Oak Park is home to the National Centre for Arable Crops Research. Situated on 225 hectare research farm, the main objective of the work programme at Oak Park is to support the arable crops sector of Irish agriculture. The task ahead is to adapt new challenges in developing sustainable and environmentally sensitive agricultural systems which will provide farmers with adequate incomes and consumers with quality food at reasonable prices.

Recent Submissions

  • 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.
  • 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.
  • Experimental comparison of two methods to study barley responses to partial submergence

    Miricescu, Alexandra; Byrne, Tomás; Doorly, Catherine M; Ng, Carl K Y; Barth, Susanne; Graciet, Emmanuelle; Department of Agriculture, Food and the Marine; Maynooth University Kathleen Lonsdale Institute for Human Health.; 14/S/819 (Biomed Central, 2021-04-13)
    Background Crop yield is dependent on climate conditions, which are becoming both more variable and extreme in some areas of the world as a consequence of global climate change. Increased precipitation and flooding events are the cause of important yield losses due to waterlogging or (partial) submergence of crops in the field. Our ability to screen efficiently and quickly for varieties that have increased tolerance to waterlogging or (partial) submergence is important. Barley, a staple crop worldwide, is particularly sensitive to waterlogging. Screening for waterlogging tolerant barley varieties has been ongoing for many years, but methods used to screen vary greatly, from the type of soil used to the time at which the treatment is applied. This variation makes it difficult to cross-compare results. Results Here, we have devised a scoring system to assess barley tolerance to waterlogging and compare two different methods when partial submergence is applied with either water or a starch solution at an early developmental stage, which is particularly sensitive to waterlogging or partial submergence. The use of a starch solution has been previously shown to result in more reducing soil conditions and has been used to screen for waterlogging tolerance. Conclusions Our results show that the two methods provide similar results to qualitatively rank varieties as tolerant or sensitive, while also affecting plants differently, in that application of a starch solution results in stronger and earlier symptoms than applying partial submergence with water.
  • 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.
  • In vitro screening of different Pseudomonas fluorescens isolates to study lytic enzyme production and growth inhibition during antagonism of Fusarium oxysporum f. sp. cumini, wilt causing pathogen of cumin

    Rathore, Ridhdhi; Vakharia, Dinesh K.; Singh Rathore, Dheeraj (Springer Open, 2020-05-12)
    Land plants exist in close association with bacterial and fungal microbes, where some associations can be pathogenic and others can be mutualistic/beneficial. One such relation exists between host plant, Cuminum cyminum L. (Cumin) and Fusarium oxysporum f. sp. cumini (Foc), the causal pathogen of cumin wilt and Pseudomonas fluorescens (Pf), where Pf acts as a bio-agent for inhibiting Foc and promoting plant growth of cumin. In this study, antagonism by 10 different Pf isolates against Foc was studied under laboratory conditions through percent growth inhibition and biochemical mechanisms. Among these Pf isolates, Pf-5 exhibited the highest in vitro growth inhibition (82.51%). A positive correlation was observed between percent growth inhibition and specific activities of hydrolytic enzymes, chitinase, β-1, 3 glucanase, and protease, where a negative correlation was observed with cell wall degrading enzymes, cellulase and polygalacturonase. To conclude, isolate Pf-5 could be a potential biocontrol agent for Fusarium wilt disease of cumin.
  • Plant Sciences and Crop Husbandry: Research Report 1989

    Rea, Joe; Butler, Thomas; Fottrell, P; Harvey, Maurice; McDaid, Donal; O'Dowd, Helen; O'Dwyer, Michael; Power, Patrick; Walshe, Mary; Walshe, Padraig; et al. (2021-12-09)
    This report summarizes the research undertaken by Teagasc in the areas of Plant Sciences and Crop Husbandry in 1989
  • The Double Spade Method: a ‘mini-profile’ visual soil evaluation technique

