The aim of the Teagasc Crops, Environment and Land Use Programme is to develop and transfer cost-effective crop production systems, along with evidence-based knowledge to support and underpin the development of an environmentally sustainable, competitive and profitable agri-food sector.

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  • Comparison of photosynthetic performance of Fagus sylvatica seedlings under natural and artificial shading

    Sevillano, Ignacio; Short, Ian; Campion, Jerry; Grant, Olga M.; Grant, Jim; O’Reilly, Conor; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme (Elsevier, 2018-03-14)
    Commitment to sustainable forest management (alternatives to clearfelling) has led to a renewed interest in continuous cover forestry systems, which promote the control of light to produce stand benefits. Physiological performance of shade-tolerant European beech (Fagus sylvatica L.) in response to light availability was investigated in natural regeneration below the canopy in contrast to planted seedlings under artificial-shade conditions. Although beech seedlings had higher photosynthetic capacity with increasing light availability, they were able to maintain positive CO2 assimilation rates under low light levels in both field and controlled conditions. Leaves of seedlings under low light had the ability to use light more efficiently (higher PSII efficiency) than those in high light, which offer some physiological explanation for the ability of beech seedlings to grow under very low light conditions. Whilst caution is advised to interpret results from controlled to field studies, the overall general correspondence in the trend of the physiological response to light levels within beech grown below the canopy and under artificial-shade conditions suggests that it might be possible to extrapolate results from studies performed under artificial shade (nets) to field conditions. Hence, the use of nets may be an alternative way of assessing the potential physiological responses of seedlings to light availability.
  • Influence of stormflow and baseflow phosphorus pressures on stream ecology in agricultural catchments

    Shore, Mairead; Murphy, Sinead; Mellander, Per-Erik; Shortle, Ger; Melland, Alice R.; Crockford, Lucy; O'Flaherty, Vincent; Williams, Lauren; Morgan, Ger; Jordan, Philip; et al. (Elsevier, 2017-03-09)
    Stormflow and baseflow phosphorus (P) concentrations and loads in rivers may exert different ecological pressures during different seasons. These pressures and subsequent impacts are important to disentangle in order to target and monitor the effectiveness of mitigation measures. This study investigated the influence of stormflow and baseflow P pressures on stream ecology in six contrasting agricultural catchments. A five-year high resolution dataset was used consisting of stream discharge, P chemistry, macroinvertebrate and diatom ecology, supported with microbial source tracking and turbidity data. Total reactive P (TRP) loads delivered during baseflows were low (1–7% of annual loads), but TRP concentrations frequently exceeded the environmental quality standard (EQS) of 0.035 mg L− 1 during these flows (32–100% of the time in five catchments). A pilot microbial source tracking exercise in one catchment indicated that both human and ruminant faecal effluents were contributing to these baseflow P pressures but were diluted at higher flows. Seasonally, TRP concentrations tended to be highest during summer due to these baseflow P pressures and corresponded well with declines in diatom quality during this time (R2 = 0.79). Diatoms tended to recover by late spring when storm P pressures were most prevalent and there was a poor relationship between antecedent TRP concentrations and diatom quality in spring (R2 = 0.23). Seasonal variations were less apparent in the macroinvertebrate indices; however, there was a good relationship between antecedent TRP concentrations and macroinvertebrate quality during spring (R2 = 0.51) and summer (R2 = 0.52). Reducing summer point source discharges may be the quickest way to improve ecological river quality, particularly diatom quality in these and similar catchments. Aligning estimates of P sources with ecological impacts and identifying ecological signals which can be attributed to storm P pressures are important next steps for successful management of agricultural catchments at these scales.
  • Development of a scoring method to identify important areas of plant diversity in Ireland

