• 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.
    • A disease resistance locus on potato and tomato chromosome 4 exhibits a conserved multipartite structure displaying different rates of evolution in different lineages

      Destefanis, M.; Nagy, Istvan; Rigney, Brian; Bryan, Glenn J; McLean, Karen; Hein, Ingo; Griffin, Denis; Milbourne, Dan; Teagasc Walsh Fellowship Programme; Department of Agriculture, Food and the Marine, Ireland; et al. (Biomed Central, 24/10/2015)
      Background In plant genomes, NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. R-gene sequences mostly differentiate by accumulating point mutations and gene conversion events. Potato and tomato chromosome 4 harbours a syntenic R-gene locus (known as the R2 locus in potato) that has mainly been examined in central American/Mexican wild potato species on the basis of its contribution to resistance to late blight, caused by the oomycete pathogen Phytophthora infestans. Evidence to date indicates the occurrence of a fast evolutionary mode characterized by gene conversion events at the locus in these genotypes. Results A physical map of the R2 locus was developed for three Solanum tuberosum genotypes and used to identify the tomato syntenic sequence. Functional annotation of the locus revealed the presence of numerous resistance gene homologs (RGHs) belonging to the R2 gene family (R2GHs) organized into a total of 4 discrete physical clusters, three of which were conserved across S. tuberosum and tomato. Phylogenetic analysis showed clear orthology/paralogy relationships between S. tuberosum R2GHs but not in R2GHs cloned from Solanum wild species. This study confirmed that, in contrast to the wild species R2GHs, which have evolved through extensive sequence exchanges between paralogs, gene conversion was not a major force for differentiation in S. tuberosum R2GHs, and orthology/paralogy relationships have been maintained via a slow accumulation of point mutations in these genotypes. Conclusions S. tuberosum and Solanum lycopersicum R2GHs evolved mostly through duplication and deletion events, followed by gradual accumulation of mutations. Conversely, widespread gene conversion is the major evolutionary force that has shaped the locus in Mexican wild potato species. We conclude that different selective forces shaped the evolution of the R2 locus in these lineages and that co-evolution with a pathogen steered selection on different evolutionary paths.
    • Distribution and incidence of viruses in Irish seed potato crops

      Hutton, Fiona; Spink, John; Griffin, Denis; Kildea, Steven; Bonner, D.; Doherty, G.; Hunter, A. (Teagasc (Agriculture and Food Development Authority), Ireland, 30/12/2015)
      Virus diseases are of key importance in potato production and in particular for the production of disease-free potato seed. However, there is little known about the frequency and distribution of potato virus diseases in Ireland. Despite a large number of samples being tested each year, the data has never been collated either within or across years. Information from all known potato virus testing carried out in the years 2006–2012 by the Department of Agriculture Food and Marine was collated to give an indication of the distribution and incidence of potato virus in Ireland. It was found that there was significant variation between regions, varieties, years and seed classes. A definition of daily weather data suitable for aphid flight was developed, which accounted for a significant proportion of the variation in virus incidence between years. This use of weather data to predict virus risk could be developed to form the basis of an integrated pest management approach for aphid control in Irish potato crops.
    • The Double Spade Method: a ‘mini-profile’ visual soil evaluation technique

      Emmet-Booth, J.P.; Forristal, P.D.; Fenton, Owen; Bondi, G.; Holden, N.M (2021-11-23)
      Visual Soil Evaluation (VSE) methods are established for soil quality assessment and focus on the examination of soil structure and associated anthropogenic impacts. VSE techniques, of which numerous types exist, are successfully used internationally both in soil research and as sustainable soil management tools. Techniques are generally categorised into profile and spade methods. Profile methods examine entire soil profiles in soil-pits to depths of ~ 1.5 m, exploring interactions between inherent soil features and anthropic management at specific sample points. Spade methods examine the upper soil profile, often by extracting sample blocks of topsoil by spade and focus on anthropic impacts. The VESS method (Guimarães et al., 2011) is a widely used spade method and involves assessment of soil sample blocks to 25 cm depth. However, in arable soils, important structural features may occur just below this depth such as plough pans, which VESS may not capture. The SubVESS method (Ball et al., 2015) follows principles of VESS but allows assessment to ~ 1 m depth. However, the later involves soil-pit excavation by mechanical means, which may be destructive, costly, time consuming and limit replication. When used in on-farm situations by farmers or advisors, full soil-pit excavation may not be desirable. Here we describe a method previously outlined (Emmet-Booth et al. 2018) called the Double Spade Method (DS) designed to examine miniprofiles in soil pits to 40 cm depth, therefore capturing potential structural features below the VESS assessment depth, without requiring full soil-pit excavation.
    • The effect of entomopathogenic fungal culture filtrate on the immune response and haemolymph proteome of the large pine weevil, Hylobius abietis

