• The health status of Irish honeybee colonies in 2006

      Coffey, M. F.; Barth, Susanne; Hayes, K.; Breen, J.; European Agricultural Guidance and Guarantee Fund; Department of Agriculture, Food and the Marine, Ireland (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      This study assessed the health status of Irish honeybee colonies and provides a snapshot of the incidence of a number of important colony parasites/pathogens including: the mite Varroa destructor; three associated viruses (deformed wing virus (DWV), acute bee paralysis virus (ABPV) and Kashmir virus (KBV)); the tracheal mite Acarapis woodi; the microsporidian Nosema spp., and the insect Braula coeca. During June/July 2006, 135 samples of adult bees were collected from productive colonies throughout Ireland and standard techniques were used to determine the presence and absence of the parasites and pathogens. Varroa destructor was positively identified in 72.6% of the samples and was widely distributed. Although the samples were analysed for three viruses, DWV, ABPV and KBV, only DWV was detected (frequency = 12.5%). Acarapis woodi and Nosema spp. occurred in approximately 11% and 22% of the samples, respectively, while B. coeca, a wingless dipteran that was once common in Irish honeybee colonies, was very rare (3.7%). Samples where all the pathogens/parasites were jointly absent were statistically under-represented in Leinster and DWV was statistically over-represented in Munster. In Ulster, there was over-representation of the categories where all parasites/pathogens were jointly absent and for A. woodi, and underrepresentation of V. destructor.
    • A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover

      Nagy, Istvan; Barth, Susanne; Mehenni-Ciz, Jeanne; Abberton, Michael T; Milbourne, Dan; Department of Agriculture, Food and the Marine, Ireland; RSF 07–566 (Biomed Central, 13/02/2013)
      Background: White clover (Trifolium repens L.) is an allotetraploid species possessing two highly collinear ancestral sub-genomes. The apparent existence of highly similar homeolog copies for the majority of genes in white clover is problematic for the development of genome-based resources in the species. This is especially true for the development of genetic markers based on single nucleotide polymorphisms (SNPs), since it is difficult to distinguish between homeolog-specific and allelic variants. Robust methods for categorising single nucleotide variants as allelic or homeolog-specific in large transcript datasets are required. We illustrate one potential approach in this study. Results: We used 454-pyrosequencing sequencing to generate ~760,000 transcript sequences from an 8th generation white clover inbred line. These were assembled and partially annotated to yield a reference transcript set comprising 71,545 sequences. We subsequently performed Illumina sequencing on three further white clover samples, generating 14 million transcript reads from a mixed sample comprising 24 divergent white clover genotypes, and 50 million reads on two further eighth generation white clover inbred lines. Mapping these reads to the reference transcript set allowed us to develop a significant SNP resource for white clover, and to partition the SNPs from the inbred lines into categories reflecting allelic or homeolog-specific variation. The potential for using haplotype reconstruction and progenitor genome comparison to assign haplotypes to specific ancestral sub-genomes of white clover is demonstrated for sequences corresponding to genes encoding dehydration responsive element binding protein and acyl-coA oxidase. Conclusions: In total, 208,854 independent SNPs in 31,715 reference sequences were discovered, approximately three quarters of which were categorised as representing allelic or homeolog-specific variation using two inbred lines. This represents a significant resource for white clover genomics and genetics studies. We discuss the potential to extend the analysis to identify a “core set” of ancestrally derived homeolog specific variants in white clover.
    • 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.
    • 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.
    • An insight into the impact of arable farming on Irish biodiversity: A scarcity of studies hinders a rigorous assessment