    Walsh, Aidan; Sullivan, C. A.; Waldren, Stephen; Finn, John A.; Irish Research Council; Teagasc Walsh Fellowship Programme; PD/2011/2150; 2011012 (Elsevier, 2018-10-28)
    In the face of accelerating biodiversity loss it is more important than ever to identify important areas of biodiversity and target limited resources for conservation. We developed a method to identify areas of important plant diversity using known species’ distributions and evaluations of the species importance. We collated distribution records of vascular plants and developed a scoring method of spatial prioritisation to assign conservation value to the island of Ireland at the hectad scale (10 km × 10 km) and at the tetrad scale (2 km × 2 km) for two counties where sufficient data were available. Each plant species was assigned a species conservation value based on both its conservation status and distribution in Ireland. For each cell, the species conservation values within the cell were summed, thereby differentiating between areas of high and low conservation value across the landscape. Areas with high conservation value represent the most important areas for plant conservation. The protected area cover and the number of species present in these important areas were also examined by first defining threshold values using two different criteria. Species representation was high in the important areas; the identified important areas of plant diversity maintained high representation of species of conservation concern and achieved high species representation overall, requiring a low number of sites (<8%) to do so. The coincidence of protected areas and important areas for plant diversity was found to be low and while some important areas of plant diversity might benefit from the general protection afforded by these areas, our research highlights the need for conservation outside of protected areas.
  • Quantitative risk assessment of antimicrobials in biosolids applied on agricultural land and potential translocation into food

    Clarke, Rachel; Healy, Mark G.; Fenton, Owen; Cummins, Enda; European Union ERASMUS+; 2014-1-MT01-K200-000327 (Elsevier, 2017-12-30)
    The use of biosolids as a fertiliser may be an indirect route for contaminants into the food chain. One of the main concerns regarding the spreading of biosolids on agricultural land is the potential uptake of contaminants into plants which may bio-transfer into grazing animals that supply the food chain directly (e.g. meat and milk) and hence are subsequently consumed. The aim of this project was to create a quantitative risk assessment model to estimate the fate and translocation of triclosan (TCS) and triclocarban (TCC) into the feed (grass) and food chain with subsequent human exposure. The model's results indicate that TCS and TCC have low potential to transfer into milk and beef following the ingestion of contaminated grass by dairy cows. Mean estimated TCS and TCC residues in milk and beef show that TCC had the greatest concentration (mean values of 7.77 × 10− 6 mg kg− 1 in milk and 1.36 × 10− 4 mg kg− 1 in beef). Human exposure results show that TCC was greater for milk consumption in infants (1–4 years) (mean value 1.14 × 10− 7 mg kg− 1 bw d− 1) and for beef consumption by teens (12–17 years) (mean value 6.87 × 10− 8 mg kg− 1 bw d− 1). Concentrations of TCS and TCC were well below the estimated acceptable daily intake (ADI). Human health risk was estimated by evaluation of the hazard quotient (HQ), which used the NOAEL as a toxicity endpoint, combined with milk and beef human exposure estimates. HQ results show that all values were < 0.01 (no existing risk). A sensitivity analysis revealed that the Kow and initial concentration in biosolids as the parameters of greatest importance (correlation coefficients 0.91 and 0.19, respectively). This highlights the importance of physio-chemical properties of the compounds and their detection in biosolids post wastewater treatment along with their persistence in soil following application. This model is a valuable tool in which to ascertain the potential transfer of contaminants in the environment into animal forage with knock on consequences for exposure through the human food chain.
  • 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.
  • Novel Approaches to Optimise Early Growth in Willow Crops

