Thomas Didion

Frequency, type, and distribution of EST-SSRs from three genotypes of Lolium perenne, and their conservation across orthologous sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa

BackgroundSimple sequence repeat (SSR) markers are highly informative and widely used for genetic and breeding studies in several plant species. They are used for cultivar identification, variety protection, as anchor markers in genetic mapping, and in marker-assisted breeding. Currently, a limited number of SSR markers are publicly available for perennial ryegrass (Lolium perenne). We report on the exploitation of a comprehensive EST collection in L. perenne for SSR identification. The objectives of this study were 1) to analyse the frequency, type, and distribution of SSR motifs in ESTs derived from three genotypes of L. perenne, 2) to perform a comparative analysis of SSR motif polymorphisms between allelic sequences, 3) to conduct a comparative analysis of SSR motif polymorphisms between orthologous sequences of L. perenne, Festuca arundinacea, Brachypodium distachyon, and O. sativa, 4) to identify functionally associated EST-SSR markers for application in comparative genomics and breeding.ResultsFrom 25,744 ESTs, representing 8.53 megabases of nucleotide information from three genotypes of L. perenne, 1,458 ESTs (5.7%) contained one or more SSRs. Of these SSRs, 955 (3.7%) were non-redundant. Tri-nucleotide repeats were the most abundant type of repeats followed by di- and tetra-nucleotide repeats. The EST-SSRs from the three genotypes were analysed for allelic- and/or genotypic SSR motif polymorphisms. Most of the SSR motifs (97.7%) showed no polymorphisms, whereas 22 EST-SSRs showed allelic- and/or genotypic polymorphisms. All polymorphisms identified were changes in the number of repeat units. Comparative analysis of the L. perenne EST-SSRs with sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa identified 19 clusters of orthologous sequences between these four species. Analysis of the clusters showed that the SSR motif generally is conserved in the closely related species F. arundinacea, but often differs in length of the SSR motif. In contrast, SSR motifs are often lost in the more distant related species B. distachyon and O. sativa.ConclusionThe results indicate that the L. perenne EST-SSR markers are a valuable resource for genetic mapping, as well as evaluation of co-location between QTLs and functionally associated markers.

MADS-box genes from perennial ryegrass differentially expressed during transition from vegetative to reproductive growth

In contrast to well-studied dicot plants like Arabidopsis and Antirrhinum, relatively few genes controlling the transition to flowering and flower development of agronomically important monocot species have been identified. In perennial ryegrass (Lolium perenne) the transition from vegetative to reproductive growth is triggered by an obligate vernalization period (primary induction) of at least 12 weeks at temperatures below 5 degrees C under short days, followed by increased temperature and day length (secondary induction). Here we report the isolation of nine ryegrass MADS-box (LpMADS) genes by a differential display method specific to this family of transcription factors. Three of the nine MADS-box genes show homology to the APETALA 1 (AP1) subfamily, two to the SEPALLATA (SEP) subfamily, one to the AGAMOUS-LIKE 6 (AGL6) subfamily, and three show homology to the newly identified OsMADS1 subfamily. The three AP1 homologues are up-regulated, both in the shoot apex and in leaves, in response to vernalization, while expression of the other six are increased by secondary induction during inflorescence development, although not in leaves. Differences in the sequence and hierarchy of flowering gene expression patterns indicate that the Arabidopsis-based flowering model is not completely applicable to explain the molecular events leading to the floral transition in grasses.

Floral inhibition in red fescue (Festuca rubra L.) through expression of a heterologous flowering repressor from Lolium

Extension of the vegetative growth phase through delay of flowering is an important goal in todays breeding programs of both forage and turf grasses. In forage grasses, the stem and inflorescence production comprise a significant reduction in the digestibility, nutritional value and productivity of the crop, and in turf grasses the stems that start to emerge during the growth season suppress the formation of new shoots and affect the quality, density and persistence of the sward. We have tested the potential of the strong floral repressor LpTFL1 from perennial ryegrass (Lolium perenne L.) to manipulate the transition to flowering in red fescue (Festuca rubra L.), a cool-season turf grass. Expression of LpTFL1 from the constitutive maize ubiquitin promoter represses flowering in red fescue, and the flowering repression phenotype correlates well with the level of LpTFL expression. Transgenic lines showing low to intermediate expression of LpTFL1 flowered approximately two weeks later than the controls, and transgenic lines showing very high LpTFL1 expression levels still remained non-flowering after exposure to natural vernalization conditions (Danish winter) in two successive years. There were no other phenotypic effects associated with the LpTFL transgene expression during vegetative growth. However, there was a tendency towards an LpTFL1-mediated reduction in stem length among the flowering lines. Expression of a truncated LpTFL, caused by transgene rearrangements during the transformation, lead to increased flowering and stem production and a decrease in panicle size. This is to our knowledge the first report on full inhibition of floral development in a commercially important grass species.

