• Laboratory Development of a Passive Proportional Sampler for Overland FlowStudies in Agricultural Fields

      Ryan, T. Declan; Forristal, Dermot (Canadian Society for Bioengineering / Société Canadienne de Génie Agroalimentaire et de Bioingénierie, 06/02/2015)
      Water-quality in many rivers remains poor and needs to be improved. Diffuse pollution continues to cause difficulties. Some instruments are available which can monitor pollution of rivers from land. They allow measurement and sampling of overland flow (OLF), but they do not offer the precision required (proportional sampling and samples 0.1% of OLF). A laboratory unit was constructed to mimic instrument performance in the field. This was used to test three sampler designs. A V-notch weir was used in the first sampler and a Sutro weir in the second and third as this unit possessed a proportional discharge to head ratio, which the Vnotch weir did not have. Other parameters investigated included ground slope, sampler slope, pipe size and port location. The remaining issues of nozzle size (0.7, 1.0 and 2.0 mm), the number of 1.0 mm nozzles and the effect of aspiration were investigated. The arrangement with the Sutro weir and three 1.0 mm nozzles in series gave proportional discharge and the target low sampling rate of 0.1%. This will allow the calculation of sediment and chemical losses for the monitored area and will put the loss in context with other losses in a catchment.
    • MAJOR AND MICRO NUTRIENT ADVICE FOR PRODUCTIVE AGRICULTURAL CROPS

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

      McEniry, Joseph; O'Kiely, Padraig; Clipson, Nicholas J.W.; Forristal, P.D.; Doyle, Evelyn M.; Teagasc Walsh Fellowship Programme (Teagasc, Oak Park, Carlow, Ireland, 2007)
      Baled silage composition frequently differs from that of comparable conventional precision-chop silage. The lower final concentration of fermentation products in baled silage makes it more conducive to the activities of undesirable microorganisms. Silage additives can be used to encourage beneficial microbial activity and/or inhibit detrimental microbial activity. The experiment was organised in a 2 (chop treatments) × 6 (additive treatments) × 2 (stages of ensilage) factorial arrangement of treatments (n = 3 silos/treatment) to suggest additive treatments for use in baled silage production that would help create conditions more inhibitory to the activities of undesirable microorganisms and realise an outcome comparable to precision-chop silage. Chopping the herbage prior to ensiling, in the absence of an additive treatment, improved the silage fermentation. In the unchopped herbage, where the fermentation was poorer, the lactic acid bacterial inoculant resulted in an immediate increase (P < 0.001) in lactic acid concentration and a faster decline (P < 0.001) in pH with a subsequent reduction in butyric acid (P < 0.001) and ammonia-N (P < 0.01) concentrations. When sucrose was added in addition to the lactic acid bacterial inoculant, the combined treatment had a more pronounced effect on pH, butyric acid and ammonia-N values at the end of ensilage. The formic acid based additive and the antimicrobial mixture restricted the activities of undesirable microorganisms resulting in reduced concentrations of butyric acid (P < 0.001) and ammonia-N (P < 0.01). These additives offer a potential to create conditions in baled silage more inhibitory to the activities of undesirable microorganisms.
    • Markers associated with heading and aftermath heading in perennial ryegrass full-sib families

      Arojju, Sai Krishna; Barth, Susanne; Milbourne, Dan; Conaghan, Patrick; Velmurugan, Janaki; Hodkinson, Trevor R; Byrne, Stephen L.; Department of Agriculture, Food and the Marine, Ireland; Teagasc Walsh Fellowship Programme; EU Marie-Sklodowska-Curie Fellowship; et al. (Biomed Central, 16/07/2016)
      Background Heading and aftermath heading are important traits in perennial ryegrass because they impact forage quality. So far, genome-wide association analyses in this major forage species have only identified a small number of genetic variants associated with heading date that overall explained little of the variation. Some possible reasons include rare alleles with large phenotypic affects, allelic heterogeneity, or insufficient marker density. We established a genome-wide association panel with multiple genotypes from multiple full-sib families. This ensured alleles were present at the frequency needed to have sufficient statistical power to identify associations. We genotyped the panel via partial genome sequencing and performed genome-wide association analyses with multi-year phenotype data collected for heading date, and aftermath heading. Results Genome wide association using a mixed linear model failed to identify any variants significantly associated with heading date or aftermath heading. Our failure to identify associations for these traits is likely due to the extremely low linkage disequilibrium we observed in this population. However, using single marker analysis within each full-sib family we could identify markers and genomic regions associated with heading and aftermath heading. Using the ryegrass genome we identified putative orthologs of key heading genes, some of which were located in regions of marker-trait associations. Conclusion Given the very low levels of LD, genome wide association studies in perennial ryegrass populations are going to require very high SNP densities. Single marker analysis within full-sibs enabled us to identify significant marker-trait associations. One of these markers anchored proximal to a putative ortholog of TFL1, homologues of which have been shown to play a key role in continuous heading of some members of the rose family, Rosaceae.
    • The microbiological and chemical composition of baled and precision-chop silages on a sample of farms in County Meath

