Showing papers by "Agriculture and Agri-Food Canada published in 2018"
TL;DR: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
Abstract: 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.
2,118 citations
Norwich Research Park1, Bayer2, University of Toronto3, Agriculture and Agri-Food Canada4, University of Saskatchewan5, Paris Diderot University6, Institut national de la recherche agronomique7, National Research Council8, Technische Universität München9, University of Melbourne10, University of Maryland, College Park11
TL;DR: This study leverages 850 wheat RNA-sequencing samples, alongside the annotated genome, to determine the similarities and differences between homoeolog expression across a range of tissues, developmental stages, and cultivars and suggests that the transposable elements in promoters relate more closely to the variation in the relative expression of homoeologicals across tissues than to a ubiquitous effect across all tissues.
Abstract: The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world's major crops. Here we combine extensive gene expression datasets to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varies between tissues, with ~30% of wheat homoeologs showing nonbalanced expression. We found expression asymmetries along wheat chromosomes, with homoeologs showing the largest inter-tissue, inter-cultivar, and coding sequence variation, most often located in high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps toward neo- or subfunctionalization of wheat homoeologs. Coexpression networks reveal extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in wheat.
609 citations
TL;DR: Research indicates that these products are improving aerobic stability, but feeding studies are not yet sufficient to make conclusions about effects on animal performance, so future silage additives are expected to directly inhibit clostridia and other detrimental microorganisms, mitigate high mycotoxin levels on harvested forages during ensiling.
423 citations
TL;DR: Overall, progress has been made in understanding the functional and bioactive components of soy, however, more studies are required to further identify their target organs, and elucidate their biological mechanisms of action in order to be potentially used as functional foods or even therapeutics for the prevention or treatment of chronic diseases.
Abstract: Soy consumption has been associated with many potential health benefits in reducing chronic diseases such as obesity, cardiovascular disease, insulin-resistance/type II diabetes, certain type of cancers, and immune disorders. These physiological functions have been attributed to soy proteins either as intact soy protein or more commonly as functional or bioactive peptides derived from soybean processing. These findings have led to the approval of a health claim in the USA regarding the ability of soy proteins in reducing the risk for coronary heart disease and the acceptance of a health claim in Canada that soy protein can help lower cholesterol levels. Using different approaches, many soy bioactive peptides that have a variety of physiological functions such as hypolipidemic, anti-hypertensive, and anti-cancer properties, and anti-inflammatory, antioxidant, and immunomodulatory effects have been identified. Some soy peptides like lunasin and soymorphins possess more than one of these properties and play a role in the prevention of multiple chronic diseases. Overall, progress has been made in understanding the functional and bioactive components of soy. However, more studies are required to further identify their target organs, and elucidate their biological mechanisms of action in order to be potentially used as functional foods or even therapeutics for the prevention or treatment of chronic diseases.
261 citations
University of Gothenburg1, Paris Diderot University2, University of Copenhagen3, Uppsala University4, Umeå University5, Royal Cornwall Hospital6, National Institutes of Health7, Harvard University8, Catholic University of Portugal9, Oslo and Akershus University College of Applied Sciences10, French Institute of Health and Medical Research11, Carlos III Health Institute12, Centre national de la recherche scientifique13, University of Warwick14, Agriculture and Agri-Food Canada15, Centre for Environment, Fisheries and Aquaculture Science16
TL;DR: Four key areas were identified where research is urgently needed: the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.
255 citations
TL;DR: A number of areas of future prospect for effective management of GTDs worldwide, which, if addressed, will provide a positive outlook on the longevity of vineyards in the future are identified.
Abstract: Fungal trunk diseases are some of the most destructive diseases of grapevine in all grape growing areas of the world. Management of GTDs has been intensively studied for decades with some great advances made in our understanding of the causal pathogens, their epidemiology, impact, and control. However, due to the breadth and complexity of the problem, no single effective control measure has been developed. Management of GTD must be holistic and integrated, with an interdisciplinary approach conducted in both nurseries and vineyards that integrates plant pathology, agronomy, viticulture, microbiology, epidemiology, biochemistry, physiology, and genetics. In this review, we identify a number of areas of future prospect for effective management of GTDs worldwide, which, if addressed, will provide a positive outlook on the longevity of vineyards in the future.
246 citations
TL;DR: The dynamic mechanisms driving utilization of pectins by Bacteroides thetaiotaomicron are described, where specific polysaccharide-utilization loci target specific pectin molecules with the products available for use by other bacteria.