      Mc Namara, Louise; Griffin, Christine T.; Fitzpatrick, David; Kavanagh, Kevin; Carolan, James C.; Department of Agriculture, Food and the Marine; Science Foundation Ireland; 10/RD/MCOP/NUIM/720; 12/RI/2346 (3) (Elsevier, 2018-07-17)
      The large pine weevil Hylobius abietis L. is a major forestry pest in 15 European countries, where it is a threat to 3.4 million hectares of forest. A cellular and proteomic analysis of the effect of culture filtrate of three entomopathogenic fungi (EPF) species on the immune system of H. abietis was performed. Injection with Metarhizium brunneum or Beauvaria bassiana culture filtrate facilitated a significantly increased yeast cell proliferation in larvae. Larvae co-injected with either Beauvaria caledonica or B. bassiana culture filtrate and Candida albicans showed significantly increased mortality. Together these results suggest that EPF culture filtrate has the potential to modulate the insect immune system allowing a subsequent pathogen to proliferate. Injection with EPF culture filtrate was shown to alter the abundance of protease inhibitors, detoxifing enzymes, antimicrobial peptides and proteins involved in reception/detection and development in H. abietis larvae. Larvae injected with B. caledonica culture filtrate displayed significant alterations in abundance of proteins involved in cellulolytic and other metabolic processes in their haemolymph proteome. Screening EPF for their ability to modulate the insect immune response represents a means of assessing EPF for use as biocontrol agents, particularly if the goal is to use them in combination with other control agents.
    • Effect of Harvest Timing and Soil Moisture Content on Compaction, Growth and Harvest Yield in a Miscanthus Cropping System

      O'Flynn, Michael G.; Finnan, John; Curley, Edna M.; McDonnell, Kevin; Science Foundation Ireland; CP/E001 (MDPI, 2018-09-22)
      Harvesting Miscanthus × giganteus (J.M. Greef & Deuter ex Hodkinson & Renvoize) after shoot emergence is known to reduce yields in subsequent seasons. This research was conducted in Miscanthus to assess the effects on crop response and soil compaction of annually repeated traffic, applied both before new growth in the rhizomes (early harvest) and after shoot emergence (late harvest), at two different soil moisture contents. While an annual early harvest, yields more than a late harvest, because damage to new shoots is avoided, soil compaction may be increased following repeated harvests. Five treatments were tested: (a) An untrafficked control, (b) early-traffic on soil with typical soil moisture content (SMC) (early-normal), (c) early-traffic on soil with elevated SMC (early-elevated), (d) late-traffic on soil with typical SMC (late-normal) and (e) late-traffic on soil with elevated SMC (late-wet). The experiment was conducted on a Gleysol in Co. Dublin, Ireland during 2010 and 2011. Crop response effects were assessed by measuring stem numbers, stem height, trafficked zone biomass yield (November) and overall stem yield (January). Compaction effects were assessed by measuring penetration resistance, bulk density and water infiltration rate. Trafficked zone biomass yield in the early-dry and early-wet treatments was, respectively, 18% and 23% lower than in the control, but was, respectively, 39% and 31% higher than in the late-dry treatment. Overall, stem yield was significantly lower in the late-normal and late-wet treatments (10.4 and 10.1 tdm ha−1 respectively) when compared with the control (12.4 tdm ha−1), but no significant difference was recorded in overall stem yield between both early-traffic treatments and the control. Penetration resistance values were significantly higher in all trafficked treatments when compared with the control at depths of 0.15 m (≥54–61%) and 0.30 m (≥27–57%) and were significantly higher in 2011 when compared with 2010 at depths of 0.15 and 0.30 m. Baler system traffic in Miscanthus significantly reduced yields and significantly increased compaction annually. Miscanthus harvested early, on a dry soil, yielded 1.1 tdm ha−1 more than when harvested late on a dry soil. The yield advantage increased to 1.3 tdm ha−1 when early harvesting on a soil with 40–43% moisture content was compared with late harvesting on a wetter soil (51–52% moisture content). In this study, the magnitude of yield losses from compaction or other causes in early harvests was substantially lower than the yield losses, which resulted from shoot damage in late harvests. It is likely in similar climates that the results of this study would also apply to other perennial crops growing in similar soil types
    • Effect of nitrogen fertilizer application timing on nitrogen use efficiency and grain yield of winter wheat in Ireland.