    Donnelly, Isabella; McDonnell, Kevin; Finnan, John; Teagasc Walsh Fellowship Programme (MDPI, 2019-06-03)
    Willow is a fast growing, high yielding biomass crop that can help reduce reliance on fossil fuels. However, long establishment times to get to profitability and sustainable yield may deter interest in planting the crop. A number of different approaches were investigated to optimise and accelerate early growth. These approaches were water immersion, plastic application, altering stem orientation at planting, altering coppicing timings and applying growth hormone. Glasshouse and field trials were used to test the different approaches. In this work, planting material was soaked for a varying number of days and plastic was applied or not applied in field trials. In the planting orientation approach, stems were planted diagonally or vertically with half of the planting material above the ground level or horizontally below ground level. Additionally, willow crops were coppiced at different times throughout their first growing season and a growth hormone trial was also incorporated in this work. Water soaking, plastic application, coppicing during the growing season or hormone application did not improve early growth or yield. However, early growth and yield were increased by manipulating the planting orientation of willow stems. Planting orientation treatments in which part of the stem was left above the ground increased early growth and yield significantly compared to the control without requiring extra inputs at planting. The beneficial effects of coppicing can be achieved by manipulating the planting procedure so that the first year’s growth is not disregarded.
  • Risk Assessment of E. coli Survival Up to the Grazing Exclusion Period After Dairy Slurry, Cattle Dung, and Biosolids Application to Grassland

    Ashekuzzaman, S. M.; Richards, Karl G.; Ellis, Stephanie; Tyrrel, Sean; O'Leary, Emma; Griffiths, Bryan; Ritz, Karl; Fenton, Owen; European Union; 265269 (Frontiers, 2018-07-10)
    Grassland application of dairy slurry, cattle dung, and biosolids offers an opportunity to recycle valuable nutrients (N, P, and K), which may all introduce pathogens to the soil environment. Herein, a temporal risk assessment of the survival of Escherichia coli (E. coli) up to 40 days in line with the legislated grazing exclusion time points after application was examined across six scenarios: (1) soil and biosolids mixture, (2) biosolids amended soil, (3) dairy slurry application, (4) cattle dung on pasture, (5) comparison of scenario 2, 3, and 4, and (6) maximum legal vs. excess rate of application for scenario 2 and 3. The risk model input parameters were taken or derived from regressions within the literature and an uncertainty analysis (n = 1,000 trials for each scenario) was conducted. Scenario 1 results showed that E. coli survival was higher in the soil/biosolids mixture for higher biosolids portion, resulting in the highest 20 day value of residual E. coli concentration (i.e., C20, log10 CFU g−1 dw) of 1.0 in 100% biosolids or inoculated soil and the lowest C20 of 0.098 in 75/25 soil/biosolids ratio, respectively, in comparison to an average initial value of ~6.4 log10 CFU g−1 dw. The E. coli survival across scenario 2, 3, and 4 showed that the C20 value of biosolids (0.57 log10 CFU g−1 dw) and dairy slurry (0.74 log10 CFU ml−1) was 2.9–3.7 times smaller than that of cattle dung (2.12 log10 CFU g−1 dw). The C20 values of biosolids and dairy slurry associated with legal and excess application rates ranged from 1.14 to 1.71 log10 CFU ha−1, which is a significant reduction from the initial concentration range (12.99 to 14.83 log10 CFU ha−1). The E. coli survival in un-amended soil was linear with a very low decay rate resulting in a higher C20 value than that of biosolids or dairy slurry. The risk assessment and uncertainly analysis showed that the residual concentrations in biosolids/dairy slurry applied soil after 20 days would be 45–57% lower than that of the background soil E. coli concentration. This means the current practice of grazing exclusion times is safe to reduce the risk of E. coli transmission into the soil environment.
  • A Novel Multivariate Approach to Phenotyping and Association Mapping of Multi-Locus Gametophytic Self-Incompatibility Reveals S, Z, and Other Loci in a Perennial Ryegrass (Poaceae) Population