      McEniry, Joseph; O'Kiely, Padraig; Clipson, Nicholas J.W.; Forristal, P.D.; Doyle, Evelyn M.; Teagasc Walsh Fellowship Programme; (Teagasc, Oak Park, Carlow, Ireland, 2006)
      Baled and precision-chop silages were examined on a sample of farms in the Irish midlands to determine microbiological and chemical composition at feedout. Silage making practices and chemical composition were similar to those in national surveys. Wilting was an integral part of baled silage production and was reflected in a more restricted fermentation (higher pH and water-soluble carbohydrates, with lower fermentation acids and buffering capacity) compared to precision-chop silage. Yeast numbers were higher in baled silage, suggesting a more aerobic environment within the bale. Although the fermentation appeared similar in the outer and inner horizons of baled silage, yeast, lactic acid bacteria and Enterobacteria numbers were higher in the outer horizon suggesting less exacting anaerobiosis adjacent to the surface of the bale.
    • Mustard catch crop enhances denitrification in shallow groundwater beneath a spring barley field

      Jahangir, Mohammad M. R.; Minet, E.; Johnston, Paul; Premrov, Alina; Coxon, Catherine E.; Hackett, Richard; Richards, Karl G.; Department of Agriculture, Food and the Marine, Ireland; RSF 06383 (Elsevier, 26/12/2013)
      Over-winter green cover crops have been reported to increase dissolved organic carbon (DOC) concentrations in groundwater, which can be used as an energy source for denitrifiers. This study investigates the impact of a mustard catch crop on in situ denitrification and nitrous oxide (N2O) emissions from an aquifer overlain by arable land. Denitrification rates and N2O-N/(N2O-N + N2-N) mole fractions were measured in situ with a push–pull method in shallow groundwater under a spring barley system in experimental plots with and without a mustard cover crop. The results suggest that a mustard cover crop could substantially enhance reduction of groundwater nitrate NO3--N via denitrification without significantly increasing N2O emissions. Mean total denitrification (TDN) rates below mustard cover crop and no cover crop were 7.61 and 0.002 μg kg−1 d−1, respectively. Estimated N2O-N/(N2O-N + N2-N) ratios, being 0.001 and 1.0 below mustard cover crop and no cover crop respectively, indicate that denitrification below mustard cover crop reduces N2O to N2, unlike the plot with no cover crop. The observed enhanced denitrification under the mustard cover crop may result from the higher groundwater DOC under mustard cover crop (1.53 mg L−1) than no cover crop (0.90 mg L−1) being added by the root exudates and root masses of mustard. This study gives insights into the missing piece in agricultural nitrogen (N) balance and groundwater derived N2O emissions under arable land and thus helps minimise the uncertainty in agricultural N and N2O-N balances.
    • A note on the conservation characteristics of baled grass silages ensiled with different additives.

      Keles, G.; O'Kiely, Padraig; Forristal, P.D. (Teagasc, Oak Park, Carlow, Ireland, 2010)
      The effects of contrasting conventional silage additives on chemical composition, aerobic stability and deterioration, and mould development in baled silage were investigated. Herbage from a grassland sward was wilted for 24 h and treated with acid (formic or sulphuric), sugar (molasses), bacterial (Lactobacillus plantarum, L. plantarum + Serratia rubidaea + Bacillus subtilis, or L. buchneri) or sugar + bacterial (molasses + L. plantarum) additives prior to baling and wrapping. Silage made without an additive preserved well and had a low incidence of mould growth, and the effects of additives were minor or absent. It is concluded that little practical benefit was realised when conventional additives were applied to wilted, leafy, easy-to-ensile grass prior to baling and ensilage.
    • A note on the early transcriptional response in leaves and root of potato plants to cadmium exposure