      Efretuei, A.; Gooding, M.; White, E.M.; Spink, John; Hackett, Richard (Teagasc (Agriculture and Food Development Authority), Ireland, 2016-12-01)
      The objectives of this work were to determine the effects of initiating application of fertilizer nitrogen (N) to winter wheat at different growth stages (GSs) on grain yield and N use efficiency (NUE). A factorial experiment was carried out in two growing seasons (2011 and 2012) with five timings of first N application (GS 24/26 [tillering], GS 30, GS 31, GS 32 or GS 37) and an unfertilized control, two sowing densities (100 and 400 seeds/m2) and a cattle slurry treatment (with or without slurry). The latter was included to simulate variation in soil N supply (SNS). Delaying the first application of N from the tillering stage until GS 30 had no significant effect on grain yield in either year. Further delaying the initial N application until GS 31 caused a significant yield reduction in 2011, in comparison to GS 30 application, but not in 2012. Differences in efficiency of recovery and use of fertilizer N by the crop among the first three application timings were small. There was no evidence to support alteration in the timing of the first application of N in response to low plant density. Slurry application did not influence SNS, so the interaction between SNS and fertilizer N application timing could not be determined. It is concluded that in order to maximise yield and NUE, the first N application should be applied to winter wheat between late tillering and GS 30 and that delaying the first N until GS 31 can lead to yield reductions compared to the yield obtained with earlier application.
    • Effects of over-winter green cover on groundwater nitrate and dissolved organic carbon concentrations beneath tillage land

      Premrov, Alina; Coxon, Catherine E.; Hackett, Richard; Kirwan, Laura; Richards, Karl G. (Elsevier, 13/09/2012)
      Application of over-winter green cover (e.g. cover crops) as a measure for reducing nitrate losses from tillage land has been frequently investigated, especially in the unsaturated zone. Monitoring of groundwater is less common in these studies. Studies on groundwater responses to different land treatments can be challenging because they can be influenced by various conditions, such as recharge, seasonal variations, and aquifer properties, often occurring at different time scales than surface water processes. The aim of this study was to evaluate groundwater nitrate (NO3−single bondN) and dissolved organic carbon (DOC) concentration responses to different over-winter green covers: mustard, natural regeneration and no cover. A field experiment was designed and run for three years on tillage land underlain by a vulnerable sand and gravel aquifer in the south-east of Ireland. Results showed that over-winter green cover growth on tillage land can be an effective measure to reduce groundwater NO3−single bondN concentrations. A significant decrease in groundwater NO3−single bondN concentrations was observed under the mustard cover compared to no cover. All treatments, including no cover, showed a decline in groundwater NO3−single bondN concentrations over time. A significant increase in groundwater DOC was also observed under the mustard cover. Although the overall groundwater DOC concentrations were low, the increased DOC occurrence in groundwater should be accounted for in carbon balances and could potentially enhance groundwater denitrification in cases where aquifer conditions may favour it.
    • The Effects of Seed Treatment, Sowing date, Cultivar and Harvest date on the Yield and Quality of Sugar Beet

