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PubMed | Punjab Agricultural University, Institute Salud Carlos III, Kibi International University, Hill International and 11 more.
Type: Journal Article | Journal: Pest management science | Year: 2016

Evolved resistance to fungicides is a major problem limiting our ability to control agricultural, medical and veterinary pathogens and is frequently associated with substitutions in the amino acid sequence of the target protein. The convention for describing amino acid substitutions is to cite the wild-type amino acid, the codon number and the new amino acid, using the one-letter amino acid code. It has frequently been observed that orthologous amino acid mutations have been selected in different species by fungicides from the same mode of action class, but the amino acids have different numbers. These differences in numbering arise from the different lengths of the proteins in each species. The purpose of the present paper is to propose a system for unifying the labelling of amino acids in fungicide target proteins. To do this we have produced alignments between fungicide target proteins of relevant species fitted to a well-studied archetype species. Orthologous amino acids in all species are then assigned numerical labels based on the position of the amino acid in the archetype protein. 2016 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.


News Article | December 26, 2016
Site: www.eurekalert.org

Tens of millions of ash trees across Europe are dying from the Hymenoscyphus fraxinea fungus - the most visible signs that a tree is infected with ash dieback fungus are cankers on the bark and dying leaves. Project leader Dr Richard Buggs from QMUL's School of Biological and Chemical Sciences said: "This ash tree genome sequence lays the foundations for accelerated breeding of ash trees with resistance to ash dieback." A small percentage of ash trees in Denmark show some resistance to the fungus and the reference genome is the first step towards identifying the genes that confer this resistance. The ash tree genome also contains some surprises. Up to quarter of its genes are unique to ash. Known as orphan genes, they were not found in ten other plants whose genomes have been sequenced. Dr Buggs added: "Orphan genes present a fascinating evolutionary conundrum as we have no idea how they evolved." This research is published today in the journal Nature. It involved a collaboration between scientists at: QMUL, the Earlham Institute, Royal Botanic Gardens Kew, University of York, University of Exeter, University of Warwick, Earth Trust, University of Oxford, Forest Research, Teagasc, John Innes Centre, and National Institute of Agricultural Botany. The reference genome from QMUL was used by scientists at York University who discovered genes that are associated with greater resistance to ash dieback. They have used these to predict the occurrence of more resistant trees in parts of the UK not yet affected by the disease, which is spreading rapidly. The genome sequence will also help efforts to combat the beetle Emerald Ash Borer, which has killed hundreds of millions of ash trees in North America. Ash trees have a huge significance in culture and society - they are one of the most common trees in Britain and over 1,000 species, from wildflowers to butterflies, rely on its ecosystem for shelter or sustenance. Ash timber has been used for years for making tools and sport handles, for example hammers and hockey sticks, and is used often for furniture. The work was funded by NERC, BBSRC, Defra, ESRC, the Forestry Commission, the Scottish Government, Marie Sklodowska-Curie Actions, Teagasc - the Agriculture and Food Development Authority. 'Genome sequence and genetic diversity of European ash trees' by E. Sollars et al is published in the journal Nature on Monday 26 December 2016. For further details, images or to arrange interviews with the author please contact the press office. Could disease 'tolerance' genes give new life to UK ash trees? Researchers at the University of York have identified genetic markers for disease tolerance that suggest UK ash trees may have a fighting chance against a fungal infection, which has the potential to wipe out 90% of the European ash tree population. The disease, called ash dieback, was first identified in Poland, where it devastated the native ash tree population. It rapidly spread across northern Europe, and was discovered in the UK in 2012. Results from the latest study, a collaboration between the University of York and Queen Mary University of London, could contribute to breeding new varieties of ash that are tolerant to the disease. The disease is aggressive, spreads quickly through the population, and has no cure, other than individual natural tolerance to the infection. It is spread on the wind or via the transfer of infected saplings between areas. Symptoms include loss of leaves and lesions, which are a useful way to diagnose fungal ash dieback, as they leave a characteristic diamond shape scar on the bark. Professor Ian Bancroft, plant biologist at the University of York, said: "This disease has spread across Europe