Showing papers by "Agriculture and Agri-Food Canada published in 2017"
TL;DR: Improvements in the relative accuracy considering the amount of variation explained, in comparison to the previous version of SoilGrids at 1 km spatial resolution, range from 60 to 230%.
Abstract: This paper describes the technical development and accuracy assessment of the most recent and improved version of the SoilGrids system at 250m resolution (June 2016 update). SoilGrids provides global predictions for standard numeric soil properties (organic carbon, bulk density, Cation Exchange Capacity (CEC), pH, soil texture fractions and coarse fragments) at seven standard depths (0, 5, 15, 30, 60, 100 and 200 cm), in addition to predictions of depth to bedrock and distribution of soil classes based on the World Reference Base (WRB) and USDA classification systems (ca. 280 raster layers in total). Predictions were based on ca. 150,000 soil profiles used for training and a stack of 158 remote sensing-based soil covariates (primarily derived from MODIS land products, SRTM DEM derivatives, climatic images and global landform and lithology maps), which were used to fit an ensemble of machine learning methods-random forest and gradient boosting and/or multinomial logistic regression-as implemented in the R packages ranger, xgboost, nnet and caret. The results of 10-fold cross-validation show that the ensemble models explain between 56% (coarse fragments) and 83% (pH) of variation with an overall average of 61%. Improvements in the relative accuracy considering the amount of variation explained, in comparison to the previous version of SoilGrids at 1 km spatial resolution, range from 60 to 230%. Improvements can be attributed to: (1) the use of machine learning instead of linear regression, (2) to considerable investments in preparing finer resolution covariate layers and (3) to insertion of additional soil profiles. Further development of SoilGrids could include refinement of methods to incorporate input uncertainties and derivation of posterior probability distributions (per pixel), and further automation of spatial modeling so that soil maps can be generated for potentially hundreds of soil variables. Another area of future research is the development of methods for multiscale merging of SoilGrids predictions with local and/or national gridded soil products (e.g. up to 50 m spatial resolution) so that increasingly more accurate, complete and consistent global soil information can be produced. SoilGrids are available under the Open Data Base License.
2,228 citations
University of Sydney1, Agriculture and Agri-Food Canada2, Institut national de la recherche agronomique3, Natural Resources Conservation Service4, Centre national de la recherche scientifique5, National Taiwan University6, Nanjing Agricultural University7, Indian Institute of Technology Kharagpur8, James Hutton Institute9, Landcare Research10, Rural Development Administration11, Bidhan Chandra Krishi Viswavidyalaya12, British Geological Survey13, Wageningen University and Research Centre14, University College Dublin15, Colorado State University16, World Agroforestry Centre17, Université catholique de Louvain18
TL;DR: In this paper, the authors surveyed the soil organic carbon (SOC) stock estimates and sequestration potentials from 20 regions in the world (New Zealand, Chile, South Africa, Australia, Tanzania, Indonesia, Kenya, Nigeria, India, China Taiwan, South Korea, China Mainland, United States of America, France, Canada, Belgium, England & Wales, Ireland, Scotland, and Russia).
1,171 citations
California Institute of Technology1, Agricultural Research Service2, University of Tsukuba3, University of Guelph4, University of Texas at Austin5, Princeton University6, Kuwait University7, University of Valencia8, University of Salamanca9, Agriculture and Agri-Food Canada10, University of Southern California11, European Academy of Bozen12, University of Grenoble13, Finnish Meteorological Institute14, National Autonomous University of Mexico15, University of Twente16, Comisión Nacional de Actividades Espaciales17, Vienna University of Technology18, Monash University19, Goddard Space Flight Center20, Massachusetts Institute of Technology21
TL;DR: The NASA Soil Moisture Active Passive (SMAP) mission has utilized a set of core validation sites as the primary methodology in assessing the soil moisture retrieval algorithm performance as mentioned in this paper.
487 citations
University of California, Davis1, Agricultural Research Service2, Johns Hopkins University School of Medicine3, University of Georgia4, China Agricultural University5, Technische Universität München6, Norwich Research Park7, Institut national de la recherche agronomique8, Agriculture and Agri-Food Canada9, University of Arizona10, University of Zurich11, Johns Hopkins University12
TL;DR: It is proposed that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.
Abstract: Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.