      O'Brien, Martin; Spillane, Charles; Meade, Connor; Mullins, Ewen; Environmental Protection Agency; 2006-B-MS-46 (Royal Irish Academy, 27/08/2008)
      To help understand and counteract future agronomic challenges to farmland biodiversity, it is essential to know how present farming practices have affected biodiversity on Irish farms. We present an overview of existing research data and conclusions, describing the impact of crop cultivation on biodiversity on Irish arable farms. An extensive literature review clearly indicates that peer-reviewed publications on research conducted in Ireland on this topic are quite scarce: just 21 papers investigating the effect of conventional crop cultivation on Irish biodiversity have been published within the past 30 years. Principally, these studies have concluded that conventional crop cultivation has had an adverse impact on biodiversity on Irish farms, with 15 of the 21 studies demonstrating negative trends for the taxa investigated. Compared to other EU states, the relative dearth of baseline data and absence of monitoring programmes designed to assess the specific impacts of crop cultivation on Irish biodiversity highlight the need to develop long-term research studies. With many new challenges facing Irish agriculture, a research programme must be initiated to measure current levels of biodiversity on arable land and to assess the main farming ‘pressures’ causing significant biodiversity loss or gains in these systems.
    • Insights from the Fungus Fusarium oxysporum Point to High Affinity Glucose Transporters as Targets for Enhancing Ethanol Production from Lignocellulose

      Ali, Shahin S; Nugent, Brian; Mullins, Ewen; Doohan, Fiona; Department of Agriculture, Food and the Marine, Ireland; RSF 07 513 (PLOS, 30/01/2013)
      Ethanol is the most-widely used biofuel in the world today. Lignocellulosic plant biomass derived from agricultural residue can be converted to ethanol via microbial bioprocessing. Fungi such as Fusarium oxysporum can simultaneously saccharify straw to sugars and ferment sugars to ethanol. But there are many bottlenecks that need to be overcome to increase the efficacy of microbial production of ethanol from straw, not least enhancement of the rate of fermentation of both hexose and pentose sugars. This research tested the hypothesis that the rate of sugar uptake by F. oxysporum would enhance the ethanol yields from lignocellulosic straw and that high affinity glucose transporters can enhance ethanol yields from this substrate. We characterized a novel hexose transporter (Hxt) from this fungus. The F. oxysporum Hxt represents a novel transporter with homology to yeast glucose signaling/transporter proteins Rgt2 and Snf3, but it lacks their C-terminal domain which is necessary for glucose signalling. Its expression level decreased with increasing glucose concentration in the medium and in a glucose uptake study the Km(glucose) was 0.9 mM, which indicated that the protein is a high affinity glucose transporter. Post-translational gene silencing or over expression of the Hxt in F. oxysporum directly affected the glucose and xylose transport capacity and ethanol yielded by F. oxysporum from straw, glucose and xylose. Thus we conclude that this Hxt has the capacity to transport both C5 and C6 sugars and to enhance ethanol yields from lignocellulosic material. This study has confirmed that high affinity glucose transporters are ideal candidates for improving ethanol yields from lignocellulose because their activity and level of expression is high in low glucose concentrations, which is very common during the process of consolidated processing.
    • Insights from the Fungus Fusarium oxysporum Point to High Affinity Glucose Transporters as Targets for Enhancing Ethanol Production from Lignocellulose

      Ali, Shahin S; Nugent, Brian; Mullins, Ewen; Doohan, Fiona (PLOS, 30/01/2013)
      Ethanol is the most-widely used biofuel in the world today. Lignocellulosic plant biomass derived from agricultural residue can be converted to ethanol via microbial bioprocessing. Fungi such as Fusarium oxysporum can simultaneously saccharify straw to sugars and ferment sugars to ethanol. But there are many bottlenecks that need to be overcome to increase the efficacy of microbial production of ethanol from straw, not least enhancement of the rate of fermentation of both hexose and pentose sugars. This research tested the hypothesis that the rate of sugar uptake by F. oxysporum would enhance the ethanol yields from lignocellulosic straw and that high affinity glucose transporters can enhance ethanol yields from this substrate. We characterized a novel hexose transporter (Hxt) from this fungus. The F. oxysporum Hxt represents a novel transporter with homology to yeast glucose signaling/transporter proteins Rgt2 and Snf3, but it lacks their C-terminal domain which is necessary for glucose signalling. Its expression level decreased with increasing glucose concentration in the medium and in a glucose uptake study the Km(glucose) was 0.9 mM, which indicated that the protein is a high affinity glucose transporter. Post-translational gene silencing or over expression of the Hxt in F. oxysporum directly affected the glucose and xylose transport capacity and ethanol yielded by F. oxysporum from straw, glucose and xylose. Thus we conclude that this Hxt has the capacity to transport both C5 and C6 sugars and to enhance ethanol yields from lignocellulosic material. This study has confirmed that high affinity glucose transporters are ideal candidates for improving ethanol yields from lignocellulose because their activity and level of expression is high in low glucose concentrations, which is very common during the process of consolidated processing.
    • Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation

      Zuniga-Soto, Evelyn; Doohan, Fiona; Mullins, Ewen; Fitzpatrick, David; Science Foundation Ireland; Teagasc Walsh Fellowship Programme; 11/RFP.1/GEN/3420; 2011210 (Springer Science and Business Media LLC, 2019-07-17)
      The ability to engineer plant genomes has been primarily driven by the soil bacterium Agrobacterium tumefaciens but recently the potential of alternative rhizobia such as Rhizobium etli and Ensifer adhaerens OV14, the latter of which supports Ensifer Mediated Transformation (EMT) has been reported. Surprisingly, a knowledge deficit exists in regards to understanding the whole genome processes underway in plant transforming bacteria, irrespective of the species. To begin to address the issue, we undertook a temporal RNAseq-based profiling study of E. adhaerens OV14 in the presence/absence of Arabidopsis thaliana tissues. Following co-cultivation with root tissues, 2333 differentially expressed genes (DEGs) were noted. Meta-analysis of the RNAseq data sets identified a clear shift from plasmid-derived gene expression to chromosomal-based transcription within the early stages of bacterium-plant co-cultivation. During this time, the number of differentially expressed prokaryotic genes increased steadily out to 7 days co-cultivation, a time at which optimum rates of transformation were observed. Gene ontology evaluations indicated a role for both chromosomal and plasmid-based gene families linked specifically with quorum sensing, flagellin production and biofilm formation in the process of EMT. Transcriptional evaluation of vir genes, housed on the pCAMBIA 5105 plasmid in E. adhaerens OV14 confirmed the ability of E. adhaerens OV14 to perceive and activate its transcriptome in response to the presence of 200 µM of acetosyringone. Significantly, this is the first study to characterise the whole transcriptomic response of a plant engineering bacterium in the presence of plant tissues and provides a novel insight into prokaryotic genetic processes that support T-DNA transfer.
    • An Investigation of Seed Treatments for the Control of Crow Damage to Newly-Sown Wheat

      Kennedy, T.F.; Connery, J. (Teagasc, 28/02/2007)
      Seed treatments for the control of crow damage to newly-sown winter and spring wheat were evaluated in field trials from 2004 to 2007. Treatments included six fungicides, three insecticides, a product marketed as a bird repellent and three possible repellents. Various rates of selected compounds were investigated. Winter wheat was sown in December and spring wheat in late-January to mid-February. Sowing depth was 2 to 4 cm while some selected treatments were also sown at 5 to 9 cm deep. Crow damage was assessed by recording plant density and grain yield. Severe damage by crows was recorded. The plant population for untreated spring wheat seed in 2004, 2005 and 2006 was reduced by 59%, 72% and 89%, respectively. The corresponding reductions caused by crows to winter wheat sown in December 2004, 2005 and 2006 was 97%, 89% and 96%. Best control of crow damage was provided by the fungicide Thiram. Increasing the rate of Thiram applied to seed improved the control of crow damage by increasing plant density in the range 42 to 70% and 36 to 57%, respectively, for spring and winter wheat when compared with untreated seed. Anchor, which contains the fungicides Thiram and Carboxin, also gave reasonably good control. The commonly used fungicide product panoctine gave poor control of crow damage. Other treatments investigated were ineffective in controlling damage. Increasing the sowing depth to more than 4.6 cm significantly reduced damage to both treated and untreated seed when compared with similar treatments sown less than this depth.
    • Ireland’s Rural Environment: Research Highlights from Johnstown Castle

      O hUallachain, Daire; Fenton, Owen; Foley, M (Teagasc, 2013)
      This booklet gives a flavour of the current research in Teagasc Johnstown Castle Research Centre and introduces you to the staff involved. It covers the areas of Nutrient Efficiency, Gaseous emissions, Agricultural Ecology, Soils and Water quality.
    • 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.
    • 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 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.