in less than 10 years so there is some urgency to understand how we can better support breeding programmes for the species. "Ash trees can be found in home gardens, parks, and roadsides and are an important woodland species that support a number of insects and fungi. It is not known exactly how the loss of this tree species will impact the eco-system, but from past examples, we know that the extinction of any species can fundamentally alter the environment." The York team had previously tested a genetic screening process on Danish trees. Using this data alongside information from the ash tree genome, which was sequenced by researchers at Queen Mary University of London (QMUL), they were able to improve the genetic markers for disease tolerance, and use them to predict the tolerance of a sample of trees from across the UK. Early indications suggest that the proportion of UK trees with tolerance to ash dieback is greater than that of the Danish and Polish trees, but it is still unknown whether the UK trees have previously been infected with the disease and built tolerance or whether their genetic tolerance is yet to be tested. Dr Andrea Harper, plant biologist at the University of York, said: "Working with DEFRA, the next stage of this work will be to establish a UK panel suitable for identifying additional, UK-specific, markers for tolerance. This will improve our predictions on individual trees, and provide more information about why some trees are tolerant to the disease. It will also support breeding programmes to develop tolerant varieties of ash." The research, funded by BBSRC and Defra, is published in the journal, Nature. Supportive press release from University of Exeter and University of Warwick: Ash trees which can resist the killer dieback fungus may be more vulnerable to attacks by insects, according to new research. Scientists from the universities of Exeter and Warwick examined trees which are resistant to ash dieback and - unexpectedly - found they had very low levels of chemicals which defend against insects. With efforts under way to protect ash trees from dieback, the scientists warn that selecting trees for fungal resistance could put them at risk from insects. Aside from ash dieback, the other major threat to European ash trees is the Emerald Ash Borer beetle, which has already devastated vast tracts of ash in the USA and is currently spreading westwards across Europe. "Our research highlights the danger of selecting trees for resilience to ash dieback at the expense of resistance to insects that threaten this iconic UK tree species," said joint lead author Dr Christine Sambles, of the University of Exeter. "Ash dieback, which is caused by a fungus called Hymenoscyphus fraxineus, can kill young trees in a season, while older trees tend to decline and die over several years." The research, published in the journal Nature, is part of a study involving several universities and Government institutes which looked at the DNA of ash trees in the hope of identifying ash dieback resistance. Instead of focussing on DNA, the Exeter and Warwick scientists looked at differences in chemical composition between tolerant and susceptible ash trees. "Plants use a vast range of chemicals to defend against fungal attack, and the primary objective was to identify differences which could be used to screen young ash trees and choose the best ones for replanting," said co-author Professor Murray Grant, Elizabeth Creak Chair in Food Security at the University of Warwick. "Our findings underline the need for further research to ensure that we select ash trees resilient to present and future threats." Co-author Dr David Studholme, of the University of Exeter, added: "These findings highlight Exeter's world-class expertise in high-impact, integrative plant science underpinned by key research infrastructure, such as the Mass Spectrometry facility." Researchers have identified genetic markers for disease tolerance that suggest UK ash trees may have a fighting chance against a fungal infection that has the potential to wipe out 90% of the European ash tree population. The disease, called ash dieback, was first identified in Poland, where it devastated the native ash tree population. It rapidly spread across northern Europe, and was discovered in the UK in 2012. Results from the latest study published in Nature, a UK collaboration between Queen Mary University of London (QMUL), University of York, Earlham Institute (EI), John Innes Centre (JIC), NIAB and the University of Copenhagen, could contribute to breeding new varieties of ash that are tolerant to the disease. Much like Dutch elm disease, ash dieback is aggressive, spreads quickly through the ash tree population, and has no cure, other than individual natural tolerance to the infection. It is spread on the wind or via the transfer of infected saplings between areas. Symptoms include loss of leaves and lesions, which are a useful way to diagnose fungal ash dieback, as they leave a characteristic diamond-shaped scar on the bark. The York team had previously tested a genetic screening process on Danish trees identified by collaborators at the University of Copenhagen as