute of Agricultural Botany (NIAB), Cambridge, UK.
authors.forename: Sabine
authors.initials: S
authors.lastname: Mameaux
authors.forename: James
authors.initials: J
authors.lastname: Cockram
authors.forename: Thomas
authors.initials: T
authors.lastname: Thiel
authors.forename: Burkhard
authors.initials: B
authors.lastname: Steuernagel
authors.forename: Nils
authors.initials: N
authors.lastname: Stein
authors.forename: Stefan
authors.initials: S
authors.lastname: Taudien
authors.forename: Peter
authors.initials: P
authors.lastname: Jack
authors.forename: Peter
authors.initials: P
authors.lastname: Werner
authors.forename: John C
authors.initials: JC
authors.lastname: Gray
authors.forename: Andy J
authors.initials: AJ
authors.lastname: Greenland
authors.forename: Wayne
authors.initials: W
authors.lastname: Powell
mesh_terms: D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D023281:Genomics / Q000379:methods*; D001467:Hordeum / Q000201:enzymology / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D010088:Oxidoreductases / Q000235:genetics*; D010802:Phylogeny; D020161:Physical Chromosome Mapping; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D006109:Poaceae / Q000201:enzymology* / Q000235:genetics*; D012639:Seeds / Q000201:enzymology / Q000235:genetics; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D059467:Transcriptome / Q000235:genetics; D014908:Triticum / Q000201:enzymology / Q000235:genetics
chemical_list: D010940:Plant Proteins; D010088:Oxidoreductases; C019984:cytokinin oxidase