Abstract: The major nutrients available to human colonic Bacteroides species are glycans, exemplified by pectins, a network of covalently linked plant cell wall polysaccharides containing galacturonic acid (GalA). Metabolism of complex carbohydrates by the Bacteroides genus is orchestrated by polysaccharide utilization loci (PULs). In Bacteroides thetaiotaomicron, a human colonic bacterium, the PULs activated by different pectin domains have been identified; however, the mechanism by which these loci contribute to the degradation of these GalA-containing polysaccharides is poorly understood. Here we show that each PUL orchestrates the metabolism of specific pectin molecules, recruiting enzymes from two previously unknown glycoside hydrolase families. The apparatus that depolymerizes the backbone of rhamnogalacturonan-I is particularly complex. This system contains several glycoside hydrolases that trim the remnants of other pectin domains attached to rhamnogalacturonan-I, and nine enzymes that contribute to the degradation of the backbone that makes up a rhamnose-GalA repeating unit. The catalytic properties of the pectin-degrading enzymes are optimized to protect the glycan cues that activate the specific PULs ensuring a continuous supply of inducing molecules throughout growth. The contribution of Bacteroides spp. to metabolism of the pectic network is illustrated by cross-feeding between organisms.
230 citations
École Polytechnique Fédérale de Lausanne1, University of Kassel2, University of Nebraska–Lincoln3, Punjab Agricultural University4, Université Paris-Saclay5, Colorado State University6, Institut national de la recherche agronomique7, University of Bologna8, University of Lausanne9, Agriculture and Agri-Food Canada10, ETH Zurich11, Ghent University12, Bangor University13, University of Göttingen14, Technische Universität München15, Commonwealth Scientific and Industrial Research Organisation16, University of Antwerp17, Université catholique de Louvain18, University of Sydney19, Braunschweig University of Technology20
TL;DR: In this article, a total of 20 different soil organic carbon fractionation methods were tested by participating laboratories for their suitability to isolate fractions with varying turnover rates, using agricultural soils from three experimental sites with vegetation change from C3 to C4 22-36 years ago.
Abstract: Fractionation of soil organic carbon (SOC) is crucial for mechanistic understanding and modeling of soil organic matter decomposition and stabilization processes. It is often aimed at separating the bulk SOC into fractions with varying turnover rates, but a comprehensive comparison of methods to achieve this is lacking. In this study, a total of 20 different SOC fractionation methods were tested by participating laboratories for their suitability to isolate fractions with varying turnover rates, using agricultural soils from three experimental sites with vegetation change from C3 to C4 22–36 years ago. Enrichment of C4-derived carbon was traced and used as a proxy for turnover rates in the fractions. Methods that apply a combination of physical (density, size) and chemical (oxidation, extraction) fractionation were identified as most effective in separating SOC into fractions with distinct turnover rates. Coarse light SOC separated by density fractionation was the most C4-carbon enriched fraction, while oxidation-resistant SOC left after extraction with NaOCl was the least C4-carbon enriched fraction. Surprisingly, even after 36 years of C4 crop cultivation in a temperate climate, no method was able to isolate a fraction with more than 76% turnover, which challenges the link to the most active plant-derived carbon pools in models. Particles with density >2.8 g cm−3 showed similar C4-carbon enrichment as oxidation-resistant SOC, highlighting the importance of sesquioxides for SOC stabilization. The importance of clay and silt-sized particles (
225 citations
TL;DR: A comprehensive understanding of the dietary, animal, and management factors that affect eating and ruminating behavior in dairy cows is provided and an overview of the physiological importance of chewing is presented with emphasis on recent developments and practical implications for feeding and managing the modern housed dairy cow.
210 citations
Queen's University Belfast1, Ben-Gurion University of the Negev2, Commonwealth Scientific and Industrial Research Organisation3, Université Paris-Saclay4, University of Auvergne5, University of California, Davis6, Swedish University of Agricultural Sciences7, Spanish National Research Council8, University of Alberta9, Agriculture and Agri-Food Canada10, Scotland's Rural College11, University of Aberdeen12, University of Edinburgh13, University of Wisconsin-Madison14, Aberystwyth University15, Universidade Estadual de Maringá16, Universidade Federal de Viçosa17, AgResearch18, Wageningen University and Research Centre19, Robert Gordon University20
TL;DR: Advances in computational tools, high-throughput sequencing technologies and cultivation-independent “omics” approaches continue to revolutionize the understanding of the rumen microbiome, which will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.