having a range of different levels of disease susceptibility. Using this data alongside information from the ash tree genome, which was sequenced by researchers at QMUL by utilising EI's reference gene models, they were able to improve the genetic markers for disease tolerance, and use them to predict the tolerance of a sample of trees from across the UK. Leading to these research findings, EI (previously 'The Genome Analysis Centre') generated the transcriptome and re-sequencing (together with the Institute's previous analysis of the resistant 'Tree 35' from Denmark released in 2013) data to conduct the bioinformatics analysis of the UK ash tree, in alignment with the Nornex Consortium to combat Ash Dieback, funded by DEFRA and BBSRC. The analysis was carried out on a subset of the tree's genetic regions, with high coverage across the samples. This increased the number of potential markers that could be used to sustain ash tree diversity for breeding programmes. EI also sequenced 37 trees originating from across Europe to investigate genomic diversity in ash. The data were analysed by researchers at QMU, JIC and NIAB finding evidence for apparent long-term decline in effective population size. The EI team generated the most comprehensive annotation of ash genes to date, and this will aid researchers in identifying genetic variants linked to specific traits associated with the killer tree disease. This will help seek out the suspected tolerant genes and support future breeding programmes of ash trees with low susceptibility to the disease. Dr David Swarbreck, Regulatory Genomics Group Leader at EI, said: "Having a more comprehensive annotation of ash genes has improved the identification of markers for ash dieback and will aid future functional studies into this prevalent disease." Professor Mario Caccamo, previously at EI, now Head of Crop Bioinformatics at NIAB, added: "This effort is a great example of team-work across several leading UK research organisations responding to the devastating threat of ash dieback. The identification of markers for tolerance will be a very important tool in the toolbox that complements other ongoing efforts to manage the threat of this disease. We have also generated important genomic resources that will support other studies and offer the foundations for more research into tackling the epidemic." Professor Allan Downie, Emeritus Fellow at JIC and coordinator of the NORNEX programme, commented: "This work represents significant new progress in our understanding of ash dieback disease and the patterns of inheritance of tolerance to this disease. Our success has been built on excellent national and international collaborations. These have brought the strengths of genomics and transcriptomics research in the UK together with the excellent analyses of disease susceptibility done in Denmark, to enhance our research into UK ash trees. This progress has been breath-taking in its speed and as a research coordinator based at JIC; I have been delighted by the spirit of collaboration and determination brought to this project by my Danish and UK collaborators. Early indications suggest that the proportion of UK trees with tolerance to ash dieback is greater than that of the Danish and Polish trees, but it is still unknown whether the UK trees have previously been infected with the disease and built tolerance or whether this is due to their genetic tolerance, is yet to be tested. The study, "Genome sequence and genetic diversity of European ash trees" is published in the journal, Nature. A team of scientists have successfully decoded the genetic sequence of the ash tree, to help the fight against the fungal disease, ash dieback. In a paper published by the journal Nature today, a team of researchers led by Richard Buggs, who heads up plant health research at the Royal Botanic Gardens, Kew, assembled a reference genome and analysed the diversity of ash trees throughout Europe. Their collaborators have used this resource to identify genes that may be associated with low susceptibility to ash dieback. They used these to predict the effect that ash dieback will have on ash trees all over Britain. The genome sequence will also help efforts to combat the beetle Emerald Ash Borer, which has already killed hundreds of millions of ash trees in North America. Project Leader Dr Richard Buggs, Senior Research Leader (Plant Health) at RBG Kew who conducted the work at Queen Mary University of London's (QMUL) School of Biological and Chemical Sciences said: "This is the first time a plant genome has been rapidly sequenced in response to an emerging disease threat, leading to an assessment of the susceptibility of as yet uninfected populations. Kew is continuing to work with the latest genomic technologies to increase the armoury of methods that can be deployed against plant pests and pathogens." There are 520 specimens of the Ash tree at Kew and its Sussex site, Wakehurst (227 of these are at Kew). At Kew's Millennium Seed bank scientists are also involved in gathering seed of different ash populations around Britain to help inform broader efforts to control disease spread and drive plant health policy.


