Agriculture and Agri-Food Canada

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

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.

The antioxidant activities and total phenolics of 28 plant products, including sunflower seeds, flaxseeds, wheat germ, buckwheat, and several fruits, vegetables, and medicinal plants were determined. The total phenolic content, determined according to the Folin−Ciocalteu method, varied from 169 to 10548 mg/100 g of dry product. Antioxidant activity of methanolic extract evaluated according to the β-carotene bleaching method expressed as AOX (Δ log A470/min), AA (percent inhibition relative to control), ORR (oxidation rate ratio), and AAC (antioxidant activity coefficient) ranged from 0.05, 53.7, 0.009, and 51.7 to 0.26, 99.1, 0.46, and 969.3, respectively. The correlation coefficient between total phenolics and antioxidative activities was statistically significant. Keywords: Antioxidant activity; phenolics; medicinal plants; oilseeds; buckwheat; vegetables; fruits; wheat products

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

The Northern Circumpolar Soil Carbon Database was developed in order to determine carbon pools in soils of the northern circumpolar permafrost region. The area of all soils in the northern permafrost region is approximately 18,782 × 10 3 km 2 , or approximately 16% of the global soil area. In the northern permafrost region, organic soils (peatlands) and cryoturbated permafrost‐affected mineral soils have the highest mean soil organic carbon contents (32.2–69.6 kg m −2 ). Here we report a new estimate of the carbon pools in soils of the northern permafrost region, including deeper layers and pools not accounted for in previous analyses. Carbon pools were estimated to be 191.29 Pg for the 0–30 cm depth, 495.80 Pg for the 0–100 cm depth, and 1024.00 Pg for the 0–300 cm depth. Our estimate for the first meter of soil alone is about double that reported for this region in previous analyses. Carbon pools in layers deeper than 300 cm were estimated to be 407 Pg in yedoma deposits and 241 Pg in deltaic deposits. In total, the northern permafrost region contains approximately 1672 Pg of organic carbon, of which approximately 1466 Pg, or 88%, occurs in perennially frozen soils and deposits. This 1672 Pg of organic carbon would account for approximately 50% of the estimated global belowground organic carbon pool.

Honeybees Can't Do It Alone The majority of food crops require pollination to set fruit with the honeybee providing a pollination workhorse, with both feral and managed populations an integral component of crop management (see the Perspective by Tylianakis , published online 28 February). Garibaldi et al. (p. 1608 , published online 28 February) now show that wild pollinators are also a vital part of our crop systems. In more than 40 important crops grown worldwide, wild pollinators improved pollination efficiency, increasing fruit set by twice that facilitated by honeybees. Burkle et al. (p. 1611 , published online 28 February) took advantage of one of the most thorough and oldest data sets available on plant-pollinator interaction networks and recollected data on plant-pollinator interactions after more than 120 years of climate change and landscape alteration. The historical data set consists of observations collected by Charles Robertson near Carlinville, Illinois (USA), in the late 1800s on the phenology of plants and their pollinating insects, as well as information about which plants and pollinators interacted with one another. Many sites were revisited in the early 1970s and in 2009 and 2010 to collect similar plant-pollinator data. Pollinator function has declined through time, with bees showing lower visitation rates and lower fidelity to individual plant species.

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

Agricultural lands occupy 37% of the earth's land surface. Agriculture accounts for 52 and 84% of global anthropogenic methane and nitrous oxide emissions. Agricultural soils may also act as a sink or source for CO2, but the net flux is small. Many agricultural practices can potentially mitigate greenhouse gas (GHG) emissions, the most prominent of which are improved cropland and grazing land management and restoration of degraded lands and cultivated organic soils. Lower, but still significant mitigation potential is provided by water and rice management, set-aside, land use change and agroforestry, livestock management and manure management. The global technical mitigation potential from agriculture (excluding fossil fuel offsets from biomass) by 2030, considering all gases, is estimated to be approximately 5500-6000Mt CO2-eq.yr-1, with economic potentials of approximately 1500-1600, 2500-2700 and 4000-4300Mt CO2-eq.yr-1 at carbon prices of up to 20, up to 50 and up to 100 US$ t CO2-eq.-1, respectively. In addition, GHG emissions could be reduced by substitution of fossil fuels for energy production by agricultural feedstocks (e.g. crop residues, dung and dedicated energy crops). The economic mitigation potential of biomass energy from agriculture is estimated to be 640, 2240 and 16 000Mt CO2-eq.yr-1 at 0-20, 0-50 and 0-100 US$ t CO2-eq.-1, respectively.

Polyphenols are the biggest group of phytochemicals, and many of them have been found in plant-based foods. Polyphenol-rich diets have been linked to many health benefits. This paper is intended to review the chemistry and biochemistry of polyphenols as related to classification, extraction, separation and analytical methods, their occurrence and biosynthesis in plants, and the biological activities and implications in human health. The discussions are focused on important and most recent advances in the above aspects, and challenges are identified for future research.