Abstract: The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security As the world population is predicted to reach approximately 97 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in "omic" data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies Advances in computational tools, high-throughput sequencing technologies and cultivation-independent "omics" approaches continue to revolutionize our understanding of the rumen microbiome This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges
210 citations
TL;DR: It is argued that improving the functionality of probiotics can be achieved by adapting fermentation technologies in order to produce high levels of probioactives in the supplements or in fermented foods.
Abstract: Probiotic bacteria are increasingly marketed in supplements and in foods. In order to ensure their functionality (effectiveness), the focus has traditionally been to simply maintain cell viability. However, the bioactive metabolites that are specifically the result of probiotics (probioactives), are increasingly being identified. Thus, ensuring the presence of the probioactives in the products will contribute to health functionality. It is argued that improving the functionality of probiotics can be achieved by adapting fermentation technologies in order to produce high levels of probioactives in the supplements or in fermented foods. Also, probiotics will need to demonstrate multiple benefits in foods, including delaying spoilage.
TL;DR: There is an association between HEs and PAV events, particularly in recent Brassica napus synthetic accessions, and these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species.
Abstract: Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In the present study we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterisation of the association between HEs and PAVs in B. napus at the pangenome level. This article is protected by copyright. All rights reserved.
TL;DR: The past and current achievements of research on structural characterizations of a range of RS prepared from different sources of native starches as a result of a variety of processing conditions are focused on.
Abstract: Resistant starch (RS) is defined as the fraction of starch that escapes digestion in the small intestine due to either difficult enzyme/starch contact or to the strength of the crystalline regions formed both in native starch and in those retrograded starch. RS occurs naturally in some foods, and some may be generated in others as the results of several processing conditions. Varieties of techniques have been employed to obtain structural characteristics of RS such as their crystallinity, structural order, chain-length distribution and conformation, helicity, and double-helical structures. These structures play an important role in determining the physiological properties of RS such as their prebiotic and hypoglycaemic properties. However, such topic on structural characterization of RS and their structure-physiological function relationship have not been reviewed in previous literatures. Therefore, this review focuses on the past and current achievements of research on structural characterization...
TL;DR: The results indicated that Arla-10, J FR-1, and JFR-5 strains grew well on both MRS and BHI media at growth temperature tested whereas TSB-8 strain, unable to grow at 20 °C, provides useful information on potential application of bacteriocinogenic LAB in food fermentation processes.
Abstract: There has been continued interest in bacteriocins research from an applied perspective as bacteriocins have potential to be used as natural preservative. Four bacteriocinogenic lactic acid bacteria (LAB) strains of Lactobacillus curvatus (Arla-10), Enterococcus faecium (JFR-1), Lactobacillus paracasei subsp. paracasei (JFR-5) and Streptococcus thermophilus (TSB-8) were previously isolated and identified in our lab. The objective of this study was to determine the optimal growth conditions for both LAB growth and bacteriocins production. In this study, various growth conditions including culture media (MRS and BHI), initial pH of culture media (4.5, 5.5, 6.2, 7.4 and 8.5), and incubation temperatures (20, 37 and 44 °C) were investigated for LAB growth measured as optical density (OD), bacteriocin activity determined as arbitrary unit and viability of LAB expressed as log CFU ml−1. Growth curves of the bacteriocinogenic LAB were generated using a Bioscreen C. Our results indicated that Arla-10, JFR-1, and JFR-5 strains grew well on both MRS and BHI media at growth temperature tested whereas TSB-8 strain, unable to grow at 20 °C. LAB growth was significantly affected by the initial pH of culture media (p < 0.001) and the optimal pH was found ranging from 6.2 to 8.5. Bacteriocin activity was significantly different in MRS versus BHI (p < 0.001), and the optimal condition for LAB to produce bacteriocins was determined in MRS broth, pH 6.2 at 37 °C. This study provides useful information on potential application of bacteriocinogenic LAB in food fermentation processes.
TL;DR: The utility of this technology is demonstrated through foliar applications of dsRNAs to the leaf surface that significantly decreased fungal infection and S. sclerotiorum disease symptoms, providing compelling evidence of the adaptability and flexibility of thistechnology in protecting plants against devastating fungal pathogens.
Abstract: Sclerotinia sclerotiorum, the causal agent of white stem rot, is responsible for significant losses in crop yields around the globe. While our understanding of S. sclerotiorum infection is becoming clearer, genetic control of the pathogen has been elusive and effective control of pathogen colonization using traditional broad-spectrum agro-chemical protocols are less effective than desired. In the current study, we developed species-specific RNA interference-based control treatments capable of reducing fungal infection. Development of a target identification pipeline using global RNA sequencing data for selection and application of double stranded RNA (dsRNA) molecules identified single gene targets of the fungus. Using this approach, we demonstrate the utility of this technology through foliar applications of dsRNAs to the leaf surface that significantly decreased fungal infection and S. sclerotiorum disease symptoms. Select target gene homologs were also tested in the closely related species, Botrytis cinerea, reducing lesion size and providing compelling evidence of the adaptability and flexibility of this technology in protecting plants against devastating fungal pathogens.