    Thorogood, Daniel; Yates, Steven; Manzanares, Chloé; Skot, Leif; Hegarty, Matthew; Blackmore, Tina; Barth, Susanne; Studer, Bruno; Biotechnology and Biological Sciences Research Council; Swiss National Science Foundation; et al. (Frontiers, 2017-08-02)
    Self-incompatibility (SI) is a mechanism that many flowering plants employ to prevent fertilisation by self- and self-like pollen ensuring heterozygosity and hybrid vigour. Although a number of single locus mechanisms have been characterised in detail, no multi-locus systems have been fully elucidated. Historically, examples of the genetic analysis of multi-locus SI, to make analysis tractable, are either made on the progeny of bi-parental crosses, where the number of alleles at each locus is restricted, or on crosses prepared in such a way that only one of the SI loci segregates. Perennial ryegrass (Lolium perenne L.) possesses a well-documented two locus (S and Z) gametophytic incompatibility system. A more universal, realistic proof of principle study was conducted in a perennial ryegrass population in which allelic and non-allelic diversity was not artificially restricted. A complex pattern of pollinations from a diallel cross was revealed which could not possibly be interpreted easily per se, even with an already established genetic model. Instead, pollination scores were distilled into principal component scores described as Compatibility Components (CC1-CC3). These were then subjected to a conventional genome-wide association analysis. CC1 associated with markers on linkage groups (LGs) 1, 2, 3, and 6, CC2 exclusively with markers in a genomic region on LG 2, and CC3 with markers on LG 1. BLAST alignment with the Brachypodium physical map revealed highly significantly associated markers with peak associations with genes adjacent and four genes away from the chromosomal locations of candidate SI genes, S- and Z-DUF247, respectively. Further significant associations were found in a Brachypodium distachyon chromosome 3 region, having shared synteny with Lolium LG 1, suggesting further SI loci linked to S or extensive micro-re-arrangement of the genome between B. distachyon and L. perenne. Significant associations with gene sequences aligning with marker sequences on Lolium LGs 3 and 6 were also identified. We therefore demonstrate the power of a novel association genetics approach to identify the genes controlling multi-locus gametophytic SI systems and to identify novel loci potentially involved in already established SI systems.
  • An Immortalized Genetic Mapping Population for Perennial Ryegrass: A Resource for Phenotyping and Complex Trait Mapping

    Velmurugan, Janaki; Milbourne, Dan; Connolly, Vincent; Heslop-Harrison, J. S.; Anhalt, Ulrike C. M.; Lynch, M. B.; Barth, Susanne; Teagasc Walsh Fellowship Programme; Teagasc (Frontiers, 2018-05-31)
    To address the lack of a truly portable, universal reference mapping population for perennial ryegrass, we have been developing a recombinant inbred line (RIL) mapping population of perennial ryegrass derived via single seed descent from a well-characterized F2 mapping population based on genetically distinct inbred parents in which the natural self-incompatibility (SI) system of perennial ryegrass has been overcome. We examined whether it is possible to create a genotyping by sequencing (GBS) based genetic linkage map in a small population of the F6 generation of this population. We used 41 F6 genotypes for GBS with PstI/MspI-based libraries. We successfully developed a genetic linkage map comprising 6074 SNP markers, placing a further 22080 presence and absence variation (PAV) markers on the map. We examined the resulting genetic map for general and RIL specific features. Overall segregation distortion levels were similar to those experienced in the F2 generation, but segregation distortion was reduced on linkage group 6 and increased on linkage group 7. Residual heterozygosity in the F6 generation was observed at a level of 5.4%. There was a high proportion of chromosomes (30%) exhibiting the intact haplotype of the original inbred parents of the F1 genotype from which the population is derived, pointing to a tendency for chromosomes to assort without recombining. This could affect the applicability of these lines and might make them more suitable for situations where repressed recombination is an advantage. Inter- and intra-chromosomal linkage disequilibrium (LD) analysis suggested that the map order was robust. We conclude that this RIL population, and subsequent F7 and F8 generations will be useful for genetic analysis and phenotyping of agronomic and biological important traits in perennial ryegrass.
  • A Pathogen-Responsive Leucine Rich Receptor Like Kinase Contributes to Fusarium Resistance in Cereals

