Oak Park is home to the National Centre for Arable Crops Research. Situated on 225 hectare research farm, the main objective of the work programme at Oak Park is to support the arable crops sector of Irish agriculture. The task ahead is to adapt new challenges in developing sustainable and environmentally sensitive agricultural systems which will provide farmers with adequate incomes and consumers with quality food at reasonable prices.

Recent Submissions

  • Gene Expression Pattern in Olive Tree Organs (Olea europaea L.)

    Ramírez-Tejero, Jorge A.; Jiménez-Ruiz, Jaime; Leyva-Pérez, María de la O; Barroso, Juan Bautista; Luque, Francisco; Regional Government of Andalusia; Spanish Ministry of Economy, Industry and Competitiveness; Spanish State Research Agency; European Union; AGR-6038; et al. (MDPI AG, 2020-05-12)
    The olive tree (Olea europaea L.) was one of the first plant species in history to be domesticated. Throughout olive domestication, gene expression has undergone drastic changes that may affect tissue/organ-specific genes. This is an RNA-seq study of the transcriptomic activity of different tissues/organs from adult olive tree cv. “Picual” under field conditions. This analysis unveiled 53,456 genes with expression in at least one tissue, 32,030 of which were expressed in all organs and 19,575 were found to be potential housekeeping genes. In addition, the specific expression pattern in each plant part was studied. The flower was clearly the organ with the most exclusively expressed genes, 3529, many of which were involved in reproduction. Many of these organ-specific genes are generally involved in regulatory activities and have a nuclear protein localization, except for leaves, where there are also many genes with a plastid localization. This was also observed in stems to a lesser extent. Moreover, pathogen defense and immunity pathways were highly represented in roots. These data show a complex pattern of gene expression in different organs, and provide relevant data about housekeeping and organ-specific genes in cultivated olive.
  • MAJOR AND MICRO NUTRIENT ADVICE FOR PRODUCTIVE AGRICULTURAL CROPS

    Wall, David, P.; Plunkett, Mark (2021-07-21)
    A major responsibility of the research staff at Johnstown Castle has been the publication of leaflets, booklets and manuals giving nutrient and trace element advice for grassland and crops. This began in the 1940s and was the scientific basis for soil analysis (Coulter 2000), since then, further updates were published by Coulter in 2004 (2nd edition), by Coulter and Lalor in 2008 (3rd edition) and by Wall and Plunkett in 2016 (4th edition. This version has now been enhanced and expanded to produce the present volume (5 th edition) published by Wall and Plunkett in 2020. New sections and information and updates based on the latest scientific findings have been made to grassland fertiliser advice section including nitrogen advice for grass–white clover swards. Many of the chapters have been reorganised to make them easier to consult and the advice and tables have been redesigned to be compliant with the latest European and Irish legislation.
  • Physiological and Transcriptional Response to Drought Stress Among Bioenergy Grass Miscanthus Species

    Vega, Jose J. De; Teshome, Abel; Klaas, Manfred; Grant, Jim; Finnan, John; Barth, Susanne; European Union; FP7-KBBE-2011-5-289461; CLNE/2017/364 (Biomed Central, 2020-07-28)
    Background: Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity, particularly in the temperate regions. This study was conducted to elucidate physiological and molecular responses of four Miscanthus species subjected to well-watered and droughted greenhouse conditions. Results: A signicant biomass loss was observed under drought conditions for all genotypes. A sterile M. x giganteus showed a lower reduction in biomass yield under drought conditions compared to the control than the other species. Under well-watered conditions, biomass yield was as good as or better than control conditions in all species tested. M. sinensis was more tolerant than M. sacchariorus to both water stress conditions. 4,389 of the 67,789 genes (6.4%) in the reference genome were differentially expressed among four Miscanthus species. Most of the genes were differentially expressed in a single species, but the enrichment analysis of gene ontology (GO) terms revealed that the same biological processes were regulated in all the species during stress conditions. Namely, upregulated differentially expressed genes were signicantly involved in sucrose and starch metabolism, redox, and water and glycerol homeostasis and channel activity. Multiple copies of starch metabolic enzymes BAM and waxy GBSS-I were strongly up-regulated in drought stress in all Miscanthus genotypes. Twelve aquaporins (PIP1, PIP2 and NIP2) were also up-regulated in drought stress across genotypes. On the other hand, downregulated differentially expressed genes were signicantly involved in protein kinase activity, cell receptor signalling and phosphorylation. Conclusions: Findings in the present study can assist in implementing molecular breeding approaches of drought resistant Miscanthus and its domestication.
  • Genetic Analysis Using a Multi-Parent Wheat Population Identifies Novel Sources of Septoria Tritici Blotch Resistance