457 citations
TL;DR: This review provides historical perspectives and summarizes key findings in the study of Bacteroidetes bacteria, highlighting a critical shift from sequence-based PUL discovery to systems-based analyses combining reverse genetics, biochemistry, enzymology, and structural biology to precisely illuminate the molecular mechanisms underpinning PUL function.
Abstract: The complex carbohydrates of terrestrial and marine biomass represent a rich nutrient source for free-living and mutualistic microbes alike. The enzymatic saccharification of these diverse substrates is of critical importance for fueling a variety of complex microbial communities, including marine, soil, ruminant, and monogastric microbiota. Consequently, highly specific carbohydrate-active enzymes, recognition proteins, and transporters are enriched in the genomes of certain species and are of critical importance in competitive environments. In Bacteroidetes bacteria, these systems are organized as polysaccharide utilization loci (PULs), which are strictly regulated, colocalized gene clusters that encode enzyme and protein ensembles required for the saccharification of complex carbohydrates. This review provides historical perspectives and summarizes key findings in the study of these systems, highlighting a critical shift from sequence-based PUL discovery to systems-based analyses combining reverse genetics, biochemistry, enzymology, and structural biology to precisely illuminate the molecular mechanisms underpinning PUL function. The ecological implications of dynamic PUL deployment by key species in the human gastrointestinal tract are explored, as well as the wider distribution of these systems in other gut, terrestrial, and marine environments.
327 citations
TL;DR: A combination of prospective experimental and modeling research on precooling uniformity, responsive food inventory management systems, and cold chains in developing countries is proposed for the improvement of the cold chain at the global scale.
Abstract: The cold chain is responsible for the preservation and transportation of perishable foods in the proper temperature range to slow biological decay processes and deliver safe and high-quality foods to consumers Studies show that the efficiency of the cold chain is often less than ideal, as temperature abuses above or below the optimal product-specific temperature range occur frequently, a situation that significantly increases food waste and endangers food safety In this work, field studies on time-temperature conditions at each critical stage of the cold chain are reviewed to assess the current state of commercial cold chains Precooling, ground operations during transportation, storage during display at retail and in domestic refrigerators, and commercial handling practices are identified and discussed as the major weaknesses in the modern cold chain The improvement in efficiency achieved through the measurement, analysis, and management of time-temperature conditions is reviewed, along with the accompanying technical and practical challenges delaying the implementation of such methods A combination of prospective experimental and modeling research on precooling uniformity, responsive food inventory management systems, and cold chains in developing countries is proposed for the improvement of the cold chain at the global scale
300 citations
TL;DR: Tannins have traditionally been regarded as “anti-nutritional factor” for monogastric animals and poultry, but recent researches have revealed some of them, when applied in appropriate manner, improved intestinal microbial ecosystem, enhanced gut health and hence increased productive performance.
274 citations
21 Aug 2017
TL;DR: This chapter discusses Insect Biodiversity in the Nearctic Region, which is dominated by Coleoptera, a Dominant Life Form in the Critical Zone of the Neotropics Terry L. Erwin and Christy J. Geraci.
