• Factors influencing the conservation characteristics of baled and precision-chop grass silages

      McEniry, Joseph; Forristal, P.D.; O'Kiely, Padraig (Teagasc (Agriculture and Food Development Authority), Ireland, 2011)
      The composition of baled silage on Irish farms frequently differs from that of comparable precision-chop silage. This paper concerns a field-scale study designed to investigate: (a) the effects of number of layers (2, 4, 6 or 8) of polyethylene stretch film and the duration of storage (7 vs. 18 months) on the conservation characteristics of baled silage, and (b) the conservation characteristics of baled (4 layers of stretch film) and precision-chop silages. All silages were made following three durations of wilting (0, 24 or 48 h). Wilting restricted silage fermentation, with silage pH being highest (P<0.001) and the concentration of fermentation products lowest (P<0.001) for the 48 h wilt treatment. Wrapping bales in only 2 layers of polyethylene stretch film resulted in extensive visible mould growth, but mould growth was practically eliminated by the application of 4 or more layers of film. Silage fermentation characteristics were generally improved by wilting, and by 4 compared to 2 layers of stretch film. Extending the storage duration of baled silage from 7 to 18 months reduced (P<0.001) the concentration of fermentation products and increased in-silo fresh weight losses (P<0.001) and visible mould growth. Whereas 4 layers of conventional stretch film are normally sufficient, 6 layers may be necessary to prevent mould growth when bales of unwilted silage are stored for a second season. Under good farm-management conditions differences observed between baled and precision-chop silages probably result mainly from differences in the concentration of dry matter in herbage at ensiling.
    • Functional Land Management: Bridging the Think-Do-Gap using a multi-stakeholder science policy interface

      O’Sullivan, Lilian; Wall, David; Creamer, Rachel; Bampa, Francesca; Schulte, Rogier P. O.; National Development Plan 2007–2013; European Union; 13S468; 635201; 677407 (Springer Science and Business Media LLC, 2017-11-24)
      Functional Land Management (FLM) is proposed as an integrator for sustainability policies and assesses the functional capacity of the soil and land to deliver primary productivity, water purification and regulation, carbon cycling and storage, habitat for biodiversity and recycling of nutrients. This paper presents the catchment challenge as a method to bridge the gap between science, stakeholders and policy for the effective management of soils to deliver these functions. Two challenges were completed by a wide range of stakeholders focused around a physical catchment model—(1) to design an optimised catchment based on soil function targets, (2) identify gaps to implementation of the proposed design. In challenge 1, a high level of consensus between different stakeholders emerged on soil and management measures to be implemented to achieve soil function targets. Key gaps including knowledge, a mix of market and voluntary incentives and mandatory measures were identified in challenge 2.
    • Gene Expression Pattern in Olive Tree Organs (Olea europaea L.)

      Ramírez-Tejero, Jorge A.; Jiménez-Ruiz, Jaime; Leyva-Pérez, María de la O; Barroso, Juan Bautista; Luque, Francisco; Regional Government of Andalusia; Spanish Ministry of Economy, Industry and Competitiveness; Spanish State Research Agency; European Union; AGR-6038; et al. (MDPI AG, 2020-05-12)
      The olive tree (Olea europaea L.) was one of the first plant species in history to be domesticated. Throughout olive domestication, gene expression has undergone drastic changes that may affect tissue/organ-specific genes. This is an RNA-seq study of the transcriptomic activity of different tissues/organs from adult olive tree cv. “Picual” under field conditions. This analysis unveiled 53,456 genes with expression in at least one tissue, 32,030 of which were expressed in all organs and 19,575 were found to be potential housekeeping genes. In addition, the specific expression pattern in each plant part was studied. The flower was clearly the organ with the most exclusively expressed genes, 3529, many of which were involved in reproduction. Many of these organ-specific genes are generally involved in regulatory activities and have a nuclear protein localization, except for leaves, where there are also many genes with a plastid localization. This was also observed in stems to a lesser extent. Moreover, pathogen defense and immunity pathways were highly represented in roots. These data show a complex pattern of gene expression in different organs, and provide relevant data about housekeeping and organ-specific genes in cultivated olive.
    • Generating Phenotypic Diversity in a Fungal Biocatalyst to Investigate Alcohol Stress Tolerance Encountered during Microbial Cellulosic Biofuel Production