    Riaz, Adnan; KockAppelgren, Petra; Hehir, James Gerard; Kang, Jie; Meade, Fergus; Cockram, James; Milbourne, Dan; Spink, John; Mullins, Ewen; Byrne, Stephen; et al. (MDPI AG, 2020-08-04)
    Zymoseptoria tritici is the causative fungal pathogen of septoria tritici blotch (STB) disease of wheat (Triticum aestivum L.) that continuously threatens wheat crops in Ireland and throughout Europe. Under favorable conditions, STB can cause up to 50% yield losses if left untreated. STB is commonly controlled with fungicides; however, a combination of Z. tritici populations developing fungicide resistance and increased restrictions on fungicide use in the EU has led to farmers relying on fewer active substances. Consequently, this serves to drive the emergence of Z. tritici resistance against the remaining chemistries. In response, the use of resistant wheat varieties provides a more sustainable disease management strategy. However, the number of varieties offering an adequate level of resistance against STB is limited. Therefore, new sources of resistance or improved stacking of existing resistance loci are needed to develop varieties with superior agronomic performance. Here, we identified quantitative trait loci (QTL) for STB resistance in the eight-founder “NIAB Elite MAGIC” winter wheat population. The population was screened for STB response in the field under natural infection for three seasons from 2016 to 2018. Twenty-five QTL associated with STB resistance were identified in total. QTL either co-located with previously reported QTL or represent new loci underpinning STB resistance. The genomic regions identified and the linked genetic markers serve as useful resources for STB resistance breeding, supporting rapid selection of favorable alleles for the breeding of new wheat cultivars with improved STB resistance.
  • Detection of Novel QTLs for Late Blight Resistance Derived from the Wild Potato Species Solanum microdontum and Solanum pampasense

    Meade, Fergus; Hutten, Ronald; Wagener, Silke; Prigge, Vanessa; Dalton, Emmet; Kirk, Hanne Grethe; Griffin, Denis; Milbourne, Dan; Department of Agriculture, Food and the Marine; IPM Potato Group; et al. (MDPI AG, 2020-06-30)
    Wild potato species continue to be a rich source of genes for resistance to late blight in potato breeding. Whilst many dominant resistance genes from such sources have been characterised and used in breeding, quantitative resistance also offers potential for breeding when the loci underlying the resistance can be identified and tagged using molecular markers. In this study, F1 populations were created from crosses between blight susceptible parents and lines exhibiting strong partial resistance to late blight derived from the South American wild species Solanum microdontum and Solanum pampasense. Both populations exhibited continuous variation for resistance to late blight over multiple field-testing seasons. High density genetic maps were created using single nucleotide polymorphism (SNP) markers, enabling mapping of quantitative trait loci (QTLs) for late blight resistance that were consistently expressed over multiple years in both populations. In the population created with the S. microdontum source, QTLs for resistance consistently expressed over three years and explaining a large portion (21–47%) of the phenotypic variation were found on chromosomes 5 and 6, and a further resistance QTL on chromosome 10, apparently related to foliar development, was discovered in 2016 only. In the population created with the S. pampasense source, QTLs for resistance were found in over two years on chromosomes 11 and 12. For all loci detected consistently across years, the QTLs span known R gene clusters and so they likely represent novel late blight resistance genes. Simple genetic models following the effect of the presence or absence of SNPs associated with consistently effective loci in both populations demonstrated that marker assisted selection (MAS) strategies to introgress and pyramid these loci have potential in resistance breeding strategies.
  • Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions

    Szoboszlay, Márton; Näther, Astrid; Mullins, Ewen; Tebbe, Christoph C.; European Union; 289706 (Public Library of Science (PLoS), 2019-12-17)
    The importance of geographic location and annual variation on the detection of differences in the rhizomicrobiome caused by the genetic modification of maize (Bt-maize, event MON810) was evaluated at experimental field sites across Europe including Sweden, Denmark, Slovakia and Spain. DNA of the rhizomicrobiome was collected at the maize flowering stage in three consecutive years and analyzed for the abundance and diversity of PCR-amplified structural genes of Bacteria, Archaea and Fungi, and functional genes for bacterial nitrite reductases (nirS, nirK). The nirK genes were always more abundant than nirS. Maize MON810 did not significantly alter the abundance of any microbial genetic marker, except for sporadically detected differences at individual sites and years. In contrast, annual variation between sites was often significant and variable depending on the targeted markers. Distinct, site-specific microbial communities were detected but the sites in Denmark and Sweden were similar to each other. A significant effect of the genetic modification of the plant on the community structure in the rhizosphere was detected among the nirK denitrifiers at the Slovakian site in only one year. However, most nirK sequences with opposite response were from the same or related source organisms suggesting that the transient differences in community structure did not translate to the functional level. Our results show a lack of effect of the genetic modification of maize on the rhizosphere microbiome that would be stable and consistent over multiple years. This demonstrates the importance of considering annual variability in assessing environmental effects of genetically modified crops.
  • Genomic prediction of crown rust resistance in Lolium perenne

    Arojju, Sai Krishna; Conaghan, Patrick; Barth, Susanne; Milbourne, Dan; Casler, Michael D.; Hodkinson, Trevor R.; Michel, Thibauld; Byrne, Stephen; Department of Agriculture Food and the Marine; European Union; et al. (Springer Science and Business Media LLC, 2018-05-29)
    Background Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability. Results Using these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set. Conclusion Using a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications.
  • Functional Land Management: Bridging the Think-Do-Gap using a multi-stakeholder science policy interface

    O’Sullivan, Lilian; Wall, David; Creamer, Rachel; Bampa, Francesca; Schulte, Rogier P. O.; National Development Plan 2007–2013; European Union; 13S468; 635201; 677407 (Springer Science and Business Media LLC, 2017-11-24)
    Functional Land Management (FLM) is proposed as an integrator for sustainability policies and assesses the functional capacity of the soil and land to deliver primary productivity, water purification and regulation, carbon cycling and storage, habitat for biodiversity and recycling of nutrients. This paper presents the catchment challenge as a method to bridge the gap between science, stakeholders and policy for the effective management of soils to deliver these functions. Two challenges were completed by a wide range of stakeholders focused around a physical catchment model—(1) to design an optimised catchment based on soil function targets, (2) identify gaps to implementation of the proposed design. In challenge 1, a high level of consensus between different stakeholders emerged on soil and management measures to be implemented to achieve soil function targets. Key gaps including knowledge, a mix of market and voluntary incentives and mandatory measures were identified in challenge 2.
  • Evaluation of the ’Irish Rules’: The Potato Late Blight Forecasting Model and Its Operational Use in the Republic of Ireland