Abstract: Preface. Acknowledgements. 1. Introduction Peter H. Adler and Robert G. Foottit . 2. The Importance of Insects G.G.E. Scudder . Part I. Insect Biodiversity: Regional Examples . 3. Insect Biodiversity in the Nearctic Region Andrew B. T. Smith and Hugh V. Danks. 4. Amazonian Rainforests and Their Richness of Coleoptera, a Dominant Life Form in the Critical Zone of the Neotropics Terry L. Erwin and Christy J. Geraci. 5. Insect Biodiversity in the Afrotropical Region C.H. Scholtz and M.W. Mansell . 6. Biodiversity of Australasian Insects Peter S. Cranston . 7. Insect Biodiversity in the Palearctic Region Alexander S. Konstantinov, Boris A. Korotyaev and Mark G. Volkovitsh. Part II. Insect Biodiversity: Taxon Examples. 8. Biodiversity of Aquatic Insects John C. Morse. 9. Biodiversity of Diptera G.W. Courtney, T. Pape, J.H. Skevington and B.J. Sinclair . 10. Biodiversity of Heteroptera Thomas J. Henry. 11. Biodiversity of Coleoptera P. Bouchard, V.V. Grebennikov, A.B.T. Smith and H. Douglas. 12. Biodiversity of Hymenoptera John T. Huber . 13. Lepidoptera Biodiversity Michael G. Pogue. Part III. Tools and Approaches . 14. The Science of Insect Taxonomy: Prospects and Needs Quentin D. Wheeler . 15. Insect Species - Concepts and Practice Michael F. Claridge . 16. Molecular Dimensions of Insect Taxonomy Felix Sperling and Amanda Roe . 17. DNA Barcodes and Insect Biodiversity Robin M. Floyd, John J. Wilson, Paul D. N. Hebert . 18. Insect Biodiversity and Informatics Norman F. Johnson . 19. Parasitoid Diversity and Insect Pest Management John Heraty . 20. Taxonomy of Crop Pests: The Aphids Gary L. Miller and Robert G. Foottit . 21. Adventive Insects: A Global Overview Alfred G. Wheeler, Jr. and E. Richard Hoebeke . 22. Biodiversity of Biting Flies: Implications for Humanity Peter H. Adler . 23. Reconciling Ethical and Scientific Issues for Insect Conservation Michael J. Samways . 24. Insect Biodiversity: Assessment and Taxonomy Ke Chung Kim. 25. Insect Biodiversity - Millions and Millions May Berenbaum. Taxonomic Index. Subject Index
259 citations
TL;DR: The cloning and characterization of J are reported, and J is identified as the ortholog of Arabidopsis thaliana EARLY FLOWERING 3 (ELF3), and an important new component in flowering-time control in soybean is identified, providing new insight into soybean adaptation to tropical regions.
Abstract: Soybean is a major legume crop originating in temperate regions, and photoperiod responsiveness is a key factor in its latitudinal adaptation. Varieties from temperate regions introduced to lower latitudes mature early and have extremely low grain yields. Introduction of the long-juvenile (LJ) trait extends the vegetative phase and improves yield under short-day conditions, thereby enabling expansion of cultivation in tropical regions. Here we report the cloning and characterization of J, the major classical locus conferring the LJ trait, and identify J as the ortholog of Arabidopsis thaliana EARLY FLOWERING 3 (ELF3). J depends genetically on the legume-specific flowering repressor E1, and J protein physically associates with the E1 promoter to downregulate its transcription, relieving repression of two important FLOWERING LOCUS T (FT) genes and promoting flowering under short days. Our findings identify an important new component in flowering-time control in soybean and provide new insight into soybean adaptation to tropical regions.
257 citations
TL;DR: Overall, consuming moderate amounts of traditionally prepared and minimally processed soy foods may offer modest health benefits while minimizing potential for any adverse health effects.
Abstract: Isoflavones (genistein, daidzein, and glycitein) are bioactive compounds with mildly estrogenic properties and often referred to as phytoestrogen. These are present in significant quantities (up to 4–5 mg·g−1 on dry basis) in legumes mainly soybeans, green beans, mung beans. In grains (raw materials) they are present mostly as glycosides, which are poorly absorbed on consumption. Thus, soybeans are processed into various food products for digestibility, taste and bioavailability of nutrients and bioactives. Main processing steps include steaming, cooking, roasting, microbial fermentation that destroy protease inhibitors and also cleaves the glycoside bond to yield absorbable aglycone in the processed soy products, such as miso, natto, soy milk, tofu; and increase shelf lives. Processed soy food products have been an integral part of regular diets in many Asia–Pacific countries for centuries, e.g. China, Japan and Korea. However, in the last two decades, there have been concerted efforts to introdu...
252 citations
TL;DR: Recent findings in animal research on butyrate and its derivatives in regard to their effects and mechanisms behind are critically reviewed and the implications of these findings for improving animal gut health and production are discussed.
TL;DR: Improved representation of vegetation phenology and water dynamics will be identified as essential to improve soil moisture retrievals, crop monitoring, and for the development of emerging drought/water stress applications.