      Mengist, M.F.; Byrne, Stephen; Griffin, Denis; Milbourne, Dan; Department of Agriculture, Food and the Marine; 11SF308 (Teagasc, 2021-03-26)
      Potato plants can accumulate a high amount of cadmium (Cd) in the tuber when grown in soils rich in Cd. The molecular mechanisms governing Cd accumulation in the potato plant are poorly understood. Here we performed an RNA-sequencing experiment to identify genes differentially expressed in the leaf and root of potato during early stages of Cd exposure. Results did not identify any significant transcriptional response in leaves under 1 or 5 mg kg−1 Cd after 72 h. However, in the roots we did identify 2,846 genes that were significantly differentially expressed after 72 h between plants grown in 5 mg kg−1 Cd and controls. These included genes involved in photosynthesis and autophagy being up-regulated, and genes involved in intracellular transport being down-regulated. This study is the first report on the transcriptome-wide response of potato to Cd stress, providing insight into the molecular mechanisms involved in the response.
    • A note on the effect of elevated concentrations of greenhouse gases on spring wheat yield in Ireland

      Donnelly, A; Finnan, John; Jones, M. B.; Burke, James I. (Teagasc (Agriculture and Food Development Authority), Ireland, 2005)
      Spring wheat (Triticum aestivum L., cv. Minaret) was grown to maturity in open-top chambers under two concentrations of CO2 (ambient and 680 μmol/mol) and two concentrations of O3 (ambient and ambient +90 nmol/mol). Elevated concentrations of CO2 increased grain yield whereas yield was reduced by elevated O3. The damaging effect of elevated O3 on grain yield was reduced when the crop was grown in a combination of elevated CO2 and elevated O3. It is concluded that wheat production in Ireland is expected to benefit from rising concentrations of atmospheric CO2.
    • 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.
    • 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.
    • 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.
    • The occurrence of herbicide-resistant Avena fatua (wild oats) populations to ACCase-inhibiting herbicides in Ireland

      Byrne, R.; Vijaya Bhaskar, A.V.; Spink, J.; Freckleton, R.; Neve, P.; Barth, Susanne (Teagasc, 2021-06-03)
      Following growers’ reports of herbicide control problems, populations of 30 wild oats, Avena fatua, were collected from the south-east main arable counties of Ireland in 2016 and investigated for the occurrence and potential for herbicide resistance to acetyl-CoA carboxylase (ACCase) inhibitors pinoxaden, propaquizafop and cycloxydim, as well as acetolactate synthase (ALS) inhibitor mesosulfuron + iodosulfuron. Plant survival ≥20% was considered as the discriminating threshold between resistant and susceptible populations, when plants were treated with full recommended field rates of ACCase/ALS inhibitors. Glasshouse sensitivity screens revealed 2 out of 30 populations were cross-resistant to all three ACCase inhibitors. While three populations were cross-resistant to both pinoxaden and propaquizafop, and additionally, two populations were resistant to propaquizafop only. Different degree of resistance and cross-resistance between resistant populations suggest the involvement of either different point mutations or more than one resistance mechanism. Nevertheless, all populations including the seven ACCase-resistant populations were equally susceptible to ALS inhibitor. An integrated weed management (cultural/non-chemical control tactics and judicious use of herbicides) approach is strongly recommended to minimize the risk of herbicide resistance evolution.
    • An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection

      Diekmann, Kerstin; Hodkinson, Trevor R; Fricke, Evelyn; Barth, Susanne; Teagasc Walsh Fellowship Programme (PLoS, 30/07/2008)
      Background Obtaining chloroplast genome sequences is important to increase the knowledge about the fundamental biology of plastids, to understand evolutionary and ecological processes in the evolution of plants, to develop biotechnological applications (e.g. plastid engineering) and to improve the efficiency of breeding schemes. Extraction of pure chloroplast DNA is required for efficient sequencing of chloroplast genomes. Unfortunately, most protocols for extracting chloroplast DNA were developed for eudicots and do not produce sufficiently pure yields for a shotgun sequencing approach of whole plastid genomes from the monocot grasses. Methodology/Principal Findings We have developed a simple and inexpensive method to obtain chloroplast DNA from grass species by modifying and extending protocols optimized for the use in eudicots. Many protocols for extracting chloroplast DNA require an ultracentrifugation step to efficiently separate chloroplast DNA from nuclear DNA. The developed method uses two more centrifugation steps than previously reported protocols and does not require an ultracentrifuge. Conclusions/Significance The described method delivered chloroplast DNA of very high quality from two grass species belonging to highly different taxonomic subfamilies within the grass family (Lolium perenne, Pooideae; Miscanthus×giganteus, Panicoideae). The DNA from Lolium perenne was used for whole chloroplast genome sequencing and detection of SNPs. The sequence is publicly available on EMBL/GenBank.
    • Parthenium hysterophorus Herbage Mulching: a Potential Source of Weeds Control in Soybean (Glycine max)