    Thapa, Ganesh; Gunupuru, Lokanadha R.; Hehir, James G.; Kahla, Amal; Mullins, Ewen; Doohan, Fiona; Department of Agriculture, Food and the Marine; Science Foundation Ireland; 11/S/103; 10/IN.1/B3028; et al. (Frontiers, 2018-06-26)
    Receptor-like kinases form the largest family of receptors in plants and play an important role in recognizing pathogen-associated molecular patterns and modulating the plant immune responses to invasive fungi, including cereal defenses against fungal diseases. But hitherto, none have been shown to modulate the wheat response to the economically important Fusarium head blight (FHB) disease of small-grain cereals. Homologous genes were identified on barley chromosome 6H (HvLRRK-6H) and wheat chromosome 6DL (TaLRRK-6D), which encode the characteristic domains of surface-localized receptor like kinases. Gene expression studies validated that the wheat TaLRRK-6D is highly induced in heads as an early response to both the causal pathogen of FHB disease, Fusarium graminearum, and its’ mycotoxic virulence factor deoxynivalenol. The transcription of other wheat homeologs of this gene, located on chromosomes 6A and 6B, was also up-regulated in response to F. graminearum. Virus-induced gene silencing (VIGS) of the barley HvLRRK-6H compromised leaf defense against F. graminearum. VIGS of TaLRRK-6D in two wheat cultivars, CM82036 (resistant to FHB disease) and cv. Remus (susceptible to FHB), confirmed that TaLRRK-6D contributes to basal resistance to FHB disease in both genotypes. Although the effect of VIGS did not generally reduce grain losses due to FHB, this experiment did reveal that TaLRRK-6D positively contributes to grain development. Further gene expression studies in wheat cv. Remus indicated that VIGS of TaLRRK-6D suppressed the expression of genes involved in salicylic acid signaling, which is a key hormonal pathway involved in defense. Thus, this study provides the first evidence of receptor like kinases as an important component of cereal defense against Fusarium and highlights this gene as a target for enhancing cereal resistance to FHB disease.
  • Cereal yield gaps across Europe

    Schils, René; Olesen, Jørgen E.; Kersebaum, Kurt-Christian; Rijk, Bert; Oberforster, Michael; Kalyada, Valery; Khitrykau, Maksim; Gobin, Anne; Kirchev, Hristofor; Manolova, Vanya; et al. (Elsevier, 2018-09-18)
    Europe accounts for around 20% of the global cereal production and is a net exporter of ca. 15% of that production. Increasing global demand for cereals justifies questions as to where and by how much Europe’s production can be increased to meet future global market demands, and how much additional nitrogen (N) crops would require. The latter is important as environmental concern and legislation are equally important as production aims in Europe. Here, we used a country-by-country, bottom-up approach to establish statistical estimates of actual grain yield, and compare these to modelled estimates of potential yields for either irrigated or rainfed conditions. In this way, we identified the yield gaps and the opportunities for increased cereal production for wheat, barley and maize, which represent 90% of the cereals grown in Europe. The combined mean annual yield gap of wheat, barley, maize was 239 Mt, or 42% of the yield potential. The national yield gaps ranged between 10 and 70%, with small gaps in many north-western European countries, and large gaps in eastern and south-western Europe. Yield gaps for rainfed and irrigated maize were consistently lower than those of wheat and barley. If the yield gaps of maize, wheat and barley would be reduced from 42% to 20% of potential yields, this would increase annual cereal production by 128 Mt (39%). Potential for higher cereal production exists predominantly in Eastern Europe, and half of Europe’s potential increase is located in Ukraine, Romania and Poland. Unlocking the identified potential for production growth requires a substantial increase of the crop N uptake of 4.8 Mt. Across Europe, the average N uptake gaps, to achieve 80% of the yield potential, were 87, 77 and 43 kg N ha−1 for wheat, barley and maize, respectively. Emphasis on increasing the N use efficiency is necessary to minimize the need for additional N inputs. Whether yield gap reduction is desirable and feasible is a matter of balancing Europe’s role in global food security, farm economic objectives and environmental targets.
  • Crop Establishment Practices Are a Driver of the Plant Microbiota in Winter Oilseed Rape (Brassica napus)