    Cucak, Mladen; Sparks, Adam; Moral, Rafael; Kildea, Steven; Lambkin, Keith; Fealy, Rowan; Department of Agriculture, Food and the Marine; 14/S/879 (MDPI AG, 2019-09-06)
    Potato late blight caused by Phytophthora infestans is one of the most important plant diseases known, requiring high pesticide inputs to prevent disease occurrence. The disease development is highly dependent on weather conditions, and as such, several forecasting schemes have been developed worldwide which seek to reduce the inputs required to control the disease. The Irish Rules, developed in the 1950s and calibrated to accommodate the meteorological network, the characteristics of potato production and the P. infestans population at the time, is still operationally utilized by the national meteorological agency, Met Éireann. However, numerous changes in the composition and dynamics of the pathosystem and the risks of production/economic consequences associated with potato late blight outbreaks have occurred since the inception of the Irish Rules model. Additionally, model and decision thresholds appear to have been selected ad hoc and without a clear criteria. We developed a systematic methodology to evaluate the model using the empirical receiver operating curve (ROC) analysis and the response surface methodology for the interpretation of the results. The methodology, written in the R language, is provided as an open, accessible and reproducible platform to facilitate the ongoing seasonal re-evaluation of the Irish Rules and corresponding decision thresholds. Following this initial analysis, based on the available data, we recommend the reduction of the thresholds for relative humidity and an initial period duration from 90% and 12 h to 88% and 10 h, respectively. Contrary to recent reports, we found that the risk of blight epidemics remains low at temperatures below 12 °C. With the availability of more comprehensive outbreak data and with greater insight into the founder population to confirm our findings as robust, the temperature threshold in the model could potentially be increased from 10 °C to 12 °C, providing more opportunities for reductions of pesticide usage. We propose a dynamic operational decision threshold between four and 11 effective blight hours (EBH) set according to frequency of the disease outbreaks in the region of interest. Although the risk estimation according to the new model calibrations is higher, estimated chemical inputs, on average, are lower than the usual grower’s practice. Importantly, the research outlined here provides a robust and reproducible methodological approach to evaluate a semi-empirical plant disease forecasting model.
  • Genotyping by Sequencing and Plastome Analysis Finds High Genetic Variability and Geographical Structure in Dactylis glomerata L. in Northwest Europe Despite Lack of Ploidy Variation

    Hodkinson, Trevor R.; Perdereau, Aude; Klaas, Manfred; Cormican, Paul; Barth, Susanne; EU; 289461 (MDPI AG, 2019-06-28)
    Large collections of the forage and bioenergy grass Dactylis glomerata were made in northwest (NW) Europe along east to west and north to south clines for genetic resource conservation and to inform breeding programmes of genetic diversity, genepools, and ploidy. Leaves were sampled for genetic analysis and seed and rhizome for ex-situ conservation. Genotyping by sequencing (GBS) was used to assay nuclear DNA diversity and plastome single nucleotide polymorphism (SNP) discovery was undertaken using a long-read PCR and MiSeq approach. Nuclear and plastid SNPs were analysed by principal component analysis (PCA) to compare genotypes. Flow cytometry revealed that all samples were tetraploid, but some genome size variation was recorded. GBS detected an average of approximately 10,000 to 15,000 SNPs per country sampled. The highest average number of private SNPs was recorded in Poland (median ca. 2000). Plastid DNA variation was also high (1466 SNPs, 17 SNPs/kbp). GBS data, and to a lesser extent plastome data, also show that genetic variation is structured geographically in NW Europe with loose clustering matching the country of plant origin. The results reveal extensive genetic diversity and genetic structuring in this versatile allogamous species despite lack of ploidy variation and high levels of human mediated geneflow via planting.
  • Exploring the sensitivity of visual soil evaluation to traffic-induced soil compaction

    Emmet-Booth, J.P.; Holden, N.M.; Fenton, Owen; Bondi, G; Forristal, P.D.; Irish Department of Agriculture, Food and the Marine; 13/S/468 (Elsevier, 2019-10-24)
    Visual Soil Evaluation (VSE) techniques are useful for assessing the impact of land management, particularly the identification and remediation of soil compaction. Despite an increasing body of VSE research, comparatively few studies have explored the sensitivity of VSE for capturing experimentally imposed compaction to estimate sensitivity and limit of detection. The aim of this research was to examine the ability of VSE techniques to indicate soil structure at different soil profile depths and to measure the associated soil productive function (yield) response to imposed compaction. A two-year experiment was conducted on sites with loam and sandy soils. Varying levels of wheeled traffic were imposed on plots in a randomised block design, prior to sowing winter barley (Hordeum vulgare L.). Quantitative crop and soil measurements were taken throughout the season in conjunction with VSE techniques, which assessed to 25 cm (VESS), 40 cm (Double Spade) and 80 cm (SubVESS) depth. Graduated changes were observed by soil and some crop quantitative measurements as traffic treatment varied. VESS and Double Spade successfully identified a graduated treatment effect at all sites to 40 cm depth, although diagnosis translated into a yield response for the loam but not the sandy soil. Correlation between VESS Sq scores and crop yield were found. SubVESS gave mixed signals and indicated impacts lower in the profile in certain instances. These impacts were not captured by quantitative soil measurements.This work highlights the capacity for VSE techniques to indicate soil structural damage, which may cause a crop yield response, therefore allowing appropriate soil management strategies to be deployed before yield penalties occur.
  • Can herbage nitrogen fractionation in Lolium perenne be improved by herbage management?

    Hoekstra, Nyncke J.; Struik, Paul; Lantinga, Egbert A.; Van Amburgh, Michael; Schulte, Rogier P.; Teagasc Walsh Fellowship Programme (Elsevier, 2009-08-20)
    The high degradability of grass protein is an important factor in the low nitrogen (N) utilization of grazing bovines in intensive European grassland systems. We tested the hypothesis that protein degradability as measured by the Cornell Net Carbohydrate and Protein System (CNCPS) protein fractionation scheme, can be manipulated by herbage management tools, with the aim to reduce N loss to the environment. A field experiment comprising the factorial combinations of three fertilizer N application rates (0, 90 and 390 kg N ha−1 year−1), three regrowth periods (2–3, 4–5, and 6–7 weeks), two perennial ryegrass (Lolium perenne L.) cultivars [Aberdart (high sugar content) and Respect (low sugar content)] and two cutting heights (approximately 8 and 12 cm) was conducted at Teagasc, Johnstown Castle Research Centre, Wexford, Ireland. The plots were sampled during four seasons [September/October 2002 (late season), April 2003 (early season), May/June 2003 (mid season) and September 2003 (late season)] and protein fractions were determined in both sheath and lamina material. The protein was highly soluble and on average 19% and 28% of total N was in the form of non-protein N, 16% and 19% in the form of buffer-soluble protein, 52% and 40% in the form of buffer-insoluble protein, and 12% and 13% in the form of potentially available cell wall N for lamina and sheath material, respectively. In both materials only 0.9% of total N was present as unavailable cell wall N. In general the herbage management tools investigated did not have much effect on protein fractionation. The effects of regrowth period, cultivar and cutting height were small and inconsistent. High N application rates significantly increased protein degradability, especially during late season. This is relevant, as it has been shown that enhanced protein degradation increases the potential N loss through urine excretion at a time when urine-N excreted onto pasture is prone to leaching. However, the effect was most evident for sheath material, which forms only a small proportion of the animals' intake. It was concluded that there appears to be little scope for manipulating the herbage-N fractionation through herbage management. The consequences for modelling herbage quality could be positive as there does not seem to be a need to model the individual N fractions; in most cases the N fractions can be expressed as a fixed proportion of total N instead.
  • Transcriptome sequencing of Festulolium accessions under salt stress

