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The gibberellin (GA)-sensitive dwarfing gene  Ddw1  provides an opportunity to genetically reduce plant height in rye. Genetic analysis in a population of recombinant inbred lines confirmed a monogenetic dominant inheritance of  Ddw1 . Significant phenotypic differences in PH between homo- and heterozygotic genotypes indicate an incomplete dominance of  Ddw1 .  De novo  transcriptome sequencing of  Ddw1  mutant as well as tall genotypes resulted in 113,547 contigs with an average length of 318 bp covering 36.18 Mbp rye DNA. A hierarchical cluster analysis based on individual groups of rye homologs of functionally characterized rice genes controlling morphological or physiological traits including plant height, flowering time, and source activity identified the gene expression profile of stems at the begin of heading to most comprehensively mirror effects of  Ddw1 . Genome-wide expression profiling identified 186 transcripts differentially expressed between semi-dwarf and tall genotypes in stems. In total, 29 novel markers have been established and mapped to a 27.2 cM segment in the distal part of the long arm of chromosome 5R.  Ddw1  could be mapped within a 0.4 cM interval co-segregating with a marker representing the C20-GA2-oxidase gene  ScGA2ox12 , that is up-regulated in stems of  Ddw1  genotypes. The increased expression of  ScGA2ox12  observed in semi-dwarf rye as well as structural alterations in transcript sequences associated with the  ScGA2ox12  gene implicate, that  Ddw1  is a dominant gain-of-function mutant. Integration of the target interval in the wheat reference genome sequence indicated perfect micro-colinearity between the  Ddw1  locus and a 831 kb segment on chromosome 5A, which resides inside of a 11.21 Mb interval carrying the GA-sensitive dwarfing gene  Rht12  in wheat. The potential of  Ddw1  as a breeder’s option to improve lodging tolerance in rye is discussed.

frontiers in plant science

Gene Expression Profiling and Fine Mapping Identifies a Gibberellin 2-Oxidase Gene Co-segregating With the Dominant Dwarfing Gene Ddw1 in Rye (Secale cereale L.)