Seasonal changes in the metabolic fingerprint of 21 grass and legume cultivars studied by nuclear magnetic resonance-based metabolomics.

A nuclear magnetic resonance (NMR)-based approach was introduced for metabolic fingerprinting of 21 grass and legume cultivars in the present study. Applying principal component analysis (PCA) on the fingerprints obtained on water extracts, it was possible to elucidate the variation between cultivars and the magnitude of changes in the metabolic fingerprint between the spring growth and the second regrowth. Consequently, the potential of the method for tracking differences and changes related to cultivar and season was demonstrated. In addition, partial least-squares (PLS) regressions revealed correlations between the NMR fingerprints and the value of the grasses as animal feed evaluated as concentration of sugars, neutral detergent fibres (NDF) (R = 0.82), indigestible neutral detergent fibres (iNDF) (R = 0.90), and in vitro organic matter digestibility (IVOMD) (R = 0.75). The correlations between these parameters and the NMR fingerprint could mainly be ascribed to differences in spectral intensities from signals assigned to malic acid (2.40 and 4.70 ppm), choline (3.27 ppm), and glucose (5.24 ppm), and the biochemical rationale for this relation is discussed.

Accuracy of Genomic Prediction in a Commercial Perennial Ryegrass Breeding Program

High accuracies for genomic prediction in a perennial ryegrass breeding program The additive genetic variance can be traced by genotyping assays Predictions work across different generations and in different traits Good prospects for the implementation of genomic selection in perennial ryegrass

Expression of a 434:VP16 chimeric activator leads to high-level activation of gene expression in stable transformants of Arabidopsis.

The performance of an expression system based on a fusion of the bacteriophage 434-repressor to the VP16 activation domain of Herpes simplex virus type 1 (434:VP16) was tested after stable integration into Arabidopsis. A special feature of this system was the use of the monocot maize ubiquitin1 and rice actin1 promoters to drive the expression of the 434:VP16 activator and 434-repressor, respectively. Our results demonstrate that the maize ubiquitin1 and the rice actin1 promoters, each of which contain introns, are active in Arabidopsis and can be used to express genes in this dicot species. Activation of gene expression after co-integration of the activator and reporter cassettes into the same genomic locus resulted in a higher activation level (84-fold activation) compared to crossing individual lines expressing only the activator or the operator reporter cassette alone (9-fold activation). Increasing the number of operator elements in the reporter cassette from 1 to 4 increased the activation level in cross-activated lines to an average of 281-fold with one combination of parental lines giving a 900-fold activation. Simultaneous expression of the 434-repressor protein driven by the rice actin promoter resulted in a significant decrease in the 434:VP16 mediated reporter gene expression. Nevertheless, an overall induction via 434:VP16 was possible even in the presence of the 434-repressor protein. This feature is important for genes which need to be absolutely repressed except under activating conditions. To our knowledge this investigation is the first report on the use of the 434:VP16 chimeric activator in an expression system in stably transformed plant lines.

Linking Dynamic Phenotyping with Metabolite Analysis to Study Natural Variation in Drought Responses of Brachypodium distachyon

Drought is an important environmental stress limiting the productivity of major crops worldwide. Understanding drought tolerance and possible mechanisms for improving drought resistance is therefore a prerequisite to develop drought-tolerant crops that produce significant yields with reduced amounts of water. Brachypodium distachyon (Brachypodium) is a key model species for cereals, forage grasses, and energy grasses. In this study, initial screening of a Brachypodium germplasm collection consisting of 138 different ecotypes exposed to progressive drought, highlighted the natural variation in morphology, biomass accumulation, and responses to drought stress. A core set of ten ecotypes, classified as being either tolerant, susceptible or intermediate, in response to drought stress, were exposed to mild or severe (respectively, 15 and 0% soil water content) drought stress and phenomic parameters linked to growth and color changes were assessed. When exposed to severe drought stress, phenotypic data and metabolite profiling combined with multivariate analysis revealed a remarkable consistency in separating the selected ecotypes into their different pre-defined drought tolerance groups. Increases in several metabolites, including for the phytohormones jasmonic acid and salicylic acid, and TCA-cycle intermediates, were positively correlated with biomass yield and with reduced yellow pixel counts; suggestive of delayed senescence, both key target traits for crop improvement to drought stress. While metabolite analysis also separated ecotypes into the distinct tolerance groupings after exposure to mild drought stress, similar analysis of the phenotypic data failed to do so, confirming the value of metabolomics to investigate early responses to drought stress. The results highlight the potential of combining the analyses of phenotypic and metabolic responses to identify key mechanisms and markers associated with drought tolerance in both the Brachypodium model plant as well as agronomically important crops.

