A5020236433- Wheat and Barley Genetics and Pathology
- Plant Disease Resistance and Genetics
- Chromosomal and Genetic Variations
- Genetic Mapping and Diversity in Plants and Animals
- Biofuel production and bioconversion
- Plant Genetic and Mutation Studies
- DNA Repair Mechanisms
- Food composition and properties
- Plant Reproductive Biology
- Molecular Biology Techniques and Applications
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Enzyme Production and Characterization
- Polysaccharides and Plant Cell Walls
- Plant tissue culture and regeneration
- Plant and Fungal Interactions Research
- RNA Research and Splicing
- Diet, Metabolism, and Disease
- Plant Molecular Biology Research
- Plant Pathogens and Resistance
- Genetics and Plant Breeding
- Agricultural Productivity and Crop Improvement
- Garlic and Onion Studies
- RNA modifications and cancer
- Photosynthetic Processes and Mechanisms
James Hutton Institute
2014-2025
University of Dundee
2014-2024
RWTH Aachen University
2021-2022
Sanden (Japan)
2008
Abstract Genetic diversity is key to crop improvement. Owing pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence species (known as ‘pan-genome’ 1 ). Multiple high-quality assemblies are an indispensable component pan-genome infrastructure. Barley ( Hordeum vulgare L.) important cereal with long history cultivation that adapted wide range agro-climatic conditions 2 . Here we report construction chromosome-scale for...
Abstract A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed barley using 20 inbred genotypes representing domesticated by generating analyzing short- long-read RNA-sequencing datasets tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific (RTDs) integrated these into linear pan-genome framework to create pan-RTD, allowing...
Pangenomes are collections of annotated genome sequences multiple individuals a species
Barley (Hordeum vulgare) is one of the most important crops worldwide and also considered a research model for large-genome small grain temperate cereals. Despite genomic resources improving all time, they are limited cv Golden Promise, efficient genotype genetic transformation. We have developed barley Promise reference assembly integrating Illumina paired-end reads, long mate-pair Dovetail Chicago in vitro proximity ligation libraries chromosome conformation capture sequencing (Hi-C) into...
The time required to analyse RNA-seq data varies considerably, due discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto Salmon overcome these problems, but require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants.A high-quality, non-redundant barley RTD database (Barley Reference Transcripts - BaRTv1.0) has been generated. BaRTv1.0, was...
SUMMARY Accurate characterisation of splice junctions (SJs) as well transcription start and end sites in reference transcriptomes allows precise quantification transcripts from RNA‐seq data, enables detailed investigations transcriptional post‐transcriptional regulation. Using novel computational methods a combination PacBio Iso‐seq Illumina short‐read sequences 20 diverse tissues conditions, we generated comprehensive highly resolved barley transcript dataset the European 2‐row spring...
Abstract Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one latest developments. Two-row spring cultivars intensely studied they source high-quality grain for malting and distilling. Here we provide data from European two-row population containing 209 different genotypes registered UK market between 1830 to 2014. The dataset encompasses RNA-sequencing six tissues across range developmental stages, phenotypic datasets two consecutive years...
(1,3;1,4)-β-Glucan is an important component of the cell walls barley grain as it affects processability during production alcoholic beverages and has significant human health benefits when consumed above recommended threshold levels. This leads to diametrically opposed quality requirements for different applications low levels (1,3;1,4)-β-glucan are required brewing distilling high positive impacts on health. We quantified content in a collection 399 2-row Spring-type, 204 Winter-type elite...
Phylogenetic analyses of cellulose synthase (CesA) and synthase-like (Csl) families from the gene superfamily were used to reconstruct their evolutionary origins selection histories. Counterintuitively, genes encoding primary cell wall CesAs have undergone extensive expansion diversification following an ancestral duplication a secondary wall-associated CesA. Selection pressure across entire CesA Csl clades appears be low, but this conceals considerable variation within individual clades....
We developed and characterised a highly mutagenised TILLING population of the barley (Hordeum vulgare) cultivar Golden Promise. Promise is 'reference' genotype for transformation primary objective using this was to be able genetically complement observed mutations directly in order prove gene function. Importantly, reference genome assembly has also recently been developed. As our interest identify genes involved meiosis recombination, characterise we focused on set 46 from literature that...
An important component of barley cell walls, particularly in the endosperm, is (1,3;1,4)-β-glucan, a polymer that has proven health benefits humans and influences processability brewing industry. Genes cellulose synthase-like (Csl) F gene family have been shown to be involved (1,3;1,4)-β-glucan synthesis but many aspects biosynthesis are still unclear. Examination sequence assembly genome revealed presence an additional three HvCslF genes (HvCslF11, HvCslF12 HvCslF13) which may synthesis....
Pangenomes are collections of annotated genome sequences multiple individuals a species. The structural variants uncovered by these datasets major asset to genetic analysis in crop plants. Here, we report pangenome barley comprising long-read sequence assemblies 76 wild and domesticated genomes short-read data 1,315 genotypes. An expanded catalogue variation the includes structurally complex loci that have become hot spots gene copy number evolutionarily recent times. To demonstrate utility...
