Exordium a novel gene in Arabidopsis identified by promoter trapping

The aim of the project was to characterize the expression of a GUS promoter trap in a transgenic line of Arabidopsis thaliana, and to investigate the Amotion of the tagged gene. GUS expression in the transgenic line, designated line EM2, was found to be localized to embryos, and to the regions of most active cell division in the seedling, notably the apical meristems and young leaves. The tagged gene was named EXORDIUM (EXO). Line EM2, which contains a single copy of the promoter trap T-DNA, was found to have no obvious phenotype when homozygous for the T-DNA insertion, and when grown under a range of nutritional and hormonal conditions in vitro. It was found that the expression of the GUS gene and of the native EXO gene, was each up-regulated by exogenous auxin and down-regulated by exogenous cytokinin. The cloned EXO promoter was introduced as a GUS fusion into transgenic plants of A. thaliana and found to be expressed ion the same tissues as EM2, and additionally in the root vascular tissues, leaves and siliques, although to different extents in different transgenic lines. It was found that the EXO mRNA abundance accumulated in seedlings treated with hydroxyurea, which induces cell-cycle arrest at the Gl-S transition. Further analysis demonstrated that EXO mRNA is preferentially abundant during M-phase of the cell cycle. Transgenic plants were produced containing sense and antisense versions of the EXO gene under the transcriptional control of the CaMV35S promoter. One antisense line exhibited an abberant phenotype, characterized by a reduced size and abnormal shoot branching pattern. EXO encodes a predicted protein of 314 amino acids, of unknown function

Optimizing Miscanthus for the Sustainable Bioeconomy:From Genes to Products

In this Research Topic we report advances in fundamental and applied aspects of the perennial C4 bioenergy crop Miscanthus (Miscanthus spp.) and its role in mitigating climate change as part of the bioeconomy. Miscanthus is extremely well suited for bioenergy, biofuel and bioproduct production over a wide geographic area including Europe and North America as well as its native Asia. Miscanthus offers a unique perspective within plant science: the challenge is to domesticate this novel crop for diverse environments and uses while simultaneously developing sustainable value chains to displace fossil fuels and contribute to climate change mitigation. Contributions to this Research Topic were offered from leading Miscanthus researchers from different parts of the world. We accepted 16 articles from 95 authors, which have generated 21,161 views at March 26 2018. Nine of the articles are the output of the European FP7 OPTIMISC project and describe multiple experiments investigating a common set of Miscanthus genotypes in Europe and Asia. These papers are complemented by seven additional articles from global authors, providing a comprehensive analysis of the state of the art of Miscanthus research and application

An interyear comparison of CO2 flux and carbon budget at a commercial-scale land-use transition from semi-improved grassland to Miscanthus x giganteus

A 6‐ha field at Aberystwyth, UK, was converted in 2012 from semi‐improved grassland to Miscanthus x giganteus for biomass production; results from transition to the end of the first 3 years are presented here. An eddy covariance sensor mast was established from year one with a second mast added from year two, improving coverage and providing replicated measurements of CO2 exchange between the ecosystem and atmosphere. Using a simple mass balance approach, above‐ground and below‐ground biomass production are combined with partitioned CO2 fluxes to estimate short‐term carbon deltas across individual years. Years one and two both ended with the site as a net source of carbon following cultivation disturbances, cumulative NEE by the end of year two was 138.57 ± 16.91 g C m−2. The site became a cumulative net sink for carbon by the end of June in the third growing season and remained so for the rest of that year; NEE by the end of year three was −616.52 ± 39.39 g C m−2. Carbon gains were primarily found in biomass pools, and SOC losses were limited to years one (−1.43 Mg C ha−1 yr−1) and two (−3.75 Mg C ha−1 yr−1). Year three saw recoupment of soil carbon at 0.74 Mg C ha−1 yr−1 with a further estimate of 0.78 Mg C ha−1 incorporated through litter inputs over the 3 years, suggesting a net loss of SOC at 3.7 Mg ha−1 from a 0‐ to 30‐cm baseline of 78.61 ± 3.28 Mg ha−1, down 4.7%. Assuming this sequestration rate as a minimum would suggest replacement of cultivation losses of SOC by year 8 of a potential 15‐ to 20‐year crop. Potential coal replacement per hectare of harvest over the three‐year study would offset 6–8 Mg of carbon emission, more than double the SOC losses

Fragments of the key flowering gene <em>GIGANTEA</em> are associated with helitron-type sequences in the Pooideae grass <em>Lolium perenne</em>

BACKGROUND: Helitrons are a class of transposable elements which have been identified in a number of species of plants, animals and fungi. They are unique in their proposed rolling-circle mode of replication, have a highly variable copy-number and have been implicated in the restructuring of coding sequences both by their insertion into existing genes and by their incorporation of transcriptionally competent gene fragments. Helitron discovery depends on identifying associated DNA signature sequences and comprehensive evaluation of helitron contribution to a particular genome requires detailed computational analysis of whole genome sequence. Therefore, the role which helitrons have played in modelling non-model plant genomes is largely unknown. RESULTS: Cloning of the flowering gene GIGANTEA (GI) from a BAC library of the Pooideae grass Lolium perenne (perennial ryegrass) identified the target gene and several GI pseudogene fragments spanning the first five exons. Analysis of genomic sequence 5' and 3' of one these GI fragments revealed motifs consistent with helitron-type transposon insertion, specifically a putative 5'-A↓T-3' insertion site containing 5'-TC and CTAG-3' borders with a sub-terminal 16 bp hairpin. Screening of a BAC library of the closely related grass species Festuca pratensis (meadow fescue) indicated similar helitron-associated GI fragments present in this genome, as well as non-helitron associated GI fragments derived from the same region of GI. In order to investigate the possible extent of ancestral helitron-activity in L. perenne, a methylation-filtered GeneThresher(® )genomic library developed from this species was screened for potential helitron 3' hairpin sequences associated with a 3'-CTRR motif. This identified 7 potential helitron hairpin-types present between at least 9 and 51 times within the L. perenne methylation-filtered library. CONCLUSION: This represents evidence for a possible ancestral role for helitrons in modelling the genomes of Lolium and related species

High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis

We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus