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SMRT–AgRenSeq-d in potato (Solanum tuberosum) as a method to identify candidates for the nematode resistance Gpa5
No full textPotato is the third most important food crop in the world. Diverse pathogens threaten sustainable crop production but can be controlled, in many cases, through the deployment of disease resistance genes belonging to the family of nucleotide-binding, leucine-rich-repeat (NLR) genes. To identify effective disease resistance genes in established varieties, we have successfully established SMRT–AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR–AgRenSeq-d. The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score. Using a SMRT–RenSeq-based sequence representation of the NLRome from the cultivar Innovator, SMRT–AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1, Rpi-R2-like, Rpi-R3a, and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations. All benchmark genes were identified with an F1 score of 1, which indicates absolute linkage in the panel. This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode (PCN) species Globodera pallida (pathotypes Pa2/3). Assuming that NLRs are involved in controlling many types of resistances, SMRT–AgRenSeq-d can readily be applied to diverse crops and pathogen systems
Drought intensity alters productivity, carbon allocation, and plant nitrogen uptake in fast versus slow grassland communities
No full textGrasslands face more frequent and extreme droughts, yet their responses to increasing drought intensity are poorly understood. Increasing drought intensity likely triggers abrupt shifts (thresholds) in grassland ecosystem functioning which can implicate recovery trajectories.
Here, we determined how drought intensity affects plant productivity, and plant-soil carbon (C) and nitrogen (N) cycling. We exposed model grassland plant communities with contrasting resource acquisition strategies (a fast- vs a slow-strategy plant community), to a gradient of drought intensity. The drought gradient ranged from well-watered to severely water-limited conditions. We identified thresholds of plant community productivity (above-ground biomass) at peak drought and two months after re-wetting, and measured net ecosystem exchange and ecosystem respiration of carbon throughout the drought and recovery phases. At peak drought and one week after re-wetting, we traced recently acquired C from plants to the soil and into microbial biomass and fatty acids using 13C pulse labelling, and measured plant and soil N.
At peak drought, slow-strategy plant communities were more drought resistant than fast-strategy communities, as the threshold in plant productivity occurred at a higher drought intensity for the slow- than the fast-strategy community. Shortly after re-wetting, microbial uptake of recent plant-assimilated C increased with increasing past drought intensity, coinciding with an increase in soil N availability and leaf N. Threshold responses to drought intensity at peak drought translated into non-linear recovery responses, with greater compensatory growth in the fast-strategy community. At peak drought, increasing drought intensity reduced C uptake and increased relative C partitioning to leaves and microbial biomass. Upon re-wetting, plant community strategy mediated drought intensity effects on plant and soil C and N dynamics and plant recovery trajectories. The fast strategy community recovered quickly, with higher leaf N than the slow community, while the slow community increased C allocation to microbial biomass
Identification and mapping of Rpi-blb4 in diploid wild potato species Solanum bulbocastanum
No full textMore than 170 years after causing the potato famine in Ireland, late blight is still considered one of the most devastating crop diseases. Commercial potato breeding efforts depend on natural sources of resistance to protect crops from the rapidly evolving late blight pathogen, Phytophthora infestans. We have identified and mapped a novel broad-spectrum disease resistance gene effective against P. infestans from the wild, diploid potato species Solanum bulbocastanum. Diagnostic resistance gene enrichment sequencing (dRenSeq) was used to confirm the uniqueness of the identified resistance. RenSeq and GenSeq-based mapping of the resistance, referred to as Rpi-blb4, alongside recombinant screening, positioned the locus responsible for the resistance to potato chromosome 5. The interval spans approximately 2.3 Mb and corresponds to the DM reference genome positions of 11.25 and 13.56 Mb
Analysis of the Milk Kefir Pan-Metagenome Reveals Four Community Types, Core Species and Associated Metabolic Pathways
Get PDFpeer-reviewedA comprehensive metagenomics-based investigation of the microorganisms present within milk kefir communities from across the globe was carried out with a view to defining the milk kefir pan-metagenome, including details relating to core and non-core components. Milk kefir samples, generated by inoculating full fat, pasteurized cow’s milk with 64 kefir grains sourced from 25 different countries, were analyzed. We identified core features, including a consistent pattern of domination by representatives from the species Lactobacillus helveticus or the sub-species Lactobacillus kefiranofaciens subsp. kefiranofaciens, Lactococcus lactis subsp. lactis or Lla. cremoris subsp. cremoris in each kefir. Notably, even in kefirs where the lactococci did not dominate, they and 51 associated metabolic pathways were identified across all metagenomes. These insights can contribute to future efforts to create tailored kefir-based microbial communities for different applications and assist regulators and producers to ensure that kefir products have a microbial composition that reflects the artisanal beverage
Mitigation of Gaseous Emissions from Livestock Systems: A Farm-Level Method to Examine the Financial Implications
No full textpeer-reviewedFeeding the world's population while minimising the contribution of agriculture to climate change is one of the greatest challenges facing modern society. This challenge is particularly pronounced for dairy production where the carbon footprint of products and the mitigation costs are high, relative to other food stuffs. This paper reviews a number of mitigation measures that may be adopted by dairy farmers to reduce greenhouse gas emissions from their farms. A simulation model is developed to assess the cost-benefit of a range of mitigation measures. The model is applied to data from Ireland, a country with a large export-oriented dairy industry, for a range of farms including top, middle and bottom performing farms from a profitability perspective. The mitigation measures modelled included animal productivity, grass production and utilisation, better reproductive performance, early compact calving, reduced crude protein, decreased fertiliser N, protected urea, white clover, slurry tank cover and low emission slurry spreading (LESS). The results show that over half of the greenhouse gas abatement potential and most of the ammonia abatement potential were realised with cost-beneficial measures. Animal and feed-related measures that increased efficiency drove the abatement of GHG emissions. Low-emission slurry spreading was beneficial for the bottom and middle one-third of farms, while protected urea and reducing nitrogen use accounted for most of the ammonia abatement potential for the most profitable farms. Results showed that combining mitigation measures resulted in a decrease of 23%, 19%, and 12% in GHG emissions below 2020 levels for the bottom, middle, and top performing dairy farms, respectively. The findings imply that top dairy farms, that are already managed efficiently and optimally, may struggle to achieve the national and international GHG reduction targets with existing technologies and practices
An investigation of extracellular vesicles in bovine colostrum, first milk and milk over the lactation curve
Get PDFpeer-reviewedExtracellular vesicles (EVs) in milk have claimed benefits ranging from conveying immunological privilege to infants to being suitable as natural delivery vehicles for therapeutic drugs. However, a longitudinal study of bovine EVs quantities and characteristics in colostrum (COL), first milk (FM) and throughout the lactation curve of mature milk (MM) had never been performed and so was our aim. COL, FM and 9 months of MM samples were collected. Caseins -overlapping size with EVs- were removed. EVs were collected by density gradient ultracentrifugation and characterised by SDS-PAGE, Bradford assay, nanoparticle tracking analysis, immunoblotting, imaging flow cytometry analysis, and transmission electron microscopy. COL and FM had substantially more EVs than MM, with COL enriched in small EVs. No significant differences were observed between months 1–9 of MM. Altogether, although COL and FM are particularly rich sources of EVs, mature milk throughout the lactation curve is also an abundant source of intact EVs
Changes in salivary biomarkers of stress, inflammation, redox status, and muscle damage due to Streptococcus suis infection in pigs
Get PDFpeer-reviewedBackground
Streptococcus suis (S. suis) is a Gram-positive bacteria that infects pigs causing meningitis, arthritis, pneumonia, or endocarditis. This increases the mortality in pig farms deriving in severe economic losses. The use of saliva as a diagnostic fluid has various advantages compared to blood, especially in pigs. In this study, it was hypothesized that saliva could reflect changes in different biomarkers related to stress, inflammation, redox status, and muscle damage in pigs with S. suis infection and that changes in these biomarkers could be related to the severity of the disease.
Results
A total of 56 growing pigs from a farm were selected as infected pigs (n = 28) and healthy pigs (n = 28). Results showed increases in biomarkers related to stress (alpha-amylase and oxytocin), inflammation (haptoglobin, inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4), total protein, S100A8-A9 and S100A12), redox status (advanced oxidation protein producs (AOPP)) and muscle damage (creatine kinase (CK), CK-MB, troponin I, lactate, aspartate aminotransferase, and lactate dehydrogenase). An increase in adenosine deaminase (ADA), procalcitonin, and aldolase in infected animals were also observed, as previously described. The grade of severity of the disease indicated a significant positive correlation with total protein concentrations, aspartate aminotransferase, aldolase, and AOPP.
Conclusions
This report revealed that S. suis infection caused variations in analytes related to stress, inflammation, redox status, and muscle damage in the saliva of pigs and these can be considered potential biomarkers for this disease.This study was supported by a Grant Reference PID2019-105950RB-100 funded by MCIN/AEI/10.13039/501100011033. It was also supported by a Grant Reference PCI2020-120712-2 from MCIN/AEI/10.13039/501100011033 and European Union “NextGenerationEU”/PRTR (1st ICRAD Joint Cofund Call). M.J.L-M. was funded by 21293/FPI/19, Fundación Séneca, Región de Murcia (Spain). D.E. was funded by the postdoctoral contract “Generational renewal to promote research” of the University of Murcia. M.L-A. has a postdoctoral fellowship “Juan de la Cierva Formación” supported by the Ministerio de Ciencia e Innovación (FJC2021-047105-I). A.M-P. T has a post-doctoral fellowship “Ramón y Cajal” supported by the Ministerio de Ciencia e Innovación, Agencia Estatal de Investigación (AEI), Spain, and The European Next Generation Funds (NextgenerationEU) (RYC2021-033660-I)
An evaluation of the Irish Science Week Festival of Farming and Food
No full textposterThe aim of the study was to evaluate the Festival of Farming and Food and its effectiveness of engagement with the general public as well as secondary school students
Is a scientific career in agri-food considered viable for girls in secondary school?
Get PDFconference posterThe Festival of Farming and Food 2022 was organised by Teagasc as part of Science Week. A key finding from the previous year’s evaluation of the event was that girls viewed science as a male-dominated career. Therefore, the 2022 festival was partially evaluated through a focus group (eight participants) with Transition Year (TY) students from an all-girls school who attended the Climate and Farming event at Teagasc Moorepark. The focus group with the TY students also served to investigate perceptions of girls towards science as a career path
Value of simplified lung lesions scoring systems to inform future codes for routine meat inspection in pigs
Get PDFpeer-reviewedBackground
Across the European Union (EU), efforts are being made to achieve modernisation and harmonisation of meat inspection (MI) code systems. Lung lesions were prioritised as important animal based measures at slaughter, but existing standardized protocols are difficult to implement for routine MI. This study aimed to compare the informative value and feasibility of simplified lung lesion scoring systems to inform future codes for routine post mortem MI.
Results
Data on lung lesions in finisher pigs were collected at slaughter targeting 83 Irish pig farms, with 201 batches assessed, comprising 31,655 pairs of lungs. Lungs were scored for cranioventral pulmonary consolidations (CVPC) and pleurisy lesions using detailed scoring systems, which were considered the gold standard. Using the data collected, scenarios for possible simplified scoring systems to record CVPC (n = 4) and pleurisy (n = 4) lesions were defined. The measurable outcomes were the prevalence and (if possible) severity scoring at batch level for CVPC and pleurisy. An arbitrary threshold was set to the upper quartile (i.e., the top 25% of batches with high prevalence/severity of CVPC or pleurisy, n = 50). Each pair of measurable outcomes was compared by calculating Spearman rank correlations and assessing if batches above the threshold for one measurable outcome were also above it for their pairwise comparison. All scenarios showed perfect agreement (k = 1) when compared among themselves and the gold standard for the prevalence of CVPC. The agreement among severity outcomes and the gold standard showed moderate to perfect agreement (k = [0.66, 1]). The changes in ranking were negligible for all measurable outcomes of pleurisy for scenarios 1, 2 and 3 when compared with the gold standard (rs ≥ 0.98), but these changes amounted to 50% for scenario 4.
Conclusions
The best simplified CVPC scoring system is to simply count the number of lung lobes affected excluding the intermediate lobe, which provides the best trade-off between value of information and feasibility, by incorporating information on CVPC prevalence and severity. While for pleurisy evaluation, scenario 3 is recommended. This simplified scoring system provides information on the prevalence of cranial and moderate and severe dorsocaudal pleurisy. Further validation of the scoring systems at slaughter and by private veterinarians and farmers is needed