    Teshome, A.; Byrne, Stephen L.; Didion, T.; De Vega, J.; Jensen, C. S; Klaas, M.; Barth, Susanne; European Union; Marie Sklodowska-Curie Actions; FP7-KBBE-2011-5-289461; et al. (Biomed Central, 2019-05-31)
    Objectives The objective of this study was to establish transcriptome assemblies of Festulolium hybrids under salt stress, and identify genes regulated across the hybrids in response to salt stress. The development of transcriptome assemblies for Festulolium hybrids and cataloguing of genes regulated under salt stress will facilitate further downstream studies. Results Plants were grown at three salt concentrations (0.5%, 1% and 1.5%) and phenotypic and transcriptomic data was collected. Salt stress was confirmed by progressive loss of green leaves as salt concentration increased from 0 to 1.5%. We generated de-novo transcriptome assemblies for two Festulolium pabulare festucoid genotypes, for a single Festulolium braunii genotype, and a single F. pabulare loloid genotype. We also identified 1555 transcripts that were up regulated and 1264 transcripts that were down regulated in response to salt stress in the Festulolium hybrids. Some of the identified transcripts showed significant sequence similarity with genes known to be regulated during salt and other abiotic stresses.
  • Equivalence analysis to support environmental safety assessment: Using nontarget organism count data from field trials with cisgenically modified potato

    van der Voet, Hilko; Goedhart, Paul W.; Lazebnik, Jenny; Kessel, Geert J. T.; Mullins, Ewen; van Loon, Joop J. A.; Arpaia, Salvatore; European Union; 289706 (Wiley, 2019-02-14)
    This paper considers the statistical analysis of entomological count data from field experiments with genetically modified (GM) plants. Such trials are carried out to assess environmental safety. Potential effects on nontarget organisms (NTOs), as indicators of biodiversity, are investigated. The European Food Safety Authority (EFSA) gives broad guidance on the environmental risk assessment (ERA) of GM plants. Field experiments must contain suitable comparator crops as a benchmark for the assessment of designated endpoints. In this paper, a detailed protocol is proposed to perform data analysis for the purpose of assessing environmental safety. The protocol includes the specification of a list of endpoints and their hierarchical relations, the specification of intended levels of data analysis, and the specification of provisional limits of concern to decide on the need for further investigation. The protocol emphasizes a graphical representation of estimates and confidence intervals for the ratio of mean abundances for the GM plant and its comparator crop. Interpretation relies mainly on equivalence testing in which confidence intervals are compared with the limits of concern. The proposed methodology is illustrated with entomological count data resulting from multiyear, multilocation field trials. A cisgenically modified potato line (with enhanced resistance to late blight disease) was compared to the original conventional potato variety in the Netherlands and Ireland in two successive years (2013, 2014). It is shown that the protocol encompasses alternative schemes for safety assessment resulting from different research questions and/or expert choices. Graphical displays of equivalence testing at several hierarchical levels and their interpretation are presented for one of these schemes. The proposed approaches should be of help in the ERA of GM or other novel plants.
  • Pooled DNA sequencing to identify SNPs associated with a major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.)

    Knorst, Verena; Byrne, Stephen; Yates, Steven; Asp, Torben; Widmer, Franco; Studer, Bruno; Kölliker, Roland; Swiss National Science Foundation; 31003A_138358 (Springer Science and Business Media LLC, 2018-11-30)
    Italian ryegrass (Lolium multiflorum Lam.) is one of the most important forage grass species in temperate regions. Its yield, quality and persistency can significantly be reduced by bacterial wilt, a serious disease caused by Xanthomonas translucens pv. graminis. Although a major QTL for bacterial wilt resistance has previously been reported, detailed knowledge on underlying genes and DNA markers to allow for efficient resistance breeding strategies is currently not available. We used pooled DNA sequencing to characterize a major QTL for bacterial wilt resistance of Italian ryegrass and to develop inexpensive sequence-based markers to efficiently target resistance alleles for marker-assisted recurrent selection. From the mapping population segregating for the QTL, DNA of 44 of the most resistant and 44 of the most susceptible F1 individuals was pooled and sequenced using the Illumina HiSeq 2000 platform. Allele frequencies of 18 × 106 single nucleotide polymorphisms (SNP) were determined in the resistant and susceptible pool. A total of 271 SNPs on 140 scaffold sequences of the reference parental genome showed significantly different allele frequencies in both pools. We converted 44 selected SNPs to KASP™ markers, genetically mapped these proximal to the major QTL and thus validated their association with bacterial wilt resistance. This study highlights the power of pooled DNA sequencing to efficiently target binary traits in biparental mapping populations. It delivers genome sequence data, SNP markers and potential candidate genes which will allow to implement marker-assisted strategies to fix bacterial wilt resistance in outcrossing breeding populations of Italian ryegrass.
  • Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses

    Della Bartola, Michele; Byrne, Stephen; Mullins, Ewen; Department of Agriculture, Food and the Marine; 15/S/618 SCOPE (MDPI AG, 2020-04-23)
    Potato virus Y (PVY) is the most economically important virus infecting cultivated potato (Solanum tuberosum L.). Accurate diagnosis is crucial to regulate the trade of tubers and for the sanitary selection of plant material for propagation. However, high genetic diversity of PVY represents a challenge for the detection and classification of isolates. Here, the diversity of Irish PVY isolates from a germplasm collection and commercial sites was investigated using conventional molecular and serological techniques. Recombinant PVY isolates were prevalent, with PVYNTNa being the predominant genotype. In addition, we evaluated Nanopore sequencing to detect and reconstruct the whole genome sequence of four viruses (PVY, PVX, PVS, PLRV) and five PVY genotypes in a subset of eight potato plants. De novo assembly of Nanopore sequencing reads produced single contigs covering greater than 90% of the viral genome and sharing greater than 99.5% identity to the consensus sequences obtained with Illumina sequencing. Interestingly, single near full genome contigs were obtained for different isolates of PVY co-infecting the same plant. Mapping reads to available reference viral genomes enabled us to generate near complete genome sequences sharing greater than 99.90% identity to the Illumina-derived consensus. This is the first report describing the use of Oxford Nanopore’s MinION to detect and genotype potato viruses. We reconstructed the genome of PVY and other RNA viruses; indicating the technologies potential for virus detection in potato production systems, and for the study of genetic diversity of highly heterogeneous viruses such as PVY.
  • Potatoes and livelihoods in Chencha, southern Ethiopia

    Tadesse, Yenenesh; Almekinders, Conny J.M.; Schulte, Rogier P.O.; Struik, Paul C.; Wageningen University and Research; Vita (Irish Aid); Teagasc Walsh Fellowship Programme (Elsevier BV, 2018-06-18)
    Potato is highly productive crop and can provide a cheap and nutritionally-rich staple food. Its potential as a cash generator and source of food is much under-utilized in many emerging economies. In this paper we study the impact of an intervention that introduced improved potato technologies in Chencha, Ethiopia on the livelihoods of smallholder farmers. We collected information through in-depth interviews in order to explore possible pathways of impact on farmers’ livelihoods; and used this information as the basis for designing a household survey. The results show changes in agronomic practices and consumption; these changes were most pronounced among wealthy farmers who participated in the intervention. Farmers used the additional income from potato in different ways: wealthier farmers improved their houses and increased their livestock, whereas poor farmers mainly invested in furniture, cooking utensils, tools and in developing small businesses like selling and buying cereals, milk and weaving products in the local markets. Some wealthy farmers, who did not participate in the project, also derived some indirect benefits from the intervention. This underscores: i) interventions that promote uniform farming technologies in themselves are not always sufficient to improve the livelihoods of poor farmers, and ii) the need to broaden the scope of interventions so as to take into account the resources available to farmers in different wealth categories, and the diversity of strategies that they employ for improving their livelihoods. Our approach allows to understand and describe the different developmental effects of a single technological intervention on the different aspects of farmers’ livelihoods.
  • Genotyping by sequencing provides new insights into the diversity of Napier grass (Cenchrus purpureus) and reveals variation in genome-wide LD patterns between collections