The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.

The ‘4 per mille Soils for Food Security and Climate’ was launched at the COP21 with an aspiration to increase global soil organic matter stocks by 4 per 1000 (or 0.4 %) per year as a compensation for the global emissions of greenhouse gases by anthropogenic sources. This paper 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). We asked whether the 4 per mille initiative is feasible for the region. The outcomes highlight region specific efforts and scopes for soil carbon sequestration. Reported soil C sequestration rates globally show that under best management practices, 4 per mille or even higher sequestration rates can be accomplished. High C sequestration rates (up to 10 per mille) can be achieved for soils with low initial SOC stock (topsoil less than 30 t C ha− 1), and at the first twenty years after implementation of best management practices. In addition, areas which have reached equilibrium will not be able to further increase their sequestration. We found that most studies on SOC sequestration only consider topsoil (up to 0.3 m depth), as it is considered to be most affected by management techniques. The 4 per mille number was based on a blanket calculation of the whole global soil profile C stock, however the potential to increase SOC is mostly on managed agricultural lands. If we consider 4 per mille in the top 1m of global agricultural soils, SOC sequestration is between 2-3 Gt C year− 1, which effectively offset 20–35% of global anthropogenic greenhouse gas emissions. As a strategy for climate change mitigation, soil carbon sequestration buys time over the next ten to twenty years while other effective sequestration and low carbon technologies become viable. The challenge for cropping farmers is to find disruptive technologies that will further improve soil condition and deliver increased soil carbon. Progress in 4 per mille requires collaboration and communication between scientists, farmers, policy makers, and marketeers.

The soil microbiome is highly diverse and comprises up to one quarter of Earth's diversity. Yet, how such a diverse and functionally complex microbiome influences ecosystem functioning remains unclear. Here we manipulated the soil microbiome in experimental grassland ecosystems and observed that microbiome diversity and microbial network complexity positively influenced multiple ecosystem functions related to nutrient cycling (e.g. multifunctionality). Grassland microcosms with poorly developed microbial networks and reduced microbial richness had the lowest multifunctionality due to fewer taxa present that support the same function (redundancy) and lower diversity of taxa that support different functions (reduced functional uniqueness). Moreover, different microbial taxa explained different ecosystem functions pointing to the significance of functional diversity in microbial communities. These findings indicate the importance of microbial interactions within and among fungal and bacterial communities for enhancing ecosystem performance and demonstrate that the extinction of complex ecological associations belowground can impair ecosystem functioning.

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort. [Supplemental material is available online at www.genome.org . Bioperl is available as open-source software free of charge and is licensed under the Perl Artistic License ( http://www.perl.com/pub/a/language/misc/Artistic.html ). It is available for download at http://www.bioperl.org . Support inquiries should be addressed to bioperl-l@bioperl.org .]

Methods for determining primary antioxidant activity were evaluated. A beta-carotene bleaching method and a free radical method using 2, 2-diphenyl-1-picrylhydrazyl (DPPH(*)) were modified to rapidly test samples for potential antioxidant activity. Malonaldehyde production in a linoleic acid emulsion system assayed by an HPLC method was also used to determine antioxidant and prooxidant activities initiated by a metal catalyst (Cu(2+)). All methods were used to assess activity of selected phenolic compounds including several anthocyanidins/anthocyanins and selected berry extracts. Most phenolic compounds had prooxidant activity at low concentrations, unlike synthetic antioxidants (BHA and BHT). Compounds with similar structures exhibited comparable trends in antioxidant activity. Antioxidant activity usually increased with an increase in the number of hydroxyl groups and a decrease in glycosylation. The antioxidant activity of many phenolic compounds and extracts was comparable to those of synthetic antioxidants using the beta-carotene bleaching and HPLC methods.

Biplot analysis has evolved into an important statistical tool in plant breeding and agricultural research. Here we review the basic principles of biplot analysis and recent developments in its application in analyzing multi-environment trail (MET) data, with the aim of providing a working guide for breeders, agronomists, and other agricultural scientists on biplot analysis and interpretation. The review is divided into four sections. The first section is a complete but succinct description of the principles of biplot analysis. The second section is a detailed treatment of biplot analysis of genotype by environment data. It addresses environment and genotype evaluation from all perspectives. The third section deals with biplot analysis of various two-way tables that can be generated from a three-way MET dataset, which is an integral and essential part to a fuller understanding and exploration of MET data. The final section discusses questions that are frequently asked about biplot analysis. Methods described in this review are available in a user-friendly, interactive software package called “GGEbiplot”. Key words: biplot analysis; genotype by environment interaction; mega-environment; multi-environment trials

