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Milne, L.

Publications and source records attributed to Milne, L..

10 recordsLinked to original sources

EoRNA2: Autonomous Data Discovery and Processing for Databasing of Gene Expression Data

We describe a major new release of the EoRNA database, a gene expression database for barley based on public data, first published in 20211. EoRNA v.2 (https://ics.hutton.ac.uk/eorna2/index.html) features an order of magnitude more samples and is based on a new automated workflow of sample discovery and processing which has enabled a dramatic scale-up the original database. EoRNA v.2 also features a major rebuild of the web user interface with rich new functionality. All infrastructure-related code and database schemas and web components are now species agnostic and publicly available for reuse with other taxa. A dedicated new reference transcript dataset has been created for EoRNA v.2 which is largely based on the recently published barley pan-transcriptome and represents the most comprehensive dataset of its kind to date.

bioinformatics↗

Barley BODYGUARD controls cuticular specialisations regulated by SHINE transcription factors

The outer epidermis of land plants secretes a cuticular layer, a hydrophobic diffusion barrier which minimises water loss into the atmosphere and protects from pests, ultraviolet light and organ fusion. Cuticles typically comprise a polyester cutin matrix embedded and overlaid with cuticular waxes, but their exact chemical make-up, structure and functions can vary widely depending on the tissue and species. Barley shows two such cuticular specialisations: (1) deposition of a thick {beta}-diketone-rich wax bloom on multiple organs at reproductive stage, common in other Poeceae species and linked to yield; and, (2) secretion of a sticky layer on the grain fruit (caryopsis) pericarp cuticle which adheres to inner floral hulls, leading to barleys distinctive covered grain used in animal feed and malting. Two SHINE/WAX-INDUCER transcription factors in barley, HvWIN1 and NUD, promote the wax bloom and hull to caryopsis adhesion, respectively, yet little is understood about other genes involved. Leveraging near-isogenic lines of wax-deficient mutants, we identify the barley BODYGUARD1 (HvBDG1) gene encoding an /{beta}-hydrolase essential for leaf cuticular integrity and wax bloom deposition. Modelling of functional and defective alleles suggests that HvBDG1 N-terminal region control of protein flexibility is important for HvBDG1 function. In addition to their role in controlling barley epicuticular wax deposition, we show that both HvBDG1 and HvWIN1 are essential for strong hull to caryopsis adhesion. Along with NUD, these gene products differentially contribute to ultrastructural changes on the pericarp associated with a cuticular building programme driven by NUD and HvWIN1 regulation of cuticle metabolism and transport and cell wall-related genes, and correlate with shifts in pericarp surface chemistry. We also show that the previously asserted grain-specific role of NUD should be revised, as our findings reveal that it is essential for maintaining leaf cuticle integrity. Our analyses in barley suggest that NUD and HvWIN1 control cuticular specialisations and cuticle integrity in part via promotion of HvBDG1 expression, while HvWIN1 and NUD likely act independently from each other. Lastly, mining tetraploid wheat mutant populations followed by crossing to combine mutated homoeologues demonstrated that BDG1 and WIN1 orthologues also control wax bloom in wheat. Taken together, our work greatly expands the genetic networks and molecular activities important for cuticle development in cereals and the underlying mechanisms for both shared and species-specific cuticular specialisations.

plant biology↗

Development of a Flex-Seq SNP panel for raspberry (Rubus idaeus L.) and validation through linkage map construction and identification of QTL for several traits of agronomic importance to raspberry breeding