Comparative exomics of Phalaris cultivars under salt stress.

BackgroundReed canary grass (Phalaris arundinacea) is an economically important forage and bioenergy grass of the temperate regions of the world. Despite its economic importance, it is lacking in public genomic data. We explore comparative exomics of the grass cultivars in the context of response to salt exposure. The limited data set poses challenges to the computational pipeline.MethodsAs a prerequisite for the comparative study, we generate the Phalaris reference transcriptome sequence, one of the first steps in addressing the issue of paucity of processed genomic data in this species. In addition, the differential expression (DE) and active-but-stable genes for salt stress conditions were analyzed by a novel method that was experimentally verified on human RNA-seq data. For the comparative exomics, we focus on the DE and stable genic regions, with respect to salt stress, of the genome.Results and conclusionsIn our comparative study, we find that phylogeny of the DE and stable genic regions of the Phalaris cultivars are distinct. At the same time we find the phylogeny of the entire expressed reference transcriptome matches the phylogeny of only the stable genes. Thus the behavior of the different cultivars is distinguished by the salt stress response. This is also reflected in the genomic distinctions in the DE genic regions. These observations have important implications in the choice of cultivars, and their breeding, for bio-energy fuels. Further, we identified genes that are representative of DE under salt stress and could provide vital clues in our understanding of the stress handling mechanisms in general.

Comparative exomics of Phalariscultivars under salt stress

BackgroundReed canary grass (Phalaris arundinacea) is an economically important forage and bioenergy grass of the temperate regions of the world. Despite its economic importance, it is lacking in public genomic data. We explore comparative exomics of the grass cultivars in the context of response to salt exposure. The limited data set poses challenges to the computational pipeline.MethodsAs a prerequisite for the comparative study, we generate the Phalaris reference transcriptome sequence, one of the first steps in addressing the issue of paucity of processed genomic data in this species. In addition, the differential expression (DE) and active-but-stable genes for salt stress conditions were analyzed by a novel method that was experimentally verified on human RNA-seq data. For the comparative exomics, we focus on the DE and stable genic regions, with respect to salt stress, of the genome.Results and conclusionsIn our comparative study, we find that phylogeny of the DE and stable genic regions of the Phalaris cultivars are distinct. At the same time we find the phylogeny of the entire expressed reference transcriptome matches the phylogeny of only the stable genes. Thus the behavior of the different cultivars is distinguished by the salt stress response. This is also reflected in the genomic distinctions in the DE genic regions. These observations have important implications in the choice of cultivars, and their breeding, for bio-energy fuels. Further, we identified genes that are representative of DE under salt stress and could provide vital clues in our understanding of the stress handling mechanisms in general.

Comparative exomics of Phalaris

BackgroundReed canary grass (Phalaris arundinacea) is an economically important forage and bioenergy grass of the temperate regions of the world. Despite its economic importance, it is lacking in public genomic data. We explore comparative exomics of the grass cultivars in the context of response to salt exposure. The limited data set poses challenges to the computational pipeline.MethodsAs a prerequisite for the comparative study, we generate the Phalaris reference transcriptome sequence, one of the first steps in addressing the issue of paucity of processed genomic data in this species. In addition, the differential expression (DE) and active-but-stable genes for salt stress conditions were analyzed by a novel method that was experimentally verified on human RNA-seq data. For the comparative exomics, we focus on the DE and stable genic regions, with respect to salt stress, of the genome.Results and conclusionsIn our comparative study, we find that phylogeny of the DE and stable genic regions of the Phalaris cultivars are distinct. At the same time we find the phylogeny of the entire expressed reference transcriptome matches the phylogeny of only the stable genes. Thus the behavior of the different cultivars is distinguished by the salt stress response. This is also reflected in the genomic distinctions in the DE genic regions. These observations have important implications in the choice of cultivars, and their breeding, for bio-energy fuels. Further, we identified genes that are representative of DE under salt stress and could provide vital clues in our understanding of the stress handling mechanisms in general.