ABSTRACT The use of genotype main effect (G) plus genotype‐by‐environment (GE) interaction (G+GE) biplot analysis by plant breeders and other agricultural researchers has increased dramatically during the past 5 yr for analyzing multi‐environment trial (MET) data. Recently, however, its legitimacy was questioned by a proponent of Additive Main Effect and Multiplicative Interaction (AMMI) analysis. The objectives of this review are: (i) to compare GGE biplot analysis and AMMI analysis on three aspects of genotype‐by‐environment data (GED) analysis, namely mega‐environment analysis, genotype evaluation, and test‐environment evaluation; (ii) to discuss whether G and GE should be combined or separated in these three aspects of GED analysis; and (iii) to discuss the role and importance of model diagnosis in biplot analysis of GED. Our main conclusions are: (i) both GGE biplot analysis and AMMI analysis combine rather than separate G and GE in mega‐environment analysis and genotype evaluation, (ii) the GGE biplot is superior to the AMMI1 graph in mega‐environment analysis and genotype evaluation because it explains more G+GE and has the inner‐product property of the biplot, (iii) the discriminating power vs. representativeness view of the GGE biplot is effective in evaluating test environments, which is not possible in AMMI analysis, and (iv) model diagnosis for each dataset is useful, but accuracy gain from model diagnosis should not be overstated.

BACKGROUND: Over the past 10-15 years, a substantial amount of work has been done by the scientific, regulatory, and business communities to elucidate the effects and risks of pharmaceuticals and personal care products (PPCPs) in the environment. OBJECTIVE: This review was undertaken to identify key outstanding issues regarding the effects of PPCPs on human and ecological health in order to ensure that future resources will be focused on the most important areas. DATA SOURCES: To better understand and manage the risks of PPCPs in the environment, we used the "key question" approach to identify the principle issues that need to be addressed. Initially, questions were solicited from academic, government, and business communities around the world. A list of 101 questions was then discussed at an international expert workshop, and a top-20 list was developed. Following the workshop, workshop attendees ranked the 20 questions by importance. DATA SYNTHESIS: The top 20 priority questions fell into seven categories: a) prioritization of substances for assessment, b) pathways of exposure, c) bioavailability and uptake, d) effects characterization, e) risk and relative risk, f ) antibiotic resistance, and g) risk management. CONCLUSIONS: A large body of information is now available on PPCPs in the environment. This exercise prioritized the most critical questions to aid in development of future research programs on the topic.

Abstract This review surveys the occurrence, analysis, and properties of glucosinolates and derived compounds in plants and products intended for humans and animal consumption. The paper, which includes references published in 1981, is also intended to compliment existing reviews on the chemistry of these sulfur‐containing natural products. Particular emphasis is placed upon members of the Brassica family because of their importance as vegetables, condiments, oilseeds, and animal feedingstuffs. Since much of the work considered here relates to glucosinolate decomposition products, biochemical information concerning the nature, occurrence, and properties of the glucosinolate‐degrading enzyme, myrosinase, is considered in Section III. The methods available for the chemical analysis of glucosinolates and their various breakdown products are discussed critically. Factors affecting the glucosinolate content of plants and plant products arc outlined in Section VII. Particular emphasis is placed upon the effect of processing on the concentration and nature of breakdown products and on the myrosinase activity. The role of glucosinolate breakdown products on flavor development is examined in Section VIII. The more general effects, both beneficial and adverse, of these compounds in food are discussed in Section X. Since such effects in animal feedingstuffs have been the subject of regular reviews, these are considered here only briefly. Contraindications in the literature are pointed out, areas which have been inadequately explored are highlighted, and suggestions are made for future research.

Different cultivars of four Vaccinium species [Vaccinium corymbosum L (Highbush), Vaccinium ashei Reade (Rabbiteye), Vaccinium angustifolium (Lowbush), and Vaccinium myrtillus L (Bilberry)] were analyzed for total phenolics, total anthocyanins, and antioxidant capacity (oxygen radical absorbance capacity, ORAC). The total antioxidant capacity of different berries studied ranged from a low of 13.9 to 45.9 μmol Trolox equivalents (TE)/g of fresh berry (63.2−282.3 μmol TE/g of dry matter) in different species and cultivars of Vaccinium. Brightwell and Tifblue cultivars of rabbiteye blueberries were harvested at 2 times, 49 days apart. Increased maturity at harvest increased the ORAC, the anthocyanin, and the total phenolic content. The growing location (Oregon vs Michigan vs New Jersey) did not affect ORAC, anthocyanin or total phenolic content of the cv. Jersey of highbush blueberries. A linear relationship existed between ORAC and anthocyanin (rxy = 0.77) or total phenolic (rxy = 0.92) content. In general, blueberries are one of the richest sources of antioxidant phytonutrients of the fresh fruits and vegetables we have studied. Keywords: Vitamin C; ascorbate; blueberry; bilberry; highbush; lowbush; rabbiteye; ORAC; HPLC