High-throughput and reproducible genotyping platforms are critical for advancing genetic research and breeding in horticultural crops. Here, the development and validation of a custom single nucleotide polymorphism (SNP) panel using the Flex-Seq genotyping platform for red raspberry (Rubus idaeus L.) is described. SNPs were derived from existing linkage maps and RNA-seq data, resulting in a panel of 5,639 high-confidence, bi-allelic markers distributed across the seven chromosomes of the R. idaeus Malling Jewel reference genome. The panel was used to genotype 457 red raspberry accessions including 161 individuals from a bi-parental mapping population (Parisx486), enabling the construction of high-density linkage maps and the identification of quantitative trait loci (QTL) for fruit size, leaf colour, plant vigour, and thorn density. Genome-wide association studies (GWAS) identified a major QTL for thornlessness on chromosome 4, co-locating with a candidate HOX3 gene, and multiple QTLs associated with anthocyanin biosynthesis genes for leaf colour. The SNP panel demonstrated utility for linkage mapping and trait association analyses, offering a powerful resource for marker-assisted selection and genetic improvement in red raspberry.

genomics↗

Transcriptional response to Phytophthora root rot in raspberry identifies RiABP19, a Germin-like protein (GLP) gene with a putative role in resistance

Most phytophthora root rot (PRR) outbreaks in symptomatic commercially cultivated raspberry varieties are associated with the prevalence of Phytophthora rubi. Reduced availability of chemical actives and the persistent presence of Phytophthora oospores in the soil contribute to its devastating impact on raspberry-growing regions. In this study, we examined the variation in root morphology in two contrasting raspberry cultivars, Latham (PRR resistant) and Glen Moy (PRR susceptible). We performed RNA-sequencing on Latham roots challenged with P. rubi, to study the transcriptomic response and uncover mechanisms underpinning resistance. We established a new raspberry reference transcript dataset that allowed quantification of raspberry root gene expression. Transcripts significantly upregulated in Latham challenged with P. rubi, included many with characterised roles in resistance, such as Pathogenesis-related proteins and a Germin-like protein, designated RiABP19. The homologous Glen Moy RiABP19 gene showed no differential transcriptional response to PRR infection, indicating a resistance cultivar-specific induction signature following PRR challenge. Three-dimensional structural modelling predicts that RiABP19 contains conserved active sites implicated in auxin-binding and superoxide dismutase activity and can form a homo-hexamer like true germins. Co-immunoprecipitation assays confirmed that RiABP19 can form both homo- and heterodimers in planta. Virus-induced gene silencing of RiABP19 orthologs of in the model plant Nicotiana benthamiana strongly impacts immune signalling, enhancing Phytophthora infestans colonization and attenuating resistance and cell death triggered by the tomato Cf4/Avr4 interaction. These findings suggest that RiABP19 functions as a positive regulator of immunity and may represent a target for future crop improvement in raspberries.

plant biology↗

Silencing of a raspberry homologue of VRN1 is associated with disruption of dormancy induction and misregulation of subsets of dormancy-associated genes.

Winter dormancy is a key process in the phenology of temperate perennials. The changing climate is severely impacting its course leading to economic losses in agriculture. A better understanding of the underlying mechanisms, as well as the genetic basis of the different responses, are necessary for the development of climate-resilient cultivars. This study aims to provide an insight into winter dormancy in red raspberry (Rubus idaeus L). We report the transcriptomic profiles during dormancy in two raspberry cultivars with contrasting responses. The cultivar Glen Ample showed a typical perennial phenology, whereas Glen Dee registered consistent dormancy dysregulation, exhibiting active growth and flowering out of season. RNA-seq combined with weighted gene co-expression network analysis (WGCNA) highlighted gene clusters in both genotypes that exhibited time-dependent expression profiles, Functional analysis of Glen Ample gene clusters highlighted the significance of the cell and structural development prior to dormancy entry as well the role of genetic and epigenetic processes such as RNAi and DNA methylation in regulating gene expression. On the contrary, dormancy release in Glen Ample was associated with upregulation of transcripts associated with the resumption of metabolism, nucleic acid biogenesis and processing signal response pathways. Many of the processes occurring in Glen Ample were dysregulated in Glen Dee and twenty-eight transcripts exhibiting time-dependent expression in Ample that also had an Arabidopsis homologue were not found in all samples from Glen Dee. These included a gene with homology to Arabidopsis VRN1 (RiVRN1.1) that exhibited a sharp decline in expression following dormancy induction in Glen Ample. Characterisation of the gene region in the Glen Dee genome revealed two large insertions upstream of the ATG start codon. We propose that non-expression of a specific VRN1 homologue in Glen Dee causes dormancy misregulation as a result of inappropriate expression of a subset of genes that are directly or indirectly regulated by RiVRN1.1. HIGHLIGHTThe raspberry cultivar Glen Dee exhibits aberrant winter dormancy status associated with insertions in the upstream promoter region of a VRN1 (RiVRN1.1) homologue that silence expression, allowing the identification of dormancy-associated genetic modules that are regulated by RiVRN1.1.