      O'Donovan, Timothy; Irish Sugar Plc; Germain’s U.K. (2002)
      Trials were carried out at Lyons Estate Research Farm during 1998 on sugar beet (Beta Vulgaris). The commercially available seed treatment ‘Advantage’ was tested across 3 sowing dates, 4 commercially available cultivars and 4 harvest dates. Trials were carried out in a factorial arrangement and subject to standard statistical analysis. Data on emergence, ground cover, yield and quality was analysed. Percentage emergence of seed was satisfactory in all experiments. The benefit of ‘Advantage’ treatment during the emergence stage of growth was clearly seen in all trials. On average ‘Advantage’ seed emerged 2-3 days earlier than untreated seed and reached the target population (>75,000 plants/ha 4 days sooner than the control seed. During the growing season, ground cover was measured until complete cover was reached. In the trials it was less clear as to the benefits of using the treatment ‘Advantage’, as it was seldom statically different from control seed. As yields can be related to the radiation intercepted, it is not surprising that there were not large differences in yields. Delaying sowing date resulted in decreased yields of clean beet, sugar and extractable sugar. The two triploid varieties, Libra and Accord gave better yields of clean beet, sugar and extractable sugar than the two diploid cultivars Zulu and Celt. Delaying harvesting gave increased yields of clean beet, sugar and extractable sugar. The ‘Experimental’ seed treatment was not superior to the ‘Advantage’ treatment. In only one of the experiments was ‘Advantage’ better than the control treatment in respect of yield of clean beet, in the time of harvest trial. This was not reflected in yield of sugar or extractable sugar. In all other situations, there were no differences between ‘Advantage’ and the control treatments. There was no benefit from using ‘Advantage’ seed in the current experiments. However earlier sowing dates require investigation with pre-treated seed.
    • Effects of ten years organic and conventional farming on early seedling traits of evolving winter wheat composite cross populations

      Bhaskar A.V., Vijaya; Baresel, Jörg Peter; Weedon, Odette; Finckh, Maria R.; German BMBF; European Union; 031A350C; 727217 (Springer Nature, 2019-06-21)
      Early vigour traits of wheat composite cross populations (CCPs) based on high yielding (Y) or high quality (Q) or Y*Q varietal intercross evolving under organic or conventional conditions in parallel populations were studied hydroponically. To eliminate storage and year effects, frozen F6, F10, F11 and F15 seeds were multiplied in one field, resulting in the respective Fx.1 generations. This eliminated generation and growing system effects on seed size for the F6.1 F10.1 and F15.1. Due to a severe winter kill affecting the F11, the generation effect persisted, leading to larger seeds and markedly different seedling traits in the F11.1 compared to the F10.1 and F15.1. Seedling traits were similar among parallel populations. Shoot length and weight increased in both systems until the F11.1 across farming systems and remained constant thereafter. Over time, seminal root length and root weight of organic CCPs increased and total- and specific- root length decreased significantly compared to the conventional CCPs. Rooting patterns under organic conditions suggests better ability to reach deeper soil nutrients. In both systems, Q and YQ CCPs were more vigorous than Y CCPs, confirming genetic differences among populations. Overall, heterogeneous populations appear very plastic and selection pressure was stronger in organic systems.
    • Ensifer-mediated Arabidopsis thaliana Root Transformation (E-ART): A Protocol to Analyse the Factors that Support Ensifer-mediated Transformation (EMT) of Plant Cells

      Rathore, Deeraj Singh; Doohan, Fiona; Mullins, Ewen; Teagasc Walsh Fellowship Programme (Bio-protocol LLC, 05/10/2017)
      Ensifer adhaerens OV14, a soil borne alpha-proteobacteria of the Rhizobiaceae family, fortifies the novel plant transformation technology platform termed ‘Ensifer-mediated transformation’ (EMT). EMT can stably transform both monocot and dicot species, and the host range of EMT is continuously expanding across a diverse range of crop species. In this protocol, we adapted a previously published account that describes the use of Arabidopsis thaliana roots to investigate the interaction of A. thaliana and Agrobacterium tumefaciens. In our laboratory, we routinely use A. thaliana root explants to examine the factors that enhance the utility of EMT. In addition, the E-ART protocol can be used to study the transcriptional response of E. adhaerens and host plant following exposure to explant tissue, the transformability of different Ensifer adhaerens strains/mutants as well as testing the susceptibility of A. thaliana mutant lines as a means to decipher the mechanisms underpinning EMT.
    • 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.
    • EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.)