Abstract: Observations from spaceborne radar contain considerable information about vegetation dynamics. The ability to extract this information could lead to improved soil moisture retrievals and the increased capacity to monitor vegetation phenology and water stress using radar data. The purpose of this review paper is to provide an overview of the current state of knowledge with respect to backscatter from vegetated (agricultural) landscapes and to identify opportunities and challenges in this domain. Much of our understanding of vegetation backscatter from agricultural canopies stems from SAR studies to perform field-scale classification and monitoring. Hence, SAR applications, theory, and applications are considered here too. An overview will be provided of the knowledge generated from ground-based and airborne experimental campaigns that contributed to the development of crop classification, crop monitoring, and soil moisture monitoring applications. A description of the current vegetation modeling approaches will be given. A review of current applications of spaceborne radar will be used to illustrate the current state of the art in terms of data utilization. Finally, emerging applications, opportunities and challenges will be identified and discussed. Improved representation of vegetation phenology and water dynamics will be identified as essential to improve soil moisture retrievals, crop monitoring, and for the development of emerging drought/water stress applications.
Murdoch University1, The Hertz Corporation2, Indian Council of Agricultural Research3, International Potato Center4, Spanish National Research Council5, Saga University6, Indian Agricultural Research Institute7, Julius Kühn-Institut8, United States Department of Agriculture9, Agriculture and Agri-Food Canada10, Universidade Federal de Viçosa11
TL;DR: The Potyviridae is the largest family of RNA plant viruses, members of which have single-stranded, positive-sense RNA genomes and flexuous filamentous particles 680–900 nm long and 11–20 nm wide.
Abstract: The Potyviridae is the largest family of RNA plant viruses, members of which have single-stranded, positive-sense RNA genomes and flexuous filamentous particles 680–900 nm long and 11–20 nm wide. There are eight genera, distinguished by the host range, genomic features and phylogeny of the member viruses. Genomes range from 8.2 to 11.3 kb, with an average size of 9.7 kb. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Potyviridae, which is available at www.ictv.global/report/potyviridae.
Goddard Space Flight Center1, Katholieke Universiteit Leuven2, Jet Propulsion Laboratory3, Agricultural Research Service4, University of Montana5, University of Guelph6, University of Toulouse7, University of Texas at Austin8, University of Salamanca9, University of Copenhagen10, University of Valencia11, Agriculture and Agri-Food Canada12, University of Southern California13, University of Grenoble14, University of Twente15, Comisión Nacional de Actividades Espaciales16, Monash University, Clayton campus17
TL;DR: The Level-4 Surface and Root-Zone Soil Moisture (L4_SM) data product is generated by assimilating SMAP L-band brightness temperature observations into the NASA Catchment land surface model as mentioned in this paper.
Abstract: The Soil Moisture Active Passive (SMAP) mission Level-4 Surface and Root-Zone Soil Moisture (L4_SM) data product is generated by assimilating SMAP L-band brightness temperature observations into the NASA Catchment land surface model. The L4_SM product is available from 31 March 2015 to present (within 3 days from real time) and provides 3-hourly, global, 9-km resolution estimates of surface (0–5 cm) and root-zone (0–100 cm) soil moisture and land surface conditions. This study presents an overview of the L4_SM algorithm, validation approach, and product assessment versus in situ measurements. Core validation sites provide spatially averaged surface (root zone) soil moisture measurements for 43 (17) “reference pixels” at 9- and 36-km gridcell scales located in 17 (7) distinct watersheds. Sparse networks provide point-scale measurements of surface (root zone) soil moisture at 406 (311) locations. Core validation site results indicate that the L4_SM product meets its soil moisture accuracy requirement, specified as an unbiased RMSE (ubRMSE, or standard deviation of the error) of 0.04 m3 m−3 or better. The ubRMSE for L4_SM surface (root zone) soil moisture is 0.038 m3 m−3 (0.030 m3 m−3) at the 9-km scale and 0.035 m3 m−3 (0.026 m3 m−3) at the 36-km scale. The L4_SM estimates improve (significantly at the 5% level for surface soil moisture) over model-only estimates, which do not benefit from the assimilation of SMAP brightness temperature observations and have a 9-km surface (root zone) ubRMSE of 0.042 m3 m−3 (0.032 m3 m−3). Time series correlations exhibit similar relative performance. The sparse network results corroborate these findings over a greater variety of climate and land cover conditions.
TL;DR: In this article, a meta-analysis of N2O emissions from agricultural soils receiving organic amendments was conducted, which yielded a global EF for all organic sources, EForg, equal to 0.30%, which is lower than the IPCC default EF of 1 for synthetic fertilizers.