TL;DR: Garnett and Christidis as mentioned in this paper argued that the lack of governance of taxonomy damages conservation efforts, harms the credibility of science, and is costly to society, and pointed out that the scientific community's failure to govern taxonomy threatens the effectiveness of global efforts to halt biodiversity loss.
Abstract: Taxonomy is a scientific discipline that has provided the universal naming and classification system of biodiversity for centuries and continues effectively to accommodate new knowledge. A recent publication by Garnett and Christidis [1] expressed concerns regarding the difficulty that taxonomic changes represent for conservation efforts and proposed the establishment of a system to govern taxonomic changes. Their proposal to “restrict the freedom of taxonomic action” through governing subcommittees that would “review taxonomic papers for compliance” and their assertion that “the scientific community’s failure to govern taxonomy threatens the effectiveness of global efforts to halt biodiversity loss, damages the credibility of science, and is expensive to society” are flawed in many respects. They also assert that the lack of governance of taxonomy damages conservation efforts, harms the credibility of science, and is costly to society. Despite its fairly recent release, Garnett and Christidis' proposition has already been rejected by a number of colleagues [2,3,4,5,6,7,8]. Herein, we contribute to the conversation between taxonomists and conservation biologists aiming to clarify some misunderstandings and issues in the proposition by Garnett and Christidis.
University of Pretoria1, Biotec2, Universidade Federal de Viçosa3, Federal University of Rio Grande do Norte4, Rovira i Virgili University5, Spanish National Research Council6, Russian Academy of Sciences7, Royal Botanic Gardens8, Eötvös Loránd University9, University of the Free State10, State University of Feira de Santana11, Naturalis12, Federal University of Pernambuco13, Ministry for Primary Industries14, Uppsala University15, University of Tartu16, Franklin & Marshall College17, Florida Museum of Natural History18, CABI19, Pontificia Universidad Católica del Ecuador20, University of Maryland College of Agriculture and Natural Resources21, Moscow State University22, University of Vienna23, Chinese Academy of Sciences24, Universidad Mayor25, University of Illinois at Urbana–Champaign26, Valparaiso University27, United States Department of Agriculture28, Harvard University29, University of North Carolina at Greensboro30, University of Oslo31, University of Palermo32, Agriculture and Agri-Food Canada33, Federal University of Bahia34, University of Antofagasta35
TL;DR: Novel species of fungi described in this study include those from various countries as follows: Angola, Gnomoniopsis angolensis and Pseudopithomyces anglensis on unknown host plants.
Abstract: Novel species of fungi described in this study include those from various countries as follows: Angola, Gnomoniopsis angolensis and Pseudopithomyces angolensis on unknown host plants. Australia, Dothiora corymbiae on Corymbia citriodora, Neoeucasphaeria eucalypti (incl. Neoeucasphaeria gen. nov.) on Eucalyptus sp., Fumagopsis stellae on Eucalyptus sp., Fusculina eucalyptorum (incl. Fusculinaceae fam. nov.) on Eucalyptus socialis, Harknessia corymbiicola on Corymbia maculata, Neocelosporium eucalypti (incl. Neocelosporium gen. nov., Neocelosporiaceae fam. nov. and Neocelosporiales ord. nov.) on Eucalyptus cyanophylla, Neophaeomoniella corymbiae on Corymbia citriodora, Neophaeomoniella eucalyptigena on Eucalyptus pilularis, Pseudoplagiostoma corymbiicola on Corymbia citriodora, Teratosphaeria gracilis on Eucalyptus gracilis, Zasmidium corymbiae on Corymbia citriodora. Brazil, Calonectria hemileiae on pustules of Hemileia vastatrix formed on leaves of Coffea arabica, Calvatia caatinguensis on soil, Cercospora solani-betacei on Solanum betaceum, Clathrus natalensis on soil, Diaporthe poincianellae on Poincianella pyramidalis, Geastrum piquiriunense on soil, Geosmithia carolliae on wing of Carollia perspicillata, Henningsia resupinata on wood, Penicillium guaibinense