      Hennessy, Rosanna C.; Doohan, Fiona; Mullins, Ewen; Department of Agriculture, Food and the Marine, Ireland; RSF 07 513 (PLOS, 16/10/2013)
      Consolidated bioprocessing (CBP) of lignocellulosic biomass offers an alternative route to renewable energy. The crop pathogen Fusarium oxysporum is a promising fungal biocatalyst because of its broad host range and innate ability to co-saccharify and ferment lignocellulose to bioethanol. A major challenge for cellulolytic CBP-enabling microbes is alcohol inhibition. This research tested the hypothesis that Agrobacterium tumefaciens - mediated transformation (ATMT) could be exploited as a tool to generate phenotypic diversity in F. oxysporum to investigate alcohol stress tolerance encountered during CBP. A random mutagenesis library of gene disruption transformants (n=1,563) was constructed and screened for alcohol tolerance in order to isolate alcohol sensitive or tolerant phenotypes. Following three rounds of screening, exposure of select transformants to 6% ethanol and 0.75% n-butanol resulted respectively in increased (≥11.74%) and decreased (≤43.01%) growth compared to the wild –type (WT). Principal component analysis (PCA) quantified the level of phenotypic diversity across the population of genetically transformed individuals and isolated candidate strains for analysis. Characterisation of one strain, Tr. 259, ascertained a reduced growth phenotype under alcohol stress relative to WT and indicated the disruption of a coding region homologous to a putative sugar transporter (FOXG_09625). Quantitative PCR (RT-PCR) showed FOXG_09625 was differentially expressed in Tr. 259 compared to WT during alcohol-induced stress (P<0.05). Phylogenetic analysis of putative sugar transporters suggests diverse functional roles in F. oxysporum and other filamentous fungi compared to yeast for which sugar transporters form part of a relatively conserved family. This study has confirmed the potential of ATMT coupled with a phenotypic screening program to select for genetic variation induced in response to alcohol stress. This research represents a first step in the investigation of alcohol tolerance in F. oxysporum and has resulted in the identification of several novel strains, which will be of benefit to future biofuel research.
    • Genetic Analysis Using a Multi-Parent Wheat Population Identifies Novel Sources of Septoria Tritici Blotch Resistance

      Riaz, Adnan; KockAppelgren, Petra; Hehir, James Gerard; Kang, Jie; Meade, Fergus; Cockram, James; Milbourne, Dan; Spink, John; Mullins, Ewen; Byrne, Stephen; et al. (MDPI AG, 2020-08-04)
      Zymoseptoria tritici is the causative fungal pathogen of septoria tritici blotch (STB) disease of wheat (Triticum aestivum L.) that continuously threatens wheat crops in Ireland and throughout Europe. Under favorable conditions, STB can cause up to 50% yield losses if left untreated. STB is commonly controlled with fungicides; however, a combination of Z. tritici populations developing fungicide resistance and increased restrictions on fungicide use in the EU has led to farmers relying on fewer active substances. Consequently, this serves to drive the emergence of Z. tritici resistance against the remaining chemistries. In response, the use of resistant wheat varieties provides a more sustainable disease management strategy. However, the number of varieties offering an adequate level of resistance against STB is limited. Therefore, new sources of resistance or improved stacking of existing resistance loci are needed to develop varieties with superior agronomic performance. Here, we identified quantitative trait loci (QTL) for STB resistance in the eight-founder “NIAB Elite MAGIC” winter wheat population. The population was screened for STB response in the field under natural infection for three seasons from 2016 to 2018. Twenty-five QTL associated with STB resistance were identified in total. QTL either co-located with previously reported QTL or represent new loci underpinning STB resistance. The genomic regions identified and the linked genetic markers serve as useful resources for STB resistance breeding, supporting rapid selection of favorable alleles for the breeding of new wheat cultivars with improved STB resistance.
    • The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry

      Byrne, Stephen; Østerbye Erthmann, Pernille; Agerbirk, Niels; Bak, Søren; Hauser, Thure Pavlo; Nagy, Istvan; Paina, Cristiana; Asp, Torben; Danish Council for Independent Research; 09–065899; et al. (Nature, 2017-01-17)
      The genus Barbarea has emerged as a model for evolution and ecology of plant defense compounds, due to its unusual glucosinolate profile and production of saponins, unique to the Brassicaceae. One species, B. vulgaris, includes two ‘types’, G-type and P-type that differ in trichome density, and their glucosinolate and saponin profiles. A key difference is the stereochemistry of hydroxylation of their common phenethylglucosinolate backbone, leading to epimeric glucobarbarins. Here we report a draft genome sequence of the G-type, and re-sequencing of the P-type for comparison. This enables us to identify candidate genes underlying glucosinolate diversity, trichome density, and study the genetics of biochemical variation for glucosinolate and saponins. B. vulgaris is resistant to the diamondback moth, and may be exploited for “dead-end” trap cropping where glucosinolates stimulate oviposition and saponins deter larvae to the extent that they die. The B. vulgaris genome will promote the study of mechanisms in ecological biochemistry to benefit crop resistance breeding.
    • Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes

      Rudder, Steven; Doohan, Fiona; Creevey, Christopher J.; Wendt, Toni; Mullins, Ewen; Science Foundation Ireland; 11/RFP.1/GEN/3420. (Biomed Central, 07/04/2014)
      Additional file 1:Figure S1. Circular representation of the four replicons of E. adhaerens OV14. Figure S2. Synteny plots showing total sequence of Ensifer adhaerens OV14 pOV14 (top bar) vs Agrobacterium tumefaciens C58 pTi (bottom bar), computed using DoubleACT version2 on tBLASTx setting with cut off set at 100. Visualised in Artemis ACT. Additional file 2; BLAST of Ensifer adhaerens OV14 replicons.xlsx. Excel file includes tables of BLAST search of individual Ensifer adhaerens OV14 replicons Additional file 3. BLAST of Agrobacterium tumefaciens C58 replicons.xlsx. Excel file includes tables of BLAST searches of individual Agrobacterium tumefaciens C58
    • Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes

      Rudder, Steven; Doohan, Fiona; Creevey, Christopher J.; Wendt, Toni; Mullins, Ewen (Biomed Central, 2014-04-07)
      Abstract Background Recently it has been shown that Ensifer adhaerens can be used as a plant transformation technology, transferring genes into several plant genomes when equipped with a Ti plasmid. For this study, we have sequenced the genome of Ensifer adhaerens OV14 (OV14) and compared it with those of Agrobacterium tumefaciens C58 (C58) and Sinorhizobium meliloti 1021 (1021); the latter of which has also demonstrated a capacity to genetically transform crop genomes, albeit at significantly reduced frequencies. Results The 7.7 Mb OV14 genome comprises two chromosomes and two plasmids. All protein coding regions in the OV14 genome were functionally grouped based on an eggNOG database. No genes homologous to the A. tumefaciens Ti plasmid vir genes appeared to be present in the OV14 genome. Unexpectedly, OV14 and 1021 were found to possess homologs to chromosomal based genes cited as essential to A. tumefaciens T-DNA transfer. Of significance, genes that are non-essential but exert a positive influence on virulence and the ability to genetically transform host genomes were identified in OV14 but were absent from the 1021 genome. Conclusions This study reveals the presence of homologs to chromosomally based Agrobacterium genes that support T-DNA transfer within the genome of OV14 and other alphaproteobacteria. The sequencing and analysis of the OV14 genome increases our understanding of T-DNA transfer by non-Agrobacterium species and creates a platform for the continued improvement of Ensifer-mediated transformation (EMT).
    • Genomic prediction of crown rust resistance in Lolium perenne

      Arojju, Sai Krishna; Conaghan, Patrick; Barth, Susanne; Milbourne, Dan; Casler, Michael D.; Hodkinson, Trevor R.; Michel, Thibauld; Byrne, Stephen; Department of Agriculture Food and the Marine; European Union; et al. (Springer Science and Business Media LLC, 2018-05-29)
      Background Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability. Results Using these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set. Conclusion Using a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications.
    • Genomic prediction of crown rust resistance in Lolium perenne

      Arojju, Sai Krishna; Conaghan, Patrick; Barth, Susanne; Milbourne, Dan; Casler, M.D.; Hodkinson, Trevor R; Michel, Thibauld; Byrne, Stephen L.; Department of Agriculture, Food and the Marine, Ireland; Marie Sklodowska-Curie; et al. (Biomed Central, 29/05/2018)
      Background Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability. Results Using these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set. Conclusion Using a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications.
    • Genotyping by Sequencing and Plastome Analysis Finds High Genetic Variability and Geographical Structure in Dactylis glomerata L. in Northwest Europe Despite Lack of Ploidy Variation

      Hodkinson, Trevor R.; Perdereau, Aude; Klaas, Manfred; Cormican, Paul; Barth, Susanne; European Union; 289461 (MDPI AG, 2019-06-28)
      Large collections of the forage and bioenergy grass Dactylis glomerata were made in northwest (NW) Europe along east to west and north to south clines for genetic resource conservation and to inform breeding programmes of genetic diversity, genepools, and ploidy. Leaves were sampled for genetic analysis and seed and rhizome for ex-situ conservation. Genotyping by sequencing (GBS) was used to assay nuclear DNA diversity and plastome single nucleotide polymorphism (SNP) discovery was undertaken using a long-read PCR and MiSeq approach. Nuclear and plastid SNPs were analysed by principal component analysis (PCA) to compare genotypes. Flow cytometry revealed that all samples were tetraploid, but some genome size variation was recorded. GBS detected an average of approximately 10,000 to 15,000 SNPs per country sampled. The highest average number of private SNPs was recorded in Poland (median ca. 2000). Plastid DNA variation was also high (1466 SNPs, 17 SNPs/kbp). GBS data, and to a lesser extent plastome data, also show that genetic variation is structured geographically in NW Europe with loose clustering matching the country of plant origin. The results reveal extensive genetic diversity and genetic structuring in this versatile allogamous species despite lack of ploidy variation and high levels of human mediated geneflow via planting.
    • Genotyping by Sequencing and Plastome Analysis Finds High Genetic Variability and Geographical Structure in Dactylis glomerata L. in Northwest Europe Despite Lack of Ploidy Variation

