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.)

Abstract

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.

Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

“…A virtual gene-order was released in 2013 10 , and a shotgun de novo genome survey of the same line became available in 2017 11 . Both resources have been rapidly adopted by researchers and breeders 12-14 , but cannot offer the same opportunities as the higher quality genome assemblies available for other Triticeae species 9, 15-19 .…”

A Convenient Co-Dominant Marker for Height-Reducing Ddw1 Allele Useful for Marker-Assisted Selection

“…REMS1218 marker, which is tightly linked to Ddw1 was improved by its combination with REMS1218 SNP marker by Tenhola-Roininen and Tanhuanpa, but was still unable to differentiate Ddw1 homozygotes from Ddw1 ddw1 heterozygotes in some cases [13]. Recently, fine mapping of Ddw1 in rye has been reported [7], however, no practical method for Ddw1 genotyping was provided. In our study we used more types, varieties and a higher number of plants compared to Tenhola-Roininen and Tanhuanpa [13], and by using capillary electrophoresis we observed one more pattern of REMS1218 PCR product (Type 3 in the current paper).…”

“…Plants (names of cultivars are according to http://wheatpedigree.net) with known dominant dwarfing (Ddw1) or recessive neutral (ddw1) alleles of Ddw1 gene were used for Ddw1 CAPS marker development: (1) winter triticale Khongor (Ddw1 Ddw1 Rht-B1b Rht-B1b); (2) winter triticale Avangard (Ddw1 Ddw1 Rht-B1a Rht-B1a); (3) winter triticale Valentin 90 (Ddw1 Ddw1); (4) winter triticale AD Zelenyi (Ddw1 Ddw1); (5) spring triticale Solovei Kharkovskii (ddw1 ddw1 Rht-B1b Rht-B1b); (6) spring triticale Dublet (ddw1 ddw1 Rht-B1b Rht-B1b); (7) winter triticale Dozor (ddw1 ddw1).…”

“…The dominant dwarfing allele of rye Ddw1 (formerly known as Hl) was discovered in the rye genome in a study of natural rye dwarf mutant EM-1 [6]. Recent data suggest that Ddw1 encodes gibberellin 2-oxidase that destroys gibberellin [7].…”

QTL mapping for plant height and fruit branch number based on RIL population of upland cotton

“…Therefore, these genes could also have a certain role in plant height determination in cotton. Evidence indicated that gibberellin caused a reduction in plant height (Monna et al 2002;Sakamoto et al 2004;Braun et al 2019;Annunziata. 2018).…”