Abstract During plant growth, sodium (Na + ) in the soil is transported via xylem from root to shoot. While excess Na toxic most plants, non-toxic concentrations have been shown improve crop yields under certain conditions, such as when K low. We quantified grain across a barley genome-wide association study panel grown non-saline conditions and identified variants of Class 1 HIGH-AFFINITY-POTASSIUM-TRANSPORTER ( HvHKT1;5 )-encoding gene responsible for content variation these conditions. A...
In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental genetic factors. To gain insights into this specialized reproductive program we used short- long-read RNA-sequencing (RNA-seq) to study the temporal dynamics transcript abundance in immuno-cytologically staged barley ( Hordeum vulgare ) anthers meiocytes. We show that most significant transcriptional changes occur at transition from pre-meiosis leptotene–zygotene,...
Abstract A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species, revealing an assortment functions that drive biological outcomes. We developed barley using twenty inbred genotypes representing domesticated* by generating analysing extensive short- long-read RNA sequencing datasets tissues. To overcome single reference bias facilitate downstream analyses we constructed genotype-specific transcript...
We profiled the grain oligosaccharide content of 154 two-row spring barley genotypes and quantified 27 compounds, mainly inulin- neoseries-type fructans, showing differential abundance. Clustering revealed two profile groups where 'high' set contained greater amounts sugar monomers, sucrose, overall but lower fructosylraffinose. A genome-wide association study (GWAS) identified a significant for variability fructan types: neoseries-DP7 inulin-DP9, which showed increased strength when...
SUMMARY The distribution of recombination events along large cereal chromosomes is uneven and generally restricted to gene‐rich telomeric ends. To understand how the lack affects diversity in pericentromeric regions, we analysed deep exome capture data from a final panel 815 Hordeum vulgare (barley) cultivars, landraces wild barleys, sampled across their eco‐geographical ranges. We defined compared variant non‐pericentromeric observing clear partitioning both within between germplasm groups....
Despite conservation of the process meiosis, recombination landscapes vary between species, with large genome grasses such as barley (Hordeum vulgare L.) exhibiting a pattern that is very heavily skewed to ends chromosomes. We have been using collection semi-sterile desynaptic meiotic mutant lines help elucidate how controlled in and role corresponding wild-type (WT) genes within this process. Here we applied combination genetic segregation analysis, cytogenetics, immunocytology genetically...
Abstract Key message Selection over 70 years has led to almost complete fixation of a haplotype spanning ~ 250 Mbp chomosome 5H in European two-rowed spring barleys, possibly originating from North Africa. Plant breeding and selection have shaped the genetic composition modern crops past decades centuries great improvements agronomic quality traits. Knowledge germplasm is essential make informed decisions programs. In this study, we characterized structure 209 barley cultivars representative...
Abstract Faced with terrestrial threats, land plants seal their aerial surfaces a lipid-rich cuticle. To breathe, interrupt cuticles adjustable epidermal pores, called stomata, that regulate gas exchange, and develop other specialised cells such as defensive hairs. Mechanisms coordinating features remain poorly understood. Addressing this, we studied two loci whose allelic variation causes both cuticular wax-deficiency misarranged stomata in barley, identifying the underlying genes, Cer-g /...
Plant breeding relies on the meiotic recombination or crossing over to generate new combinations of alleles along and among chromosomes. However, is constrained in crops such as barley by a combination low frequency biased distribution. In this study, we attempted identify genes that limit performing suppressor screen for restoration fertility semi-fertile mutant desynaptic10 ( des10 ), carrying mutation ortholog MutL-Homolog 3 HvMLH3 member MutL-homolog (MLH) family DNA mismatch repair...
(1,3;1,4)-β-Glucan is a non-cellulosic polysaccharide required for correct barley grain fill and plant development, with industrial relevance in the brewing functional food sector. Barley grains contain higher levels of (1,3;1,4)-β-glucan compared to other small cereals this influences their end use, having undesirable effects on distilling beneficial linked human health. HvCslF6 main gene contributing biosynthesis grain. Here, transcriptional regulation was investigated using an in-silico...
Abstract Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one latest developments. Two-row spring cultivars intensely studied they source high-quality grain for malting and distilling. Here we provide data from European two-row population containing 209 different genotypes registered UK market between 1830 to 2014. The dataset encompasses RNA-sequencing six tissues across range developmental stages, phenotypic datasets two consecutive years...
Automated shuttles that adhere to a fixed line, so-called virtual rail, exhibit several drawbacks, including restricted flexibility in route selection, compromised passenger safety and comfort from abrupt braking incidents, the need for operator interventions. The “EVA Shuttle” project (EVA) provided an innovative public transport service bridges first last mile using electrical, connected, automated driving shuttle buses. leading-edge concept includes breaking free routes trajectories. Due...
ABSTRACT In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental genetic factors. To gain insights into this specialised reproductive programme we used short- long-read RNA-sequencing (RNA-seq) to study the temporal dynamics transcript abundance in immuno-cytologically staged barley ( Hordeum vulgare ) anthers meiocytes. We show that most significant transcriptional changes occur at transition from pre-meiosis...