Now showing items 1-20 of 280

    • A Functional Land Management conceptual framework under soil drainage and land use scenarios

      Coyle, Cait; Creamer, Rachel E.; Schulte, Rogier P.; O'Sullivan, Lilian; Jordan, Phil; Institute of Technology, Sligo (Elsevier, 2015-11-15)
      Agricultural soils offer multiple soil functions, which contribute to a range of ecosystem services, and the demand for the primary production function is expected to increase with a growing world population. Other key functions on agricultural land have been identified as water purification, carbon sequestration, habitat biodiversity and nutrient cycling, which all need to be considered for sustainable intensification. All soils perform all functions simultaneously, but the variation in the capacity of soils to supply these functions is reviewed in terms of defined land use types (arable, bio-energy, broadleaf forest, coniferous forest, managed grassland, other grassland and Natura 2000) and extended to include the influence of soil drainage characteristics (well, moderately/imperfect, poor and peat). This latter consideration is particularly important in the European Atlantic pedo-climatic zone; the spatial scale of this review. This review develops a conceptual framework on the multi-functional capacity of soils, termed Functional Land Management, to facilitate the effective design and assessment of agri-environmental policies. A final functional soil matrix is presented as an approach to show the consequential changes to the capacity of the five soil functions associated with land use change on soils with contrasting drainage characteristics. Where policy prioritises the enhancement of particular functions, the matrix indicates the potential trade-offs for individual functions or the overall impact on the multi-functional capacity of soil. The conceptual framework is also applied by land use area in a case study, using the Republic of Ireland as an example, to show how the principle of multi-functional land use planning can be readily implemented.
    • Assessing the role of artificially drained agricultural land for climate change mitigation in Ireland

      Paul, Carsten; Fealy, Reamonn; Fenton, Owen; Lanigan, Gary; O’Sullivan, Lilian; Schulte, Rogier P.; Irish Dairy Research Fund; Teagasc Greenhouse Gas Working Group; Department of Agriculture, Food and the Marine (Elsevier, 2017-12-19)
      In 2014 temperate zone emission factor revisions were published in the IPCC Wetlands Supplement. Default values for direct CO2 emissions of artificially drained organic soils were increased by a factor of 1.6 for cropland sites and by factors ranging from 14 to 24 for grassland sites. This highlights the role of drained organic soils as emission hotspots and makes their rewetting more attractive as climate change mitigation measures. Drainage emissions of humic soils are lower on a per hectare basis and not covered by IPCC default values. However, drainage of great areas can turn them into nationally relevant emission sources. National policy making that recognizes the importance of preserving organic and humic soils’ carbon stock requires data that is not readily available. Taking Ireland as a case study, this article demonstrates how a dataset of policy relevant information can be generated. Total area of histic and humic soils drained for agriculture, resulting greenhouse gas emissions and climate change mitigation potential were assessed. For emissions from histic soils, calculations were based on IPCC emission factors, for humic soils, a modified version of the ECOSSE model was used. Results indicated 370,000 ha of histic and 426,000 ha of humic soils under drained agricultural land use in Ireland (8% and 9% of total farmed area). Calculated annual drainage emissions were 8.7 Tg CO2e from histic and 1.8 Tg CO2e from humic soils (equal to 56% of Ireland’s agricultural emissions in 2014, excluding emissions from land use). If half the area of drained histic soils was rewetted, annual saving would amount to 3.2 Tg CO2e. If on half of the deep drained, nutrient rich grasslands drainage spacing was decreased to control the average water table at −25 cm or higher, annual savings would amount to 0.4 Tg CO2e.
    • A sub-field scale critical source area index for legacy phosphorus management using high resolution data