Taylor A.,University of Warwick | Coventry E.,NIAB | Jones J.E.,University of Warwick | Clarkson J.P.,University of Warwick
Plant Pathology | Year: 2015

Sclerotinia stem rot (SSR) of oilseed rape (OSR, Brassica napus), caused by Sclerotinia sclerotiorum, is a serious problem in the UK and worldwide. As fungicide-based control approaches are not always reliable, identifying host resistance is a desirable and sustainable approach to disease management. This research initially examined the aggressiveness of 18 Sclerotinia isolates (17 S. sclerotiorum, one S. subarctica) on cultivated representatives of B. rapa, B. oleracea and B. napus using a young plant test. Significant differences were observed between isolates and susceptibility of the brassica crop types, with B. rapa being the most susceptible. Sclerotinia sclerotiorum isolates from crop hosts were more aggressive than those from wild buttercup (Ranunculus acris). Sclerotinia sclerotiorum isolates P7 (pea) and DG4 (buttercup), identified as 'aggressive' and 'weakly aggressive', respectively, were used to screen 96 B. napus lines for SSR resistance in a young plant test. A subset of 20 lines was further evaluated using the same test and also in a stem inoculation test on flowering plants. A high level of SSR resistance was observed for five lines and, although there was some variability between tests, one winter OSR (line 3, Czech Republic) and one rape kale (line 83, UK) demonstrated consistent resistance. Additionally, one swede (line 69, Norway) showed an outstanding level of resistance in the stem test. Resistant lines also had fewer sclerotia forming in stems. New pre-breeding material for the production of SSR resistant OSR cultivars relevant to conditions in the UK and Europe has therefore been identified. © 2014 British Society for Plant Pathology.


Leflon M.,CETIOM | Husken A.,Julius Kuhn Institute | Kightley S.,NIAB | Pinochet X.,CETIOM
Plant Breeding | Year: 2011

With 3 figures and 4 tables At the field scale, pollen flow between adjacent fields limits the potential of coexistence of different farming production systems, especially for allogamous crops like oilseed rape whose pollen is disseminated by insects or wind. In this article, we examine the efficiency of cleistogamy in an oilseed rape line which showed between 90% and 99% of flowers closed at flowering, in limiting deposition of allo-pollen. Five trials were established, consisting of two adjacent blocks, the one sown with the cleistogamous low-erucic acid line and the other with a classically flowering high-erucic acid line, used as source of contaminating pollen, itself artificially contaminated with a 1% mix of cleistogamous plants. Analyses showed that cross-fertilization rates of cleistogamous plants, estimated through erucic acid contents of seeds collected from them, were lower than those generally observed in oilseed rape: it averaged 10.1% on isolated plants within the erucic blocks, reached to the maximum 14% immediately adjacent to the erucic block, then decreased exponentially at higher distances. Cleistogamy appeared therefore as one imperfect means of gene bio-containment. © 2011 Blackwell Verlag GmbH.