TL;DR: Overall, the available evidence suggests non-protein soy constituents improve markers of cardiovascular health; however, additional carefully designed studies are required to independently elucidate these effects.
Abstract: The hypocholesterolemic effect of soy is well-documented and this has led to the regulatory approval of a health claim relating soy protein to a reduced risk of cardiovascular disease (CVD). However, soybeans contain additional components, such as isoflavones, lecithins, saponins and fiber that may improve cardiovascular health through independent mechanisms. This review summarizes the evidence on the cardiovascular benefits of non-protein soy components in relation to known CVD risk factors such as hypertension, hyperglycemia, inflammation, and obesity beyond cholesterol lowering. Overall, the available evidence suggests non-protein soy constituents improve markers of cardiovascular health; however, additional carefully designed studies are required to independently elucidate these effects. Further, work is also needed to clarify the role of isoflavone-metabolizing phenotype and gut microbiota composition on biological effect.
TL;DR: It has been demonstrated that essential oils have good potential as antibiotic alternatives in feeds for swine production and the combination of different essential oils and other compounds (synergistic effect) such as organic acids seems to be a promising approach to improve the efficacy and safety of essential oils in applications.
TL;DR: The findings reveal a mechanism in which antiviral defence is boosted through suppression of an miRNA that negatively regulates viral resistance, which could be manipulated to engineer virus-resistant crop plants.
Abstract: MicroRNAs (miRNAs) are key regulators of plant-pathogen interactions. Modulating miRNA function has emerged as a new strategy to produce virus resistance traits1-5. However, the miRNAs involved in antiviral defence and the underlying mechanisms remain largely elusive. We previously demonstrated that sequestration by Argonaute (AGO) proteins plays an important role in regulating miRNA function in antiviral defence pathways6. Here we reveal that cleavage-defective AGO18 complexes sequester microRNA528 (miR528) upon viral infection. We show that miR528 negatively regulates viral resistance in rice by cleaving L-ascorbate oxidase (AO) messenger RNA, thereby reducing AO-mediated accumulation of reactive oxygen species. Upon viral infection, miR528 becomes preferentially associated with AGO18, leading to elevated AO activity, higher basal reactive oxygen species accumulation and enhanced antiviral defence. Our findings reveal a mechanism in which antiviral defence is boosted through suppression of an miRNA that negatively regulates viral resistance. This mechanism could be manipulated to engineer virus-resistant crop plants.
TL;DR: This review focuses on the phytochemical composition of quinoa and amaranth seeds, the antioxidant and anti-inflammatory activities of hydrophilic and lipophilic nutrients, and how these contribute to the potential health benefits, especially in lowering the risk of the oxidative stress related diseases e.g. cancer, cardiovascular disease, diabetes, and obesity.
Abstract: Quinoa (Chenopodium quinoa Willd.) and amaranth (Amaranthus cruentus L.) are pseudocereal grains rich in both macronutrients and micronutrients including vitamins and minerals. The proteins are particularly of high nutritional quality due to the outstanding balance of essential amino acids. However, recent research strongly suggests that nonessential nutrients such as phytochemicals of quinoa and amaranth may also have potential health beneficial effects. This review focuses on the phytochemical composition of quinoa and amaranth seeds, the antioxidant and anti-inflammatory activities of hydrophilic (e.g. phenolics, betacyanins) and lipophilic (e.g. fatty acids, tocopherols, and carotenoids) nutrients, and how these contribute to the potential health benefits, especially in lowering the risk of the oxidative stress related diseases e.g. cancer, cardiovascular disease, diabetes, and obesity. The gap between current knowledge and future research needs have also been identified.
University of California, Riverside1, University of California, Davis2, Council for Scientific and Industrial Research3, International Institute of Tropical Agriculture4, Marquette University5, Bill & Melinda Gates Foundation6, National Center for Genome Resources7, Agricultural Research Service8, University of Georgia9, Illumina10, University of Virginia11, Agriculture and Agri-Food Canada12
TL;DR: Fundamental genome resources and their application to the analysis of germplasm currently in use in West African breeding programs help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.
Abstract: Summary
Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4,355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51,128 SNPs, which was then applied to five biparental RIL populations to produce a consensus genetic map containing 37,372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.
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TL;DR: It is concluded that after 7-years of fertilization, soil bacterial diversity and community structure were shaped more by changes in soil pH rather than the direct effect of nutrient addition.