      Thomas, Ian A.; Mellander, Per-Erik; Murphy, Paul; Fenton, Owen; Shine, Oliver; Djodjic, Faruk; Dunlop, Paul; Jordan, Phil; Teagasc Walsh Fellowship Programme; Department of Agriculture, Food and the Marine; et al. (Elsevier, 2016-09-25)
      Diffuse phosphorus (P) mitigation in agricultural catchments should be targeted at critical source areas (CSAs) that consider source and transport factors. However, development of CSA identification needs to consider the mobilisation potential of legacy soil P sources at the field scale, and the control of (micro)topography on runoff generation and hydrological connectivity at the sub-field scale. To address these limitations, a ‘next generation’ sub-field scale CSA index is presented, which predicts the risk of dissolved P losses in runoff from legacy soil P. The GIS-based CSA Index integrates two factors; mobile soil P concentrations (water extractable P; WEP) and a hydrologically sensitive area (HSA) index. The HSA Index identifies runoff-generating-areas using high resolution LiDAR Digital Elevation Models (DEMs), a soil topographic index (STI) and information on flow sinks and effects on hydrological connectivity. The CSA Index was developed using four intensively monitored agricultural catchments (7.5–11 km2) in Ireland with contrasting agri-environmental conditions. Field scale soil WEP concentrations were estimated using catchment and land use specific relationships with Morgan P concentrations. In-stream total reactive P (TRP) concentrations and discharge were measured sub-hourly at catchment outlet bankside analysers and gauging stations during winter closed periods for fertiliser spreading in 2009–14, and hydrograph/loadograph separation methods were used to estimate TRP loads and proportions from quickflow (surface runoff). A strong relationship between TRP concentrations in quickflow and soil WEP concentrations (r2 = 0.73) was used to predict dissolved P concentrations in runoff at the field scale, which were then multiplied by the HSA Index to generate sub-field scale CSA Index maps. Evaluation of the tool showed a very strong relationship between the total CSA Index value within the HSA and the total TRP load in quickflow (r2 = 0.86). Using a CSA Index threshold value of ≥0.5, the CSA approach identified 1.1–5.6% of catchment areas at highest risk of legacy soil P transfers, compared with 4.0–26.5% of catchment areas based on an existing approach that uses above agronomic optimum soil P status. The tool could be used to aid cost-effective targeting of sub-field scale mitigation measures and best management practices at delivery points of CSA pathways to reduce dissolved P losses from legacy P stores and support sustainable agricultural production.
    • Soil bacterial community structure and functional responses across a long-term mineral phosphorus (Pi) fertilisation gradient differ in grazed and cut grasslands

      Randall, Kate; Brennan, Fiona; Clipson, Nicholas; Creamer, Rachel; Griffiths, Bryan; Storey, Sean; Doyle, Evelyn; Programme for Research in Third-Level Institutions; European Regional Development Fund (Elsevier, 2019-03-06)
      Grasslands form a significant proportion of land used across the globe and future management is important. The objective of this study was to compare the long-term impact of inorganic phosphorus (Pi) fertilisation rates (P0, P15 and P30 ha−1 yr−1) under two grass management trials (grazed vs. cut and removed) on soil physicochemical properties, microbial biomass, phosphomonoesterase activity, bacterial community structure and abundance of a phosphorus (P) mineralising gene (phoD). Under grazing, microbial biomass and soil phosphorus concentrations (total and Pi) generally increased with Pi fertilisation rate, accompanied by significant differences in bacterial community structure between unfertilised (P0) and P30 soil. At the cut and removed site, although Pi was significantly greater in P30 soil, P concentrations (total and Pi) did not increase to the same extent as for grazing, with microbial biomass and bacterial community structures unresponsive to Pi fertilisation. Despite differences in soil P concentrations (total and Pi) and microbial biomass between sites, the abundance of bacterial phoD increased with increasing soil Pi across both sites, while phosphomonoesterase activity decreased. Amplicon sequencing revealed Acidobacteria were the dominant bacterial phylum across both grasslands, but significant differences in relative abundances of bacterial genera were detected at the grazed site only. The bacterial genera Gp6 and Gp16 increased significantly with Pi fertilisation under grazing. Conversely, Bradyrhizobium as well as unclassified genus-type groups belonging to Actinobacteria and Acidimicrobiales significantly decreased with Pi fertilisation, suggesting potential roles in P mobilisation when soil Pi concentrations are low. This study highlights the importance of long-term Pi fertilisation rates and aboveground vegetation removal in shaping soil bacterial community structure and microbial biomass, which in turn may impact soil fertility and plant productivity within agricultural soils.
    • Mushroom Virus X (MVX) prevention