    Emmet-Booth, J.P.; Forristal, P.D.; Fenton, Owen; Bondi, G.; Holden, N.M (2021-11-23)
    Visual Soil Evaluation (VSE) methods are established for soil quality assessment and focus on the examination of soil structure and associated anthropogenic impacts. VSE techniques, of which numerous types exist, are successfully used internationally both in soil research and as sustainable soil management tools. Techniques are generally categorised into profile and spade methods. Profile methods examine entire soil profiles in soil-pits to depths of ~ 1.5 m, exploring interactions between inherent soil features and anthropic management at specific sample points. Spade methods examine the upper soil profile, often by extracting sample blocks of topsoil by spade and focus on anthropic impacts. The VESS method (Guimarães et al., 2011) is a widely used spade method and involves assessment of soil sample blocks to 25 cm depth. However, in arable soils, important structural features may occur just below this depth such as plough pans, which VESS may not capture. The SubVESS method (Ball et al., 2015) follows principles of VESS but allows assessment to ~ 1 m depth. However, the later involves soil-pit excavation by mechanical means, which may be destructive, costly, time consuming and limit replication. When used in on-farm situations by farmers or advisors, full soil-pit excavation may not be desirable. Here we describe a method previously outlined (Emmet-Booth et al. 2018) called the Double Spade Method (DS) designed to examine miniprofiles in soil pits to 40 cm depth, therefore capturing potential structural features below the VESS assessment depth, without requiring full soil-pit excavation.
  • Beyond ruminants: discussing opportunities for alternative pasture uses in New Zealand

    Lucci, Gina M.; Henchion, Maeve M.; Lange, Lene; Ledgard, Stewart F.; Collie, Stewart R.; Cosgrove, Gerald P.; Meyer, Anne S.; Graichen, Florian H.M.; Barth, Susanne; Lenehan, James J. (New Zealand Grassland Association, 2019-10-28)
    The New Zealand government has set ambitious goals for primary sector growth and of zero net carbon emissions by 2050. This presents an opportunity and obligation to develop new ideas for grassland production systems to increase export value and generate new job opportunities, while reducing environmental impacts. The aim of this paper is to draw on recent research in Europe to investigate some of the alternative and complementary uses for pasture as a feedstock for a green biorefinery. A biorefinery is a facility, or a series of processes, that convert biomass into a spectrum of value-added products. For example, protein can be extracted mechanically from green biomass once harvested. The residual fibre fraction could be used as a low-nitrogen feed for ruminants to reduce urinary nitrogen, while the liquid protein fraction could be processed to make it suitable for mono-gastric or human consumption. Enzymes can promote protein extraction and controlled conversion of insoluble plant fibres and oligosaccharides to foster gut-health promoting prebiotic food ingredients. Anaerobic digestion of residues can then be used to create energy and soilimproving products. Research and demonstration of these approaches in practice, along with the results of feasibility studies, will be required to see which of these opportunities is a good fit for New Zealand pasture systems.
  • 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.
  • Grain aphids (Sitobion avenae) with knockdown resistance (kdr) to insecticide exhibit fitness trade-offs, including increased vulnerability to the natural enemy Aphidius ervi

    Jackson, Gail E.; Malloch, Gaynor; McNamara, Louise; Little, Damon; Teagasc (Public Library of Science (PLoS), 2020-11-10)
    The development of insecticide-resistance mechanisms in aphids has been associated with inhibitory, pleiotropic fitness costs. Such fitness costs have not yet been examined in the UK’s most damaging cereal aphid, Sitobion avenae (grain aphid) (Hemiptera: Aphididae). This study aimed to evaluate the fitness trade-offs of the insecticide-resistant S. avenae clone versus an insecticide-susceptible S. avenae clone. Additionally, the parasitoid, Aphidius ervi (Hymenoptera: Braconidae), was introduced to examine its potential as a biological control agent. This study found that insecticide-resistant clones had significantly lower population growth and individual relative growth rate. Furthermore, insecticide-resistant clones suffered from a significantly greater rate of parasitisation (mummification) compared to their insecticide-susceptible counterparts. The successfulness of the parasitoid as a biological control agent could prevent the spread of the insecticide-resistant genotype. However, for this to be possible, insecticide spraying regimes need to be moderated, and habitat modification and parasitoid manipulation must be considered.
  • Genome biology of the paleotetraploid perennial biomass crop Miscanthus