Abstract: Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007-2014) of applying chemical nitrogen, phosphorus and potassium (NPK) fertilizers, composted manure or their combination to acidic (pH 5.8), near-neutral (pH 6.8) or alkaline (pH 8.4) Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU) richness or Shannon diversity index, despite higher available N, P, K and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (%) of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) and Acidobacteria (12.6%); the medium dominant phyla were Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), and candidate division TM7 (1.0%); the least abundant phyla were Verrucomicrobia (0.7%), Armatimonadetes (0.6%), candidate division WS3 (0.4%) and Fibrobacteres (0.3%). In addition, Cyanobacteria and candidate division TM7 were more abundant in acidic soil, whereas more Gemmatimonadetes, Nitrospirae and candidate division WS3 were more abundant in alkaline soil. We conclude that after 7-years of fertilization, soil bacterial diversity and community structure were shaped more by changes in soil pH rather than the direct effect of nutrient addition.
TL;DR: It is suggested that vegetables grown in ground receiving raw or digested manure are at risk of contamination with manure-borne antibiotic resistant bacteria, whereas vegetables grownIn ground receiving composted manure are less so.
TL;DR: This review includes the principles of NIR spectroscopy, pre-processing methods, and multivariate analyses used for quantitative and qualitative purposes in the meat sector and the challenges of using NIRS technology in commercial applications.
Abstract: Consumer demand for quality and healthfulness has led to a higher need for quality assurance in meat production This requirement has increased interest in near-infrared (NIR) spectroscopy due to the ability for rapid, environmentally friendly, and noninvasive prediction of meat quality or authentication of added-value meat products This review includes the principles of NIR spectroscopy, pre-processing methods, and multivariate analyses used for quantitative and qualitative purposes in the meat sector Recent advances in portable NIR spectrometers that enable new online applications in the meat industry are shown and their performance evaluated Discrepancies between published studies and potential sources of variability are discussed, and further research is encouraged to face the challenges of using NIRS technology in commercial applications, so that its full potential can be achieved
University of Florence1, University of Milan2, Agro ParisTech3, Colorado State University4, University of Sassari5, Institut national de la recherche agronomique6, Canadian Real Estate Association7, University of Aberdeen8, Queensland University of Technology9, Plant & Food Research10, Agriculture and Agri-Food Canada11
TL;DR: Overall, it emerged that there is a possible impact of ill-defined pedo-climatic conditions in the unsatisfactory performance of the models, followed by limitations in the algorithms simulating the effects of management practices.
TL;DR: Results reveal that miR156 improves drought tolerance in alfalfa at least partially by silencing SPL13, and an enhanced accumulation of compatible solute and increased levels of abscisic acid (ABA) and antioxidants in miR 156OE genotypes.
TL;DR: New evidence indicates that AGP function is more complex than merely affecting enteric bacterial populations, and AGPs likely function by directly or indirectly modulating host responses such as the immune system, which will facilitate the development of effective alternatives.
TL;DR: It is concluded that S. sclerotiorum exhibits subtle signatures of enhanced mutation of secreted proteins in specific genomic compartments as a result of transposition and RIP activity, however, these signatures are not observable at the whole-genome scale.
Abstract: Sclerotinia sclerotiorum is a phytopathogenic fungus with over 400 hosts including numerous economically important cultivated species. This contrasts many economically destructive pathogens that only exhibit a single or very few hosts. Many plant pathogens exhibit a "two-speed" genome. So described because their genomes contain alternating gene rich, repeat sparse and gene poor, repeat-rich regions. In fungi, the repeat-rich regions may be subjected to a process termed repeat-induced point mutation (RIP). Both repeat activity and RIP are thought to play a significant role in evolution of secreted virulence proteins, termed effectors. We present a complete genome sequence of S. sclerotiorum generated using Single Molecule Real-Time Sequencing technology with highly accurate annotations produced using an extensive RNA sequencing data set. We identified 70 effector candidates and have highlighted their in planta expression profiles. Furthermore, we characterized the genome architecture of S. sclerotiorum in comparison to plant pathogens that exhibit "two-speed" genomes. We show that there is a significant association between positions of secreted proteins and regions with a high RIP index in S. sclerotiorum but we did not detect a correlation between secreted protein proportion and GC content. Neither did we detect a negative correlation between CDS content and secreted protein proportion across the S. sclerotiorum genome. We conclude that S. sclerotiorum exhibits subtle signatures of enhanced mutation of secreted proteins in specific genomic compartments as a result of transposition and RIP activity. However, these signatures are not observable at the whole-genome scale.