      Gaze, Richard; Grogan, Helen (Teagasc (Agriculture and Food Development Authority), IrelandHorticultural Development Council, 2007)
      This factsheet is a summary of the most important information currently available. Its objective is to provide guidance to the recognition, prevention and control of the disease.
    • Identification and control of dry bubble disease of mushrooms

      Gaze, Richard; Grogan, Helen (Teagasc (Agriculture and Food Development Authority), IrelandHorticultural Development Council, 2008)
      This factsheet is a summary of the most important information currently available on Dry bubble disease of mushrooms (Verticillium fungicola). Its objective is to provide guidance to the recognition, prevention and control of the disease.
    • Identification and control of Cobweb disease on mushrooms

      Grogan, Helen; Gaze, Richard (Teagasc (Agriculture and Food Development Authority), IrelandHorticultural Development Council, 2008)
      This factsheet is a summary of the most important information currently available on Cobweb disease (Cladobotryum spp.). Its objective is to provide guidance on the recognition, prevention and control of the disease.
    • Chronic nutrient inputs affect stream macroinvertebrate communities more than acute inputs: An experiment manipulating phosphorus, nitrogen and sediment

      Davis, Stephen J; O hUallachain, Daire; Mellander, Per-Erik; Matthaei, Christoph; Piggott, Jeremy; Kelly-Quinn, Mary; Teagasc Walsh Fellowship Programme (Elsevier, 2019-05-07)
      Freshwaters worldwide are affected by multiple stressors. Timing of inputs and pathways of delivery can influence the impact stressors have on freshwater communities. In particular, effects of point versus diffuse nutrient inputs on stream macroinvertebrates are poorly understood. Point-source inputs tend to pose a chronic problem, whereas diffuse inputs tend to be acute with short concentration spikes. We manipulated three key agricultural stressors, phosphorus (ambient, chronic, acute), nitrogen (ambient, chronic, acute) and fine sediment (ambient, high), in 112 stream mesocosms (26 days colonisation, 18 days of manipulations) and determined the individual and combined effects of these stressors on stream macroinvertebrate communities (benthos and drift). Chronic nutrient treatments continuously received high concentrations of P and/or N. Acute channels received the same continuous enrichment, but concentrations were doubled during two 3-hour periods (day 6, day 13) to simulate acute nutrient inputs during rainstorms. Sediment was the most pervasive stressor in the benthos, reducing total macroinvertebrate abundance and richness, EPT (mayflies, stoneflies, caddisflies) abundance and richness. By contrast, N or P enrichment did not affect any of the six studied community-level metrics. In the drift assemblage, enrichment effects became more prevalent the longer the experiment went on. Sediment was the dominant driver of drift responses at the beginning of the experiment. After the first acute nutrient pulse, sediment remained the most influential stressor but its effects started to fade. After the second pulse, N became the dominant stressor. In general, impacts of either N or P on the drift were due to chronic exposure, with acute nutrient pulses having no additional effects. Overall, our findings imply that cost-effective management should focus on mitigating sediment inputs first and tackle chronic nutrient inputs second. Freshwater managers should also take into account the length of exposure to high nutrient concentrations, rather than merely the concentrations themselves.
    • Spent Mushroom Compost 'Fertilizer or Fuel'

      Walsh, Gerry (Bord Bia, 2009-05-21)
    • 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, A. 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

      McNamara, Louise B.; 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.