    Mitros, Therese; Barth, Susanne; Klaas, Manfred; U.S. Department of Energy; DE-SC0018420; DE-AC02-05CH11231.; 289461; DE-SC0006634; DE-SC0012379. (Nature, 2020-10-28)
    Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.
  • Transcriptomic response of maize primary roots to low temperatures at seedling emergence

    Di Fenza, Mauro; Hogg, Bridget; Grant, Jim; Barth, Susanne; Irish Department of Agriculture, Food and the Marine; RSF 07 501 (PeerJ, 2017-01-05)
    Background. Maize (Zea mays) is a C4 tropical cereal and its adaptation to temperate climates can be problematic due to low soil temperatures at early stages of establishment. Methods. In the current study we have firstly investigated the physiological response of twelve maize varieties, from a chilling condition adapted gene pool, to sub-optimal growth temperature during seedling emergence. To identify transcriptomic markers of cold tolerance in already adapted maize genotypes, temperature conditions were set below the optimal growth range in both control and low temperature groups. The conditions were as follows; control (18 ◦C for 16 h and 12 ◦C for 8 h) and low temperature (12 ◦C for 16 h and 6 ◦C for 8 h). Four genotypes were identified from the condition adapted gene pool with significant contrasting chilling tolerance. Results. Picker and PR39B29 were the more cold-tolerant lines and Fergus and Codisco were the less cold-tolerant lines. These four varieties were subjected to microarray analysis to identify differentially expressed genes under chilling conditions. Exposure to low temperature during establishment in the maize varieties Picker, PR39B29, Fergus and Codisco, was reflected at the transcriptomic level in the varieties Picker and PR39B29. No significant changes in expression were observed in Fergus and Codisco following chilling stress. A total number of 64 genes were differentially expressed in the two chilling tolerant varieties. These two varieties exhibited contrasting transcriptomic profiles, in which only four genes overlapped. Discussion. We observed that maize varieties possessing an enhanced root growth ratio under low temperature were more tolerant, which could be an early and inexpensive measure for germplasm screening under controlled conditions. We have identified novel cold inducible genes in an already adapted maize breeding gene pool. This illustrates that further varietal selection for enhanced chilling tolerance is possible in an already preselected gene pool.
  • Temporal and spatial field evaluations highlight the importance of the presymptomatic phase in supporting strong partial resistance in Triticum aestivum against Zymoseptoria tritici

    Hehir, J. G.; Connolly, C.; O'Driscoll, A.; Lynch, J. P.; Spink, John; Brown, J. K. M.; Doohan, F.; Mullins, Ewen; Department of Agriculture, Food and the Marine; RSF 11S121; et al. (Wiley, 2017-11-24)
    Zymoseptoria tritici, the causal agent of septoria tritici blotch (STB), remains a significant threat to European wheat production with the continuous emergence of fungicide resistance in Z. tritici strains eroding the economic sustainability of wheat production systems. The life cycle of Z. tritici is characterized by a presymptomatic phase (latent period, LP) after which the pathogen switches to an aggressive necrotrophic stage, when lesions bearing pycnidia quickly manifest on the leaf. As minimal knowledge of the possible role of the LP in supporting STB resistance/susceptibility exists, the goal of this study was to investigate the spatial and temporal association between the LP and disease progression across three locations (Ireland – Waterford, Carlow; UK – Norwich) that represent commercially high, medium and low STB pressure environments. Completed over two seasons (2013–2015) with commercially grown cultivars, the potential of the LP in stalling STB epidemics was significant as identified with cv. Stigg, whose high level of partial resistance was characterized by a lengthened LP (c. 36 days) under the high disease pressure environment of Waterford. However, once the LP concluded it was followed by a rate of disease progression in cv. Stigg that was comparable to that observed in the more susceptible commercial varieties. Complementary analysis, via logistic modelling of intensive disease assessments made at Carlow and Waterford in 2015, further highlighted the value of a lengthened LP in supporting strong partial resistance against STB disease of wheat.
  • 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.