Agriculture and Agri-Food Canada1, Agricultural Research Service2, Virginia Tech3, Oregon State University4, Washington State University5, University of Kentucky6, Pennsylvania State University7, Michigan State University8, University of Modena and Reggio Emilia9, University of Delaware10, University of Connecticut11, Rutgers University12, CABI13, University of California, Riverside14, University of Maryland, College Park15, Cornell University16, University of Arkansas17, Shepherd University18, North Carolina State University19, California Department of Food and Agriculture20, Ohio State University21, Florida Department of Agriculture and Consumer Services22, University of Turin23
TL;DR: A review of 98 indigenous natural enemy datasets spanning a variety of sampling methods, habitats, and geographic areas identifies a number of key research gaps and suggest several directions for future research.
Abstract: Since the establishment of the brown marmorated stink bug, Halyomorpha halys (Stal) (Hemiptera: Pentatomidae) in North America and Europe, there has been a large, multi-group effort to characterize the composition and impact of the indigenous community of arthropod natural enemies attacking this invasive pest. In this review, we combine 98 indigenous natural enemy datasets spanning a variety of sampling methods, habitats, and geographic areas. To date, the vast majority of H. halys biological control research has focused on the egg stage, using sentinel egg masses to characterize indigenous parasitoid and predator communities and their contribution to H. halys egg mortality. Although egg parasitism and predation levels by indigenous natural enemies are low (typically <10% each) in most surveys, total egg mortality attributable to natural enemies can be higher (typically between 5 and 25%; up to 83%)—even though these values were likely underestimated in most cases because some mortality due to biological control was not recognized. In North America, where the most data are available, it appears that the relative prevalence of different indigenous parasitoid species varies among habitat types, particularly between crop and non-crop habitats. Predator species responsible for egg mortality are much less commonly identified, but appear to include a wide variety of generalist chewing and sucking predators. To date, studies of natural enemies attacking H. halys nymphs and adults are relatively rare. Based on our review, we identify a number of key research gaps and suggest several directions for future research.
TL;DR: Evidence of beneficial contributions of root and stomatal traits to plant adaptation to drought stress is summarized and a list of candidate genes that have been identified as regulators of drought response in plants is provided.
Abstract: Abiotic stresses such as, drought, heat, salinity, and flooding threaten global food security. Crop genetic improvement with increased resilience to abiotic stresses is a critical component of crop breeding strategies. Wheat is an important cereal crop and a staple food source globally. Enhanced drought tolerance in wheat is critical for sustainable food production and global food security. Recent advances in drought tolerance research have uncovered many key genes and transcription regulators governing morpho-physiological traits. Genes controlling root architecture and stomatal development play an important role in soil moisture extraction and its retention, and therefore have been targets of molecular breeding strategies for improving drought tolerance. In this systematic review, we have summarized evidence of beneficial contributions of root and stomatal traits to plant adaptation to drought stress. Specifically, we discuss a few key genes such as, DRO1 in rice and ERECTA in Arabidopsis and rice that were identified to be the enhancers of drought tolerance via regulation of root traits and transpiration efficiency. Additionally, we highlight several transcription factor families, such as, ERF (ethylene response factors), DREB (dehydration responsive element binding), ZFP (zinc finger proteins), WRKY, and MYB that were identified to be both positive and negative regulators of drought responses in wheat, rice, maize, and/or Arabidopsis. The overall aim of this review is to provide an overview of candidate genes that have been identified as regulators of drought response in plants. The lack of a reference genome sequence for wheat and non-transgenic approaches for manipulation of gene functions in wheat in the past had impeded high-resolution interrogation of functional elements, including genes and QTLs, and their application in cultivar improvement. The recent developments in wheat genomics and reverse genetics, including the availability of a gold-standard reference genome sequence and advent of genome editing technologies, are expected to aid in deciphering of the functional roles of genes and regulatory networks underlying adaptive phenological traits, and utilizing the outcomes of such studies in developing drought tolerant cultivars.