from soil, Periconia caespitosa from leaf litter, Pseudocercospora styracina on Styrax sp., Simplicillium filiforme as endophyte from Citrullus lanatus, Thozetella pindobacuensis on leaf litter, Xenosonderhenia coussapoae on Coussapoa floccosa. Canary Islands (Spain), Orbilia amarilla on Euphorbia canariensis. Cape Verde Islands, Xylodon jacobaeus on Eucalyptus camaldulensis. Chile, Colletotrichum arboricola on Fuchsia magellanica. Costa Rica, Lasiosphaeria miniovina on tree branch. Ecuador, Ganoderma chocoense on tree trunk. France, Neofitzroyomyces nerii (incl. Neofitzroyomyces gen. nov.) on Nerium oleander. Ghana, Castanediella tereticornis on Eucalyptus tereticornis, Falcocladium africanum on Eucalyptus brassiana, Rachicladosporium corymbiae on Corymbia citriodora. Hungary, Entoloma silvae-frondosae in Carpinus betulus-Pinus sylvestris mixed forest. Iran, Pseudopyricularia persiana on Cyperus sp. Italy, Inocybe roseascens on soil in mixed forest. Laos, Ophiocordyceps houaynhangensis on Coleoptera larva. Malaysia, Monilochaetes melastomae on Melastoma sp. Mexico, Absidia terrestris from soil. Netherlands, Acaulium pannemaniae, Conioscypha boutwelliae, Fusicolla septimanifiniscientiae, Gibellulopsis simonii, Lasionectria hilhorstii, Lectera nordwiniana, Leptodiscella rintelii, Parasarocladium debruynii and Sarocladium dejongiae (incl. Sarocladiaceae fam. nov.) from soil. New Zealand, Gnomoniopsis rosae on Rosa sp. and Neodevriesia metrosideri on Metrosideros sp. Puerto Rico, Neodevriesia coccolobae on Coccoloba uvifera, Neodevriesia tabebuiae and Alfaria tabebuiae on Tabebuia chrysantha. Russia, Amanita paludosa on bogged soil in mixed deciduous forest, Entoloma tiliae in forest of Tilia × europaea, Kwoniella endophytica on Pyrus communis. South Africa, Coniella diospyri on Diospyros mespiliformis, Neomelanconiella combreti (incl. Neomelanconiellaceae fam. nov. and Neomelanconiella gen. nov.) on Combretum sp., Polyphialoseptoria natalensis on unidentified plant host, Pseudorobillarda bolusanthi on Bolusanthus speciosus, Thelonectria pelargonii on Pelargonium sp. Spain, Vermiculariopsiella lauracearum and Anungitopsis lauri on Laurus novocanariensis, Geosmithia xerotolerans from a darkened wall of a house, Pseudopenidiella gallaica on leaf litter. Thailand, Corynespora thailandica on wood, Lareunionomyces loeiensis on leaf litter, Neocochlearomyces chromolaenae (incl. Neocochlearomyces gen. nov.) on Chromolaena odorata, Neomyrmecridium septatum (incl. Neomyrmecridium gen. nov.), Pararamichloridium caricicola on Carex sp., Xenodactylaria thailandica (incl. Xenodactylariaceae fam. nov. and Xenodactylaria gen. nov.), Neomyrmecridium asiaticum and Cymostachys thailandica from unidentified vine. USA, Carolinigaster bonitoi (incl. Carolinigaster gen. nov.) from soil, Penicillium fortuitum from house dust, Phaeotheca shathenatiana (incl. Phaeothecaceae fam. nov.) from twig and cone litter, Pythium wohlseniorum from stream water, Superstratomyces tardicrescens from human eye, Talaromyces iowaense from office air. Vietnam, Fistulinella olivaceoalba on soil. Morphological and culture characteristics along with DNA barcodes are provided.
TL;DR: The challenges of the assembly of polyploid plant genomes are reviewed, and recent advances in genomic resources and functional tools in molecular genetics and breeding are presented.
Abstract: Polyploidy or duplication of an entire genome occurs in the majority of angiosperms. The understanding of polyploid genomes is important for the improvement of those crops, which humans rely on for sustenance and basic nutrition. As climate change continues to pose a potential threat to agricultural production, there will increasingly be a demand for plant cultivars that can resist biotic and abiotic stresses and also provide needed and improved nutrition. In the past decade, Next Generation Sequencing (NGS) has fundamentally changed the genomics landscape by providing tools for the exploration of polyploid genomes. Here, we review the challenges of the assembly of polyploid plant genomes, and also present recent advances in genomic resources and functional tools in molecular genetics and