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The Cyril Scott companion : unity in diversity
This Companion explores the life and work of this remarkably creative man. It provides a comprehensive analysis and appraisal of all the available music and includes a complete catalogue of his musical works, along with a discography. Several works...both music and literary are here newly catalogued and discussed. Altogether, the volume gives a broad picture of Scott's entire output in literary, dramatic and philosophical genres.--Publisher
Book
EasyGeSe – a resource for benchmarking genomic prediction methods
Background
Genomic prediction is a widely used method to predict phenotypes from genotypic data. Advances in both biological and computer science have enabled the generation of vast amounts of data and the development of new algorithms, specifically in the field of machine learning. However, systematic benchmarking of new genomic prediction methods, which is essential for objective evaluation and comparison, remains limited.
Results
Here, we present EasyGeSe, a tool that provides access to a curated collection of datasets for testing genomic prediction methods. This resource encompasses data from multiple species, including barley, common bean, lentil, loblolly pine, eastern oyster, maize, pig, rice, soybean and wheat, representing a broad biological diversity. We filtered and arranged these data in convenient formats, provided functions in R and Python for easy loading and benchmarked several modelling strategies for genomic prediction. Predictive performance, measured by Pearson’s correlation coefficient (
r
), varied significantly by species and trait (
p
< 0.001), ranging from − 0.08 to 0.96, with a mean of 0.62. Comparisons among parametric, semi-parametric and non-parametric models revealed modest but statistically significant (
p
< 1e
−10
) gains in accuracy for the non-parametric methods random forest (+ 0.014), LightGBM (+ 0.021) and XGBoost (+ 0.025). These methods also offered major computational advantages, with model fitting times typically an order of magnitude faster and RAM usage approximately 30% lower than Bayesian alternatives. However, these measurements do not account for the computational costs of hyperparameter tuning.
Conclusions
By standardizing input data and evaluation procedures, this resource simplifies benchmarking and enables fair, reproducible comparisons of genomic prediction methods. It also broadens access to genomic prediction data, encouraging data scientists and interdisciplinary researchers to test novel modelling strategies.
Journal Article
Genome-wide association study of lipase and esterase in wholegrain wheat flour (Triticum aestivum L.)
Lipase activity is one of the main causes of the lipid rancidity in wholegrain wheat flour, leading to its short shelf life. Genetically diverse wheat germplasm offers potential for the selection of wheat cultivars with low lipase activity for stable wholegrain end use. This study evaluated 300 European wheat cultivars harvested in 2015 and 2016 on the genetic association of lipase and esterase activities in wholegrain wheat flour. Esterase and lipase activities in wholegrain flour were measured photometrically with p -nitrophenyl butyrate and p -nitrophenyl palmitate as substrates, respectively. Both enzyme activities showed wide ranges among all cultivars within each year, with differences up to 2.5-fold. The two years showed low correlations between each other, indicating a large environmental impact on the enzyme activities. Cultivars ‘Julius’ and ‘Bueno’ were suggested to be better suited for stable wholegrain products, as they had consistently low esterase and lipase activities compared to the other cultivars. A genome-wide association study revealed associations with single nucleotide polymorphisms in genes located on the high-quality wheat genome sequence of the International Wheat Genome Sequencing Consortium. Eight and four candidate genes were tentatively proposed to be associated to esterase and lipase activity, respectively, in wholegrain flour. Our work shows esterase and lipase activities from a new perspective, that combines reverse genetics to understand the underlying causes. This study outlines the possibilities and limitations to improve lipid stability of wholegrain wheat by genomics-assisted breeding methods, thereby offering new opportunities to optimize the quality of wholegrain wheat flour and wholegrain products.
Journal Article
De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification
Background
Red clover (
Trifolium pratense
L.) is a versatile forage crop legume, which can tolerate a variety of soils and is suitable for silage production for winter feed and for grazing. It is one of the most important forage legumes in temperate livestock agriculture. Its beneficial attributes include ability to fix nitrogen, improve soil and provide protein rich animal feed. It is however, a short-lived perennial providing good biomass yield for two or three years. Improved persistency is thus a major breeding target. Better water-stress tolerance is one of the key factors influencing persistency, but little is known about how red clover tolerates water stress.
Results
Plants from a full sib mapping family were used in a drought experiment, in which the growth rate and relative water content (RWC) identified two pools of ten plants contrasting in their tolerance to drought. Key metabolites were measured and RNA-Seq analysis was carried out on four bulked samples: the two pools sampled before and after drought. Massively parallel sequencing was used to analyse the bulked RNA samples. A
de novo
transcriptome reconstruction based on the RNA-Seq data was made, resulting in 45181 contigs, representing ‘transcript tags’. These transcript tags were annotated with gene ontology (GO) terms. One of the most striking results from the expression analysis was that the drought sensitive plants were characterised by having approximately twice the number of differentially expressed transcript tags than the tolerant plants after drought. This difference was evident in most of the major GO terms. Before onset of drought the sensitive plants overexpressed a number of genes annotated as senescence-related. Furthermore, the concentration of three metabolites, particularly pinitol, but also proline and malate increased in leaves after drought stress.
Conclusions
This
de novo
assembly of a red clover transcriptome from leaf material of droughted and non-droughted plants provides a rich source for gene identification, single nucleotide polymorphisms (SNP) and short sequence repeats (SSR). Comparison of gene expression levels between pools and treatments identified candidate genes for further analysis of the genetic basis of drought tolerance in red clover.
Journal Article
Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement
Red clover (
Trifolium pratense
L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with
Medicago truncatula
and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.
Journal Article
Identification of Candidate Genes for Self-Compatibility in Perennial Ryegrass (Lolium perenne L.)
Self-incompatibility (SI) is a genetic mechanism preventing self-pollination in ~40% of plant species. Two multiallelic loci, called S and Z , control the gametophytic SI system of the grass family (Poaceae), which contains all major forage grasses. Loci independent from S and Z have been reported to disrupt SI and lead to self-compatibility (SC). A locus causing SC in perennial ryegrass ( Lolium perenne L.) was previously mapped on linkage group (LG) 5 in an F 2 population segregating for SC. Using a subset of the same population ( n = 68), we first performed low-resolution quantitative trait locus (QTL) mapping to exclude the presence of additional, previously undetected contributors to SC. The previously reported QTL on LG 5 explained 38.4% of the phenotypic variation, and no significant contribution from other genomic regions was found. This was verified by the presence of significantly distorted markers in the region overlapping with the QTL. Second, we fine mapped the QTL to 0.26 centimorgan (cM) using additional 2,056 plants and 23 novel sequence-based markers. Using Italian ryegrass ( Lolium multiflorum Lam.) genome assembly as a reference, the markers flanking SC were estimated to span a ~3 Mb region encoding for 57 predicted genes. Among these, seven genes were proposed as relevant candidate genes based on their annotation and function described in previous studies. Our study is a step forward to identify SC genes in forage grasses and provides diagnostic markers for marker-assisted introgression of SC into elite germplasm.
Journal Article
C3 photosynthesis in the desert plant Rhazya stricta is fully functional at high temperatures and light intensities
The C3 plant Rhazya stricta is native to arid desert environment zones, where it experiences daily extremes of heat, light intensity (PAR) and high vapour pressure deficit (VPD). We measured the photosynthetic parameters in R. stricta in its native environment to assess the mechanisms that permit it to survive in these extreme conditions.
Infrared gas exchange analysis examined diel changes in assimilation (A), stomatal conductance (g
s) and transpiration (E) on mature leaves of R. stricta. A/c
i analysis was used to determine the effect of temperature on carboxylation capacity (V
c,max) and the light- and CO2-saturated rate of photosynthesis (A
max). Combined chlorophyll fluorescence and gas exchange light response curve analysis at ambient and low oxygen showed that both carboxylation and oxygenation of Rubisco acted as the major sinks for the end products of electron transport.
Physiological analysis in conjunction with gene expression analysis suggested that there are two isoforms of Rubisco activase which may provide an explanation for the ability of R. stricta to maintain Rubisco function at high temperatures.
The potential to exploit this ability to cope with extreme temperatures is discussed in the context of future crop improvement.