plant biology↗

BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

Accurate characterization of splice junctions as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data and enable detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset (RTD) from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the splice junctions and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared to an earlier version, BaRTv1.0. The accuracy of transcript level quantification, splice junctions and transcript start and end sites has been validated extensively using parallel technologies and analysis, including high resolution RT PCR and 5 RACE. BaRTv2.18 contains 39,434 genes and 148,260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.

plant biology↗

A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

BackgroundAccurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single molecule long read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation or incomplete cDNA synthesis. ResultsWe present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 160k transcripts - twice that of the best current Arabidopsis transcriptome and including over 1,500 novel genes. 79% of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We developed novel methods to determine splice junctions and transcription start and end sites accurately. Mis- match profiles around splice junctions provided a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identified high confidence transcription start/end sites and removed fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provided higher resolution of transcript expression profiling and identified cold- and light-induced differential transcription start and polyadenylation site usage. ConclusionsAtRTD3 is the most comprehensive Arabidopsis transcriptome currently available. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single molecule sequencing analysis from any species.

plant biology↗

EoRNA, a barley gene and transcript abundance database.

A high-quality, barley gene reference transcript dataset (BaRTv1.0), was used to quantify gene and transcript abundances from 22 RNA-seq experiments, covering 843 separate samples. Using the abundance data we developed a Barley Expression Database (EoRNA* - Expression of RNA) to underpin a visualisation tool that displays comparative gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes. EoRNA provides gene and transcript models for all of the transcripts contained in BaRTV1.0, and these can be conveniently identified through either BaRT or HORVU gene names, or by direct BLAST of query sequences. Browsing the quantification data reveals cultivar, tissue and condition specific gene expression and shows changes in the proportions of individual transcripts that have arisen via alternative splicing. TPM values can be easily extracted to allow users to determine the statistical significance of observed transcript abundance variation among samples or perform meta analyses on multiple RNA-seq experiments. * Eorna is the Scottish Gaelic word for Barley

genomics↗

A genome assembly of the barley 'transformation reference' cultivar Golden Promise

BackgroundBarley (Hordeum vulgare) is one of the most important crops worldwide and is also considered a research model for the large-genome small grain temperate cereals. Despite genomic resources improving all the time, they are limited for the cv. Golden Promise, the most efficient genotype for genetic transformation. FindingsWe have developed a barley cv. Golden Promise reference assembly integrating Illumina paired-end reads, long mate-pair reads, Dovetail Chicago in vitro proximity ligation libraries and chromosome conformation capture sequencing (Hi-C) libraries into a contiguous reference assembly. The assembled genome of 7 chromosomes and 4.13Gb in size, has a super-scaffold N50 after Chicago libraries of 4.14Mb and contains only 2.2% gaps. Using BUSCO (benchmarking universal single copy orthologous genes) as evaluation the genome assembly contains 95.2% of complete and single copy genes from the plant database. ConclusionsA high-quality Golden Promise reference assembly will be useful and utilised by the whole barley research community but will prove particularly useful for CRISPR-Cas9 experiments.

genomics↗

BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

BackgroundTime consuming computational assembly and quantification of gene expression and splicing analysis from RNA-seq data vary considerably. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants.\n\nResultsA high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts - BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al., 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al., 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5 and 3 UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2,791 differentially alternatively spliced genes and 2,768 transcripts with differential transcript usage.\n\nConclusionA high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.

genomics↗