      Studer, Bruno; Kolliker, Roland; Muylle, Hilde; Asp, Torben; Frei, Ursula; Roldan-Ruiz, Isabel; Barre, Philippe; Tomaszewski, Celine; Meally, Helena; Barth, Susanne; et al. (Biomed Central, 16/08/2010)
      Background: Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm. Results: A set of 204 expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2. Conclusions: The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species.
    • Evaluation of rape-seed oil production, extraction and use as fuel in modified diesel engines

      Rice, B.; Sustainable Energy Ireland (Teagasc, 01/09/2009)
      It is now well established that rape-seed oil can provide a sustainable source of renewable fuel for diesel engines. The main problem is a high viscosity and vaporisation temperature, which could lead to pumping, atomisation and combustion difficulties. These problems can be overcome in either of two ways: by further processing of the oil to improve its pumping and combustion properties (usually achieved by esterification and layer separation to produce biodiesel) or by some peripheral modifications to the engine to allow it to cope with the more viscous fuel. Engine conversion kits for this purpose are widely available. The second option has attractions in Ireland, at least in the short-term, for a number of reasons. Plants can be established quickly, and so could make an immediate if small contribution to the achievement of Ireland’s substitution target in the Transport Biofuels Directive (Commission of European Communities, 2003). The small operating scale of coldpressing oil extraction plants could be achieved without undue difficulty, and the capital investment required to launch such a project is relatively low. In the event of a biodiesel plant being established at some stage in the future, the option of sourcing some of the oil requirement from these extraction plants would still be available.
    • 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.
    • Examining the physiological and genetic response of maize to low temperature conditions

      Di Fenza, Mauro; Teagasc Walsh Fellowship Programme (2013-01)
      Maize (Zea mays) is an emerging forage crop in Ireland, originating in warmer climates. Under Irish climate conditions establishment can be problematic due to low soil temperatures at early stages of establishment. Maize varieties with improved chilling tolerance have been developed and are on the market, but maize in Ireland is still established under plastic and further varietal improvements are required to make this crop more economically viable. To date, varieties are selected principally by phenotypic traits rather than genetic response. Investigation of the physiological and genetic response of maize towards cold/chilling stress at early developmental stage, in particular the response of developing maize roots to cold stress, can make a contribution towards the understanding of the molecular mechanisms conferring plant cold tolerance. The objectives of this study were aimed to create, at first, an experimental design to test the physiological response to low temperatures, under controlled environmental conditions, of various commercial maize cultivars adapted to grow in temperate climates. Responses to abiotic stresses such as cold involve changes in gene expression, therefore, once indentified the hybrids showing contrasting degrees of cold tolerance, these were profilied to examine gene expression and identify possible cold regulated genes. The physiological experiments on twelve maize varieties identified four genotypes with contrasting cold tolerance. Microarray analysis profiling these varieties was used to identify up and down regulated genes under cold/chilling conditions. The stress induced by the cold temperature in the genotypes Picker, PR39B29, Fergus and Codisco was reflected only on the expression profiles of the two varieties with superior cold tolerance, Picker and PR39B29. No significant changes in expression were observed in Fergus and Codisco in response to cold stress. The overall number of genes up and down regulated in the two cold tolerant varieties amounted to 69, which were, however, divided in a group of 39 genes in PR39B29 and 30 genes in Picker, as the two varieties exhibited two different trancriptomic patterns in which only four genes (RNA binding protein, pathogenesis-related protein 1 and two unknown proteins) were shared, although not all with the same degree of regulation. No cold regulated genes ware detected. The gene expression of the four-shared genes was further investigated with qRT-PCR in order to estimate the expression pattern over time. Five time points were used to analyse the expression trend of the genes. The gene expression was not maintained over the five time points, but it was subjected to fluctuation. However, with the exception of the RNA binding protein gene, the expression pattern was similar between the two varieties, indicating a common response to chilling stress.
    • Exploiting the inter-strain divergence of Fusarium oxysporum for microbial bioprocessing of lignocellulose to bioethanol