    Rathore, Ridhdhi; Dowling, David N.; Forristal, P.D.; Spink, John; Cotter, Paul D.; Bulgarelli, Davide; Germaine, Kieran J.; Teagasc Walsh Fellowship Programme; Marie Curie Actions; Royal Society of Edinburgh/Scottish Government Personal Research Fellowship (Frontiers, 2017-08-09)
    Gaining a greater understanding of the plant microbiota and its interactions with its host plant heralds a new era of scientific discovery in agriculture. Different agricultural management practices influence soil microbial populations by changing a soil’s physical, chemical and biological properties. However, the impact of these practices on the microbiota associated with economically important crops such as oilseed rape, are still understudied. In this work we investigated the impact of two contrasting crop establishment practices, conventional (plow based) and conservation (strip–tillage) systems, on the microbiota inhabiting different plant microhabitats, namely rhizosphere, root and shoot, of winter oilseed rape under Irish agronomic conditions. Illumina 16S rRNA gene sequence profiling showed that the plant associated microhabitats (root and shoot), are dominated by members of the bacterial phyla Proteobacteria, Actinobacteria and Bacteroidetes. The root and shoot associated bacterial communities displayed markedly distinct profiles as a result of tillage practices. We observed a very limited ‘rhizosphere effect’ in the root zone of WOSR, i.e., there was little or no increase in bacterial community richness and abundance in the WOSR rhizosphere compared to the bulk soil. The two tillage systems investigated did not appear to lead to any major long term differences on the bulk soil or rhizosphere bacterial communities. Our data suggests that the WOSR root and shoot microbiota can be impacted by management practices and is an important mechanism that could allow us to understand how plants respond to different management practices and environments.
  • 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
  • Distribution and extent of High Nature Value farmland in the Republic of Ireland (tetrad scale)

    Matin, Shafique; Sullivan, C. A.; Finn, John A.; O'hUallacháin, Daire; Green, Stuart; Meredith, David; Moran, James (2019-05-06)
    High Nature Value (HNV) farmland is extensively managed farmland that has high biodiversity. This farmland is important for the conservation of semi-natural habitats and the plants and animals linked with them. Supporting this type of farmland will ensure high levels of farmland biodiversity, vibrant rural communities, high water, air and soil quality and resistance to flooding among other things. To map the likely distribution of HNV farmland in the Republic of Ireland (ROI) we used five indicators adapted for the Irish context and weighted based on expert knowledge and literature. The indicators used are: semi-natural habitat cover (CORINE land cover), stocking density (Land parcel information system), hedgerow/scrub cover (Teagasc), river and stream density (OSI), and soil diversity (Teagasc). Indicator data sets were included in a weighted sum model that combined raster indicator inputs, representing relative weights and the output HNV farmland had a tetrad-scale (2 km × 2 km) spatial resolution.
  • Predicted distribution of High Nature Value farmland in the Republic of Ireland

    Matin, Shafique; Sullivan, C. A.; O'hUallacháin, Daire; Meredith, David; Moran, James; Finn, John A.; Green, Stuart; Department of Agriculture, Food and the Marine; 11/S/108 (Taylor & Francis, 2016-08-31)
    High Nature Value (HNV) farmland is typically characterised by low-intensity farming associated with high biodiversity and species of conservation concern. Mapping the occurrence and distribution of such farmland are useful for appropriate targeting of conservation measures and supporting associated rural communities. We mapped the likely distribution of HNV farmland in the Republic of Ireland using a linear regression model incorporating established European indicators, adapted for Ireland and weightings based on expert opinion. The indicators used were semi-natural habitat cover, stocking density, hedgerow density, river and stream density and soil diversity, with highest weightings placed on the first two indicators (40% and 30%, respectively). The map provides information on the likely occurrence and distribution of HNV farmland in each electoral division as a reference point for future monitoring of the distribution of HNV farmland in the Republic of Ireland in order to assist with planning and policy development for the rural environment.
  • Functional Land Management: Bridging the Think-Do-Gap using a multi-stakeholder science policy interface