    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.
  • 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.
  • 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.
  • Detection of Novel QTLs for Late Blight Resistance Derived from the Wild Potato Species Solanum microdontum and Solanum pampasense

    Meade, Fergus; Hutten, Ronald; Wagener, Silke; Prigge, Vanessa; Dalton, Emmet; Kirk, Hanne Grethe; Griffin, Denis; Milbourne, Dan; Department of Agriculture, Food and the Marine; IPM Potato Group; et al. (MDPI AG, 2020-06-30)
    Wild potato species continue to be a rich source of genes for resistance to late blight in potato breeding. Whilst many dominant resistance genes from such sources have been characterised and used in breeding, quantitative resistance also offers potential for breeding when the loci underlying the resistance can be identified and tagged using molecular markers. In this study, F1 populations were created from crosses between blight susceptible parents and lines exhibiting strong partial resistance to late blight derived from the South American wild species Solanum microdontum and Solanum pampasense. Both populations exhibited continuous variation for resistance to late blight over multiple field-testing seasons. High density genetic maps were created using single nucleotide polymorphism (SNP) markers, enabling mapping of quantitative trait loci (QTLs) for late blight resistance that were consistently expressed over multiple years in both populations. In the population created with the S. microdontum source, QTLs for resistance consistently expressed over three years and explaining a large portion (21–47%) of the phenotypic variation were found on chromosomes 5 and 6, and a further resistance QTL on chromosome 10, apparently related to foliar development, was discovered in 2016 only. In the population created with the S. pampasense source, QTLs for resistance were found in over two years on chromosomes 11 and 12. For all loci detected consistently across years, the QTLs span known R gene clusters and so they likely represent novel late blight resistance genes. Simple genetic models following the effect of the presence or absence of SNPs associated with consistently effective loci in both populations demonstrated that marker assisted selection (MAS) strategies to introgress and pyramid these loci have potential in resistance breeding strategies.
  • Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions

    Szoboszlay, Márton; Näther, Astrid; Mullins, Ewen; Tebbe, Christoph C.; European Union; 289706 (Public Library of Science (PLoS), 2019-12-17)
    The importance of geographic location and annual variation on the detection of differences in the rhizomicrobiome caused by the genetic modification of maize (Bt-maize, event MON810) was evaluated at experimental field sites across Europe including Sweden, Denmark, Slovakia and Spain. DNA of the rhizomicrobiome was collected at the maize flowering stage in three consecutive years and analyzed for the abundance and diversity of PCR-amplified structural genes of Bacteria, Archaea and Fungi, and functional genes for bacterial nitrite reductases (nirS, nirK). The nirK genes were always more abundant than nirS. Maize MON810 did not significantly alter the abundance of any microbial genetic marker, except for sporadically detected differences at individual sites and years. In contrast, annual variation between sites was often significant and variable depending on the targeted markers. Distinct, site-specific microbial communities were detected but the sites in Denmark and Sweden were similar to each other. A significant effect of the genetic modification of the plant on the community structure in the rhizosphere was detected among the nirK denitrifiers at the Slovakian site in only one year. However, most nirK sequences with opposite response were from the same or related source organisms suggesting that the transient differences in community structure did not translate to the functional level. Our results show a lack of effect of the genetic modification of maize on the rhizosphere microbiome that would be stable and consistent over multiple years. This demonstrates the importance of considering annual variability in assessing environmental effects of genetically modified crops.
  • 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.

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