    Muktar, Meki S.; Teshome, Abel; Hanson, Jean; Negawo, Alemayehu T.; Habte, Ermias; Domelevo Entfellner, Jean-Baka; Lee, Ki-Won; Jones, Chris S.; Rural Development Administration of the Republic of Korea; Germany-GIZ-Deutsche Gesellschaft für Internationale Zusammenarbeit; et al. (Springer Nature, 2019-05-06)
    Napier grass is an important tropical forage-grass and of growing potential as an energy crop. One-hundred-five Napier grass accessions, encompassing two independent collections, were subjected to genotyping by sequencing which generated a set of high-density genome-wide markers together with short sequence reads. The reads, averaging 54 nucleotides, were mapped to the pearl millet genome and the closest genes and annotation information were used to select candidate genes linked to key forage traits. 980 highly polymorphic SNP markers, distributed across the genome, were used to assess population structure and diversity with seven-subgroups identified. A few representative accessions were selected with the objective of distributing subsets of a manageable size for further evaluation. Genome-wide linkage disequilibrium (LD) analyses revealed a fast LD-decay, on average 2.54 kbp, in the combined population with a slower LD-decay in the ILRI collection compared with the EMBRAPA collection, the significance of which is discussed. This initiative generated high-density markers with a good distribution across the genome. The diversity analysis revealed the existence of a substantial amount of variation in the ILRI collection and identified some unique materials from the EMBRAPA collection, demonstrating the potential of the overall population for further genetic and marker-trait-association studies.
  • Chemical composition of lamina and sheath of Lolium perenne as affected by herbage management

    Hoekstra, Nyncke J.; Struik, Paul C.; Lantinga, E. A.; Schulte, Rogier P.; Teagasc Walsh Fellowship Programme (Elsevier, 2009-08-20)
    The quality of grass in terms of form and relative amounts of energy and protein affects both animal production per unit of intake and nitrogen (N) utilization. Quality can be manipulated by herbage management and choice of cultivar. The effects of N application rate (0, 90 or 390 kg N ha−1 year−1), duration of regrowth period (2–3, 4–5, or 6–7 weeks), and cutting height (8 or 12 cm) on the mass fractions of nitrogen (N), water-soluble carbohydrates (WSC), neutral detergent fibre (NDF), acid detergent fibre (ADF), lignin and ash in lamina and sheath material of a high-sugar (Aberdart) and a low-sugar (Respect) perennial ryegrass (Lolium perenne) cultivar, were studied in a factorial field experiment during four seasons in 2002 and 2003. Expressing NDF and ADF mass fractions in g per kg WSC-free dry matter (DM) increased the consistency of treatment effects. The high-sugar cultivar had generally higher WSC mass fractions than the low-sugar cultivar, especially during the late season. Moreover, the relative difference in WSC mass fraction between the two cultivars tended to be higher for the lamina material than for the sheath material, which suggests that the high-sugar trait may be more important under grazing conditions, when lamina forms the bulk of the intake, than under mowing regimes. Longer regrowth periods and lower N application rates increased WSC mass fractions and decreased N mass fractions; interactions between regrowth period and N application rate were highly significant. The mass fractions of NDF and ADF were much less influenced. The NDF mass fraction in terms of g per kg WSC-free DM tended to be higher at lower N application rates and at longer regrowth periods. The effect of cutting height on herbage chemical composition was unclear. In conclusion, high-sugar cultivars, N application rate and length of the regrowth period are important tools for manipulating herbage quality.
  • An Analysis of Abatement Potential of Greenhouse Gas Emissions in Irish Agriculture 2021-2030

    Lanigan, Gary; Donnellan, Trevor; Hanrahan, Kevin; Carsten, Paul; Shalloo, Laurence; Krol, Dominika; Forrestal, Patrick J.; Farrelly, Niall; O’Brien, Donal; Ryan, Mary; et al. (Teagasc, 2018-06-10)
    This report has been prepared by the Teagasc Working Group on GHG Emissions, which brings together and integrates the extensive and diverse range of organisational expertise on agricultural greenhouse gases. The previous Teagasc GHG MACC was published in 2012 in response to both the EU Climate and Energy Package and related Effort Sharing Decision and in the context of the establishment of the Food Harvest 2020 production targets.

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