    O'Sullivan, Lilian; Wall, David; Creamer, Rachel E.; Bampa, Francesca; Schulte, Rogier P. O.; European Union; National Development Plan 2007–2013.; 635201; 677407; 13S468 (Springer, 2017-11)
    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.
  • Ash dieback in Ireland – A review of European management options and case studies in remedial silviculture

    Short, Ian; Hawe, Jerry; Woodland Trust NI; COFORD; Teagasc (Society of Irish Foresters, 2018)
    Ash dieback, caused by Hymenoscyphus fraxineus, is developing rapidly across the island of Ireland. Ireland’s ash (Fraxinus excelsior L.) woodlands, particularly first rotation plantations, are quite unique and are at particular risk of very rapid decline. Urgent action is required in order to minimise the economic, ecological and social impact of the disease. However, for this to happen forest owners require guidance regarding potential positive management interventions. This article outlines the wider, mainly European, experience of remedial silviculture. It presents three case studies on existing remedial silviculture trials in Ireland. In the absence of silvicultural research data specific to the evolving situation with ash dieback, this article explores the potential benefits of positive practical actions which may minimise the impact of the disease. Despite the seriousness of the situation, such silvicultural activity may even result in a positive economic outcome. It is hoped that by beginning to document potential mitigatory management options, this paper may bring some reassurance to owners and managers of ashdominated woodlands.
  • An Immortalized Genetic Mapping Population for Perennial Ryegrass: A Resource for Phenotyping and Complex Trait Mapping

    Velmurugan, Janaki; Milbourne, Dan; Connolly, Vincent; Heslop-Harrison, J. S.; Anhalt, Ulrike C. M.; Lynch, M. B.; Barth, Susanne; Teagasc Walsh Fellowship Programme (Frontiers, 2018-05-31)
    To address the lack of a truly portable, universal reference mapping population for perennial ryegrass, we have been developing a recombinant inbred line (RIL) mapping population of perennial ryegrass derived via single seed descent from a well-characterized F2 mapping population based on genetically distinct inbred parents in which the natural self-incompatibility (SI) system of perennial ryegrass has been overcome. We examined whether it is possible to create a genotyping by sequencing (GBS) based genetic linkage map in a small population of the F6 generation of this population. We used 41 F6 genotypes for GBS with PstI/MspI-based libraries. We successfully developed a genetic linkage map comprising 6074 SNP markers, placing a further 22080 presence and absence variation (PAV) markers on the map. We examined the resulting genetic map for general and RIL specific features. Overall segregation distortion levels were similar to those experienced in the F2 generation, but segregation distortion was reduced on linkage group 6 and increased on linkage group 7. Residual heterozygosity in the F6 generation was observed at a level of 5.4%. There was a high proportion of chromosomes (30%) exhibiting the intact haplotype of the original inbred parents of the F1 genotype from which the population is derived, pointing to a tendency for chromosomes to assort without recombining. This could affect the applicability of these lines and might make them more suitable for situations where repressed recombination is an advantage. Inter- and intra-chromosomal linkage disequilibrium (LD) analysis suggested that the map order was robust. We conclude that this RIL population, and subsequent F7 and F8 generations will be useful for genetic analysis and phenotyping of agronomic and biological important traits in perennial ryegrass.
  • A Pathogen-Responsive Leucine Rich Receptor Like Kinase Contributes to Fusarium Resistance in Cereals