      Khalid, S; Shehzad, M; Zahoor, F; Mubeen, K; Ahmad, A; Ali, E (FapUNIFESP (SciELO), 2018-05-28)
      Weeds have indirect effects on crop plants. Crop development is affected by allelopathy from certain weed species. Allelochemicals from allelopathic weeds can disturb the root and shoot growth of emerging crop seedlings, as well as cause several other types of damage. A study was carried out to investigate the allelopathic potential of Parthenium hysterophorus for weed response in soybean. The experiment was laid out in Randomized Complete Block Design (RCBD) with split plot arrangements and replicated thrice. Sowing methods (broadcast and line sowing) were kept in the main plot and mulching treatments (surface mulching and soil incorporation) were kept in the sub-plots. Mulching of Parthenium hysterophorus was applied at the rate of 1.0 t ha-1, 2.5 t ha-1, 5 t ha-1 with control (no parthenium). Manual weed control was also used as treatments. The results revealed that significantly higher shoot length, shoot fresh weight, shoot dry weight, root length, root fresh weigh, root dry weight, number of nodules per plant, nodules fresh and dry weight, number of branches, number of pods per plant, thousand seed weight biological yield, economic yield, dry matter yield and harvest index were recorded with the soil incorporation of Parthenium herbage at the rate of 2.5 t ha-1. Maximum weed density and weed dry biomass were recorded in control plots while weed control efficiency was seen greater in plots where Parthenium herbage was applied to surface at the rate of 5 t ha-1. The results suggested that the use of Parthenium hysterophorus herbage mulching can reduce infestation of weeds by its allelopathic effects and increase the yield of soybean under sub-humid agro-climatic conditions.
    • 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 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.
    • Pathways for Nutrient Loss to Water; Slurry and Fertilizer Spreading

      Ryan, T. Declan; Holden, Nicholas M.; Carton, Owen T.; Fitzgerald, D.; Murphy, F.; Environmental Protection Agency (Teagasc, 08/07/2008)
      There are almost 150,000 farms in Ireland and these contribute substantial quantities of N and P to inland and coastal waters. Some of these nutrients are carried from wet soils by overland flow and by leaching from dry soils. Farm practice can reduce the loss from farms by judicious management of nutrients. Improvements are required to diminish export of nutrients without impairing operations on the farm. Literature regarding nutrient loss from agriculture was reviewed in this project and maps were prepared to predict best slurry spreading times around Ireland. Two further maps were prepared to show slurry storage requirement on farms.
    • Physiological and Transcriptional Response to Drought Stress Among Bioenergy Grass Miscanthus Species

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

      De Vega, Jose J.; Teshome, Abel; Klaas, Manfred; Grant, Jim; Finnan, John; Barth, Susanne; European Union; Marie Sklodowska-Curie Actions COFUND CAROLINE; UK Research Council; FP7-KBBE-2011-5-289461; et al. (Biomed Central, 2021-03-06)
      Background Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity, resilience and photosynthetic capacity at low temperature. These qualities make Miscanthus a particularly good candidate for temperate marginal land, where yields can be limited by insufficient or excessive water supply. Differences in response to water stress have been observed among Miscanthus species, which correlated to origin. In this study, we compared the physiological and molecular responses among Miscanthus species under excessive (flooded) and insufficient (drought) water supply in glasshouse conditions. Results A significant biomass loss was observed under drought conditions in all genotypes. M. x giganteus showed a lower reduction in biomass yield under drought conditions compared to the control than the other species. Under flooded conditions, biomass yield was as good as or better than control conditions in all species. 4389 of the 67,789 genes (6.4%) in the reference genome were differentially expressed during drought among four Miscanthus genotypes from different species. We observed the same biological processes were regulated across Miscanthus species during drought stress despite the DEGs being not similar. Upregulated differentially expressed genes were significantly involved in sucrose and starch metabolism, redox, and water and glycerol homeostasis and channel activity. Multiple copies of the starch metabolic enzymes BAM and waxy GBSS-I were strongly up-regulated in drought stress in all Miscanthus genotypes, and 12 aquaporins (PIP1, PIP2 and NIP2) were also up-regulated in drought stress across genotypes. Conclusions Different phenotypic responses were observed during drought stress among Miscanthus genotypes from different species, supporting differences in genetic adaption. The low number of DEGs and higher biomass yield in flooded conditions supported Miscanthus use in flooded land. The molecular processes regulated during drought were shared among Miscanthus species and consistent with functional categories known to be critical during drought stress in model organisms. However, differences in the regulated genes, likely associated with ploidy and heterosis, highlighted the value of exploring its diversity for breeding.