      Ali, Shahin S; Khan, Mojibur; Fagan, Brian; Mullins, Ewen; Doohan, Fiona (Biomed Central, 15/03/2012)
      Microbial bioprocessing of lignocellulose to bioethanol still poses challenges in terms of substrate catabolism. A targeted evolution-based study was undertaken to determine if inter-strain microbial variability could be exploited for bioprocessing of lignocellulose to bioethanol. The microorganism studied was Fusarium oxysporum because of its capacity to both saccharify and ferment lignocellulose. Strains of F. oxysporum were isolated and assessed for their genetic variability. Using optimised solid-state straw culture conditions, experiments were conducted that compared fungal strains in terms of their growth, enzyme activities (cellulases, xylanase and alcohol dehydrogenase) and yield of bioethanol and the undesirable by-products acetic acid and xylitol. Significant inter-strain divergence was recorded in regards to the capacity of studied F. oxysporum strains to produce alcohol from untreated straw. No correlation was observed between bioethanol synthesis and either the biomass production or microbial enzyme activity. A strong correlation was observed between both acetic acid and xylitol production and bioethanol yield. The level of diversity recorded in the alcohol production capacity among closely-related microorganism means that a targeted screening of populations of selected microbial species could greatly improve bioprocessing yields, in terms of providing both new host strains and candidate genes for the bioethanol industry.
    • Exploration of flowering control in Lolium perenne L.

      Byrne, Stephen; Mur, Luis AJ; Donnisson, Iain; Guiney, Emma (Teagasc, 01/08/2009)
      Flowering or heading in Lolium perenne (perennial ryegrass) is induced by a period of vernalization, followed by long days at higher temperatures. When heading occurs there is a reduction in the feed quality of the forage and therefore extending the period of vegetative growth or eliminating heading during the growing season will improve the potential of perennial ryegrass in agriculture. Conversely, a better control of flowering time and increased heading will lead to higher seed yield for commercial producers. The aim of this project was to investigate the underlying genetic control of flowering time in perennial ryegrass. An F1 population was created by crosspollinating two lines with different heading dates and a genetic linkage map was constructed using Simple Sequence Repeat (SSR) markers. The population and genetic linkage map was then used to identify Quantitative Trait Loci (QTL) associated with heading date, spike length and spikelets per spike. A number of QTL were identified for all traits, some of which had not previously been identified in perennial ryegrass. A Suppression Subtractive Hybridization (SSH) study was also employed to identify genes differentially expressed between an extremely late flowering line and earlier flowering sibling line. Expression analysis of a number of identified genes through floral induction was performed using real time RT-PCR. This revealed a number of transcripts with expression profiles indicative of a role to play in floral induction.
    • Exploring the potential of grass feedstock from marginal land in Ireland: Does marginal mean lower yield?

      Meehan, Peter; Burke, Brendan; Doyle, Deirdre; Barth, Susanne; Finnan, John; European Union; KBBE-2011-5-289461 (Elsevier, 2017-11-02)
      The production of biomass feedstock from marginal land has attracted much attention as a means of avoiding conflict between the production of food and fuel. Yield potentials from marginal lands have generally not been quantified although it is generally assumed that lower biomass yields can be expected from marginal lands. A three year study was conducted in Ireland in order to determine if grass yields of perennial rhizomatous grasses (cocksfoot, tall fescue, reed canary grass, festulolium) for anaerobic digestion from three marginal land sites (very wet site, very dry site, site prone to flooding) could match yields from better soils. Randomised complete block designs were established on each site in 2012 with two varieties of each grass species as treatments. Three grass harvests were taken from each site in 2013 and in 2014. There was no significant difference between yields from the control site and those from the very dry site and the site prone to flooding. Biomass yields from the very wet site were 85% of those from the control site. Highest yields were obtained from festulolium which were significantly higher than yields from perennial ryegrass. An energy analysis showed that maximising the production of grass from low lying mineral marginal grassland in Ireland could provide enough energy to meet the energy requirements of both the private car fleet and the heavy goods vehicle fleet while avoiding conflict with food production which could be concentrated on conventional land.
    • 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.