Jones H.,NIAB | Mackay I.,NIAB
Theoretical and Applied Genetics | Year: 2015

Key message: Alternative methods for genomic prediction of traits and trait differences are compared and recommendations made. We make recommendations for implementing methods in the context of DUS testing. Abstract: High-throughput genotyping provides an opportunity to explore the application of genotypes in predicting plant phenotypes. We use a genome-wide prediction model to estimate the contribution of all loci and sum over multiple minor effects to predict traits. A potential use is in plant variety protection to discriminate among varieties on distinctness. We investigate this use with alternate scenarios in a set of 431 winter and spring barley varieties, with trait data from UK DUS trials comprising 28 characteristics, together with SNP genotype data. Firstly, each trait is predicted from genotypes by ridge regression with discrimination among varieties using predicted traits. Secondly, squared trait differences between each pair of varieties are regressed on genetic distances between each variety by ridge regression, with discrimination among varieties using the predicted squared trait differences directly. This latter approach is analogous to the use of phenotype and marker differences introduced to human genetic linkage analysis by Haseman and Elston and to the analysis of heritability in natural populations of plants by Ritland. We compare correlations between methods, both trait by trait and summarised across all traits. Our results show wide variation among correlations for each trait. However, the aggregate distances calculated from values predicted by genotypes show higher correlations with distances calculated from measured values than any previously reported. We discuss the applicability of these results to implementation of UPOV Model 2 in DUS testing and suggest ‘success criteria’ that should be considered by testing authorities seeking to implement UPOV Model 2. © 2015, Springer-Verlag Berlin Heidelberg.


Buckingham D.L.,Royal Society for the Protection of Birds | Bentley S.,NIAB | Dodd S.,Royal Society for the Protection of Birds | Peach W.J.,Royal Society for the Protection of Birds
Agriculture, Ecosystems and Environment | Year: 2011

We experimentally managed silage fields to provide abundant seed as a conservation measure for wintering birds. Buntings Emberiza strongly selected seeded ryegrass plots, where they fed predominantly on ryegrass Lolium seed and maintained body weights similar to those on high-quality arable wintering habitats. Bunting usage of seeded plots was positively related to Lolium seedhead density, peaking at October seedhead densities above 400seedheadsm -2. Perennial ryegrass Lolium perenne swards could only provide one early silage crop (cut by mid-late May) if sufficient seed was to be produced, while Italian ryegrass Lolium multiflorum was able to provide two silage cuts and a large seed crop. Mats of lodged seedheads ensured the continuity of seed provision, resulting in high bird usage during late winter, when most seed has been depleted from existing wild bird seed measures. The estimated cost of the measure was comparable to small-plot measures in current English agri-environment schemes. A rotational seeded ryegrass measure should constitute an effective, affordable and widely applicable conservation measure for seed-eating farmland birds in grassland-dominated farmland across NW Europe. © 2011 Elsevier B.V.


Hayot Carbonero C.,University of Manchester | Hayot Carbonero C.,Urbana University | Carbonero F.,Urbana University | Smith L.M.J.,NIAB | Brown T.A.,University of Manchester
Genetic Resources and Crop Evolution | Year: 2012

Sainfoin (Onobrychis viciifolia Scop.) is a perennial forage legume that possesses beneficial properties in the context of sustainable agriculture. In order to initiate a pre-breeding programme, we have assembled a germplasm collection of O. viciifolia from many geographic regions, as well as a collection of Onobrychis species that might be crossed with O. viciifolia to improve its biological and agronomic properties. The objective of this study was to obtain DNA sequences from a representative sample of these accessions in order to characterise their genetic diversity and to assess the robustness of the Onobrychis taxonomy. Because of potential problems with copurification of tannins and polyphenols from Onobrychis leaf tissue, three methods for DNA extraction were assessed and the most appropriate one identified. DNA sequences were obtained for the nuclear internal transcribed spacer region and the trnH-psbA and trnT-trnL intergenic spacers of the chloroplast genome. Neighbour joining trees were constructed and accessions were assigned to operational taxonomic units. The results indicated that there is substantial genetic diversity among Onobrychis species. Redundancies in species nomenclature were identified, as well as possible overlap between some of the sections into which the Onobrychis genus has been divided. A genetic distinction was apparent between O. viciifolia accessions from western Europe and those from eastern Europe and Asia, reflecting a similar division based on agronomic properties. Recognition of these different though related germplasms will be valuable in the design of breeding programmes for the rational improvement of sainfoin as a forage crop for sustainable agriculture. © 2012 Springer Science+Business Media B.V.