    Thapa, Ganesh; Gunupuru, Lokanadha R.; Hehir, James G.; Kahla, Amal; Mullins, Ewen; Doohan, Fiona; Department of Agriculture, Food and the Marine; Science Foundation Ireland; 11/S/103; 10/IN.1/B3028; et al. (Frontiers, 2018-06-26)
    Receptor-like kinases form the largest family of receptors in plants and play an important role in recognizing pathogen-associated molecular patterns and modulating the plant immune responses to invasive fungi, including cereal defenses against fungal diseases. But hitherto, none have been shown to modulate the wheat response to the economically important Fusarium head blight (FHB) disease of small-grain cereals. Homologous genes were identified on barley chromosome 6H (HvLRRK-6H) and wheat chromosome 6DL (TaLRRK-6D), which encode the characteristic domains of surface-localized receptor like kinases. Gene expression studies validated that the wheat TaLRRK-6D is highly induced in heads as an early response to both the causal pathogen of FHB disease, Fusarium graminearum, and its’ mycotoxic virulence factor deoxynivalenol. The transcription of other wheat homeologs of this gene, located on chromosomes 6A and 6B, was also up-regulated in response to F. graminearum. Virus-induced gene silencing (VIGS) of the barley HvLRRK-6H compromised leaf defense against F. graminearum. VIGS of TaLRRK-6D in two wheat cultivars, CM82036 (resistant to FHB disease) and cv. Remus (susceptible to FHB), confirmed that TaLRRK-6D contributes to basal resistance to FHB disease in both genotypes. Although the effect of VIGS did not generally reduce grain losses due to FHB, this experiment did reveal that TaLRRK-6D positively contributes to grain development. Further gene expression studies in wheat cv. Remus indicated that VIGS of TaLRRK-6D suppressed the expression of genes involved in salicylic acid signaling, which is a key hormonal pathway involved in defense. Thus, this study provides the first evidence of receptor like kinases as an important component of cereal defense against Fusarium and highlights this gene as a target for enhancing cereal resistance to FHB disease.
  • A Novel Multivariate Approach to Phenotyping and Association Mapping of Multi-Locus Gametophytic Self-Incompatibility Reveals S, Z, and Other Loci in a Perennial Ryegrass (Poaceae) Population

    Thorogood, Daniel; Yates, Steven; Manzanares, Chloé; Skot, Leif; Hegarty, Matthew; Blackmore, Tina; Barth, Susanne; Studer, Bruno; Biotechnology and Biological Sciences Research Council; Swiss National Science Foundation; et al. (Frontiers, 2017-08-02)
    Self-incompatibility (SI) is a mechanism that many flowering plants employ to prevent fertilisation by self- and self-like pollen ensuring heterozygosity and hybrid vigour. Although a number of single locus mechanisms have been characterised in detail, no multi-locus systems have been fully elucidated. Historically, examples of the genetic analysis of multi-locus SI, to make analysis tractable, are either made on the progeny of bi-parental crosses, where the number of alleles at each locus is restricted, or on crosses prepared in such a way that only one of the SI loci segregates. Perennial ryegrass (Lolium perenne L.) possesses a well-documented two locus (S and Z) gametophytic incompatibility system. A more universal, realistic proof of principle study was conducted in a perennial ryegrass population in which allelic and non-allelic diversity was not artificially restricted. A complex pattern of pollinations from a diallel cross was revealed which could not possibly be interpreted easily per se, even with an already established genetic model. Instead, pollination scores were distilled into principal component scores described as Compatibility Components (CC1-CC3). These were then subjected to a conventional genome-wide association analysis. CC1 associated with markers on linkage groups (LGs) 1, 2, 3, and 6, CC2 exclusively with markers in a genomic region on LG 2, and CC3 with markers on LG 1. BLAST alignment with the Brachypodium physical map revealed highly significantly associated markers with peak associations with genes adjacent and four genes away from the chromosomal locations of candidate SI genes, S- and Z-DUF247, respectively. Further significant associations were found in a Brachypodium distachyon chromosome 3 region, having shared synteny with Lolium LG 1, suggesting further SI loci linked to S or extensive micro-re-arrangement of the genome between B. distachyon and L. perenne. Significant associations with gene sequences aligning with marker sequences on Lolium LGs 3 and 6 were also identified. We therefore demonstrate the power of a novel association genetics approach to identify the genes controlling multi-locus gametophytic SI systems and to identify novel loci potentially involved in already established SI systems.

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