      Hodkinson, Trevor R.; Perdereau, Aude; Klaas, Manfred; Cormican, Paul; Barth, Susanne; EU; 289461 (MDPI AG, 2019-06-28)
      Large collections of the forage and bioenergy grass Dactylis glomerata were made in northwest (NW) Europe along east to west and north to south clines for genetic resource conservation and to inform breeding programmes of genetic diversity, genepools, and ploidy. Leaves were sampled for genetic analysis and seed and rhizome for ex-situ conservation. Genotyping by sequencing (GBS) was used to assay nuclear DNA diversity and plastome single nucleotide polymorphism (SNP) discovery was undertaken using a long-read PCR and MiSeq approach. Nuclear and plastid SNPs were analysed by principal component analysis (PCA) to compare genotypes. Flow cytometry revealed that all samples were tetraploid, but some genome size variation was recorded. GBS detected an average of approximately 10,000 to 15,000 SNPs per country sampled. The highest average number of private SNPs was recorded in Poland (median ca. 2000). Plastid DNA variation was also high (1466 SNPs, 17 SNPs/kbp). GBS data, and to a lesser extent plastome data, also show that genetic variation is structured geographically in NW Europe with loose clustering matching the country of plant origin. The results reveal extensive genetic diversity and genetic structuring in this versatile allogamous species despite lack of ploidy variation and high levels of human mediated geneflow via planting.
    • Genotyping by sequencing provides new insights into the diversity of Napier grass (Cenchrus purpureus) and reveals variation in genome-wide LD patterns between collections

      Muktar, Meki S.; Teshome, Abel; Hanson, Jean; Negawo, Alemayehu T.; Habte, Ermias; Domelevo Entfellner, Jean-Baka; Lee, Ki-Won; Jones, Chris S.; Rural Development Administration of the Republic of Korea; Germany-GIZ-Deutsche Gesellschaft für Internationale Zusammenarbeit; et al. (Springer Nature, 2019-05-06)
      Napier grass is an important tropical forage-grass and of growing potential as an energy crop. One-hundred-five Napier grass accessions, encompassing two independent collections, were subjected to genotyping by sequencing which generated a set of high-density genome-wide markers together with short sequence reads. The reads, averaging 54 nucleotides, were mapped to the pearl millet genome and the closest genes and annotation information were used to select candidate genes linked to key forage traits. 980 highly polymorphic SNP markers, distributed across the genome, were used to assess population structure and diversity with seven-subgroups identified. A few representative accessions were selected with the objective of distributing subsets of a manageable size for further evaluation. Genome-wide linkage disequilibrium (LD) analyses revealed a fast LD-decay, on average 2.54 kbp, in the combined population with a slower LD-decay in the ILRI collection compared with the EMBRAPA collection, the significance of which is discussed. This initiative generated high-density markers with a good distribution across the genome. The diversity analysis revealed the existence of a substantial amount of variation in the ILRI collection and identified some unique materials from the EMBRAPA collection, demonstrating the potential of the overall population for further genetic and marker-trait-association studies.
    • GM Crop Cultivation in Ireland: Ecological and Economic Considerations

      Meade, Connor; Mullins, Ewen; Department of Agriculture, Food and the Marine, Ireland; Programme for Research in Third Level Institutions (Phase 1) (Royal Irish Academy, 31/03/2005)
      Like many states in the European Union, Ireland has yet to fully commit itself to geneticallymodified (GM) crop technology. The general position of the Irish Government is ‘positive but precautionary’. However, with the European‐wide de‐facto moratorium on commercial production of GM crops now ended, many strategically important decisions regarding the commercial deployment of such crops and their co‐existence with conventional/organic crops need to be considered. To date, little research on the environmental impact of GM crops has been carried out in Ireland, and the provision of relevant local information lags far behind that available in other countries in the European Union. In this paper, we discuss much of the new ecological and economic data that have emerged since the moratorium on GM crops was introduced in 1998, assess the likely impacts of pest‐oriented GM crops should they be introduced to Ireland and examine criteria for post‐release monitoring. We also describe the likely commercial demand for these crops and the consequent priorities for ecological research. We argue that the impact of GM technology needs to be assessed in relation to the environmental impact of modern agriculture as a whole. Public unease in relation to this technology may be addressed if adequate resources are made available for independent Irish research on the issue.
    • 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.