Journal Article
Genome-Wide Association Study to Identify Candidate Loci for Biomass Formation Under Water Deficit in Perennial Ryegrass
Global warming is predicted to impact many agricultural areas, which will suffer from reduced water availability. Due to precipitation changes, mild summer droughts are expected to become more frequent, even in temperate regions. For perennial ryegrass ( Lolium perenne L.), an important forage grass of the Poaceae family, leaf growth is a crucial factor determining biomass accumulation and hence forage yield. Although leaf elongation has been shown to be temperature-dependent under normal conditions, the genetic regulation of leaf growth under water deficit in perennial ryegrass is poorly understood. Herein, we evaluated the response to water deprivation in a diverse panel of perennial ryegrass genotypes, employing a high-precision phenotyping platform. The study revealed phenotypic variation for growth-related traits and significant ( P < 0.05) differences in leaf growth under normal conditions within the subgroups of turf and forage type cultivars. The phenotypic data was combined with genotypic variants identified using genotyping-by-sequencing to conduct a genome-wide association study (GWAS). Using GWAS, we identified DNA polymorphisms significantly associated with leaf growth reduction under water deprivation. These polymorphisms were adjacent to genes predicted to encode for phytochrome B and a MYB41 transcription factor. The result obtained in the present study will increase our understanding on the complex molecular mechanisms involved in plant growth under water deficit. Moreover, the single nucleotide polymorphism (SNP) markers identified will serve as a valuable resource in future breeding programs to select for enhanced biomass formation under mild summer drought conditions.
Journal Article
Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (Lolium perenne L.)
Immature pollen can be induced to switch developmental pathways from gametogenesis to embryogenesis and subsequently regenerate into homozygous, diploid plants. Such androgenic production of doubled haploids is particularly useful for species where inbreeding is hampered by effective self-incompatibility systems. Therefore, increasing the generally low androgenic capacity of perennial ryegrass (Lolium perenne L.) germplasm would enable the efficient production of homozygous plant material, so that a more effective exploitation of heterosis through hybrid breeding schemes can be realized. Here, we present the results of a genome-wide association study in a heterozygous, multiparental population of perennial ryegrass (n = 391) segregating for androgenic capacity. Genotyping-by-sequencing was used to interrogate gene- dense genomic regions and revealed over 1,100 polymorphic sites. Between one and 10 quantitative trait loci (QTL) were identified for anther response, embryo and total plant production, green and albino plant production and regeneration. Most traits were under polygenic control, although a major QTL on linkage group 5 was associated with green plant regeneration. Distinct genetic factors seem to affect green and albino plant recovery. Two intriguing candidate genes, encoding chromatin binding domains of the developmental phase transition regulator, Polycomb Repressive Complex 2, were identified. Our results shed the first light on the molecular mechanisms behind perennial ryegrass microspore embryogenesis and enable marker-assisted introgression of androgenic capacity into recalcitrant germplasm of this forage crop of global significance.
Journal Article
Phenotyping a Dynamic Trait: Leaf Growth of Perennial Ryegrass Under Water Limiting Conditions
Water limitation is one of the major factors reducing crop productivity worldwide. In order to develop efficient breeding strategies to improve drought tolerance, accurate methods to identify when a plant reduces growth as a consequence of water deficit have yet to be established. In perennial ryegrass (
L.), an important forage grass of the Poaceae family, leaf elongation is a key factor determining plant growth and hence forage yield. Although leaf elongation has been shown to be temperature-dependent under non-stress conditions, the impact of water limitation on leaf elongation in perennial ryegrass is poorly understood. We describe a method for quantifying tolerance to water deficit based on leaf elongation in relation to temperature and soil moisture in perennial ryegrass. With decreasing soil moisture, three growth response phases were identified: first, a \"normal\" phase where growth is mainly determined by temperature, second a \"slow\" phase where leaf elongation decreases proportionally to soil water potential and third an \"arrest\" phase where leaf growth terminates. A custom R function was able to quantify the points which demarcate these phases and can be used to describe the response of plants to water deficit. Applied to different perennial ryegrass genotypes, this function revealed significant genotypic variation in the response of leaf growth to temperature and soil moisture. Dynamic phenotyping of leaf elongation can be used as a tool to accurately quantify tolerance to water deficit in perennial ryegrass and to improve this trait by breeding. Moreover, the tools presented here are applicable to study the plant response to other stresses in species with linear, graminoid leaf morphology.
Journal Article