Akhtar N.,NIAB | Tufail M.,Pakistan Institute of Engineering and Applied Sciences
International Journal of Environmental Research | Year: 2011

Wheat is a staple food in Pakistan. Production of wheat is increased with extensive use of phosphate based fertilizers in agricultural fields. Activity mass concentration of primordial radionuclides due to use of phosphate fertilizers in soil enhances the external gamma dose and due to the consumption of wheat food grown on these soils also increases the internal dose. Different types of soil, including saline and normal soil in the districts of Lahore and Faisalabad in Punjab were selected for this study. The technique of gamma ray spectroscopy was used for the determination of s levels of radioactivity 226Ra, 232Th, 40K, and the nuclear fallout 137Cs in soil, wheat and wheat made products. Radioactivity in flour, chapatti, bread, nan and rusk was determined. Maximum activity was found in the chapatti sample of highly fertilized soil. Calculations were made for the determination of external absorbed dose in air from soil and internal absorbed dose in human body due to the consumption of wheat and wheat products. The average value of wheat consumption of 140 kg was used in the estimation of ingestion dose. The value of the ingestion dose due to highly fertilized soil was 206.1 μSv/Yr, while the total ingestion dose due to unfertilized farm's food was 146.3 μSv/Yr. Risk assessment to man due to ingestion of wheat was also calculated. The cancer risk assessment due to ingestion of wheat food grown on highly fertilized soils comes as additional sufferings of 14 persons in cancer per million.


Patent
Niab | Date: 2015-02-11

A new and distinct Buglossoides arvensis plant named MALIN characterized by vigorous plant growth and abundant side shoot development. Plants flower early in May and June and do not require vernalization. Seed germination rate is typically 80%. Seeds of the plant are used in the production of the oil commercially known Ahiflower oil.


PubMed | University of Cambridge and NIAB
Type: Journal Article | Journal: TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik | Year: 2015

Four QTL conferring resistance to ergot were identified in the UK winter wheat varieties Robigus and Solstice. Two QTL co-located with semi-dwarfing alleles at the Rht loci Rht - 1B and Rht - 1D implicating a role of these DELLA proteins in infection success of Claviceps purpurea. The fungal pathogen Claviceps purpurea infects ovaries of a broad range of temperate grasses and cereals, including hexaploid wheat, causing a disease commonly known as ergot. Sclerotia produced in place of seed carry a cocktail of harmful alkaloid compounds that result in a range of symptoms in humans and animals, causing ergotism. Following a field assessment of C. purpurea infection in winter wheat, two varieties Robigus and Solstice were selected which consistently produced the largest differential effect on ergot sclerotia weights. They were crossed to produce a doubled haploid mapping population, and a marker map, consisting of 714 genetic loci and a total length of 2895cM was produced. Four ergot reducing QTL were identified using both sclerotia weight and size as phenotypic parameters; QCp.niab.2A and QCp.niab.4B being detected in the wheat variety Robigus, and QCp.niab.6A and QCp.niab.4D in the variety Solstice. The ergot resistance QTL QCp.niab.4B and QCp.niab.4D peaks mapped to the same markers as the known reduced height (Rht) loci on chromosomes 4B and 4D, Rht-B1 and Rht-D1, respectively. In both cases, the reduction in sclerotia weight and size was associated with the semi-dwarfing alleles, Rht-B1b from Robigus and Rht-D1b from Solstice. Two-dimensional, two-QTL scans identified significant additive interactions between QTL QCp.niab.4B and QCp.niab.4D, and between QCp.niab.2A and QCp.niab.4B when looking at sclerotia size, but not between QCp.niab.2A and QCp.niab.4D. The two plant height QTL, QPh.niab.4B and QPh.niab.4D, which mapped to the same locations as QCp.niab.4B and QCp.niab.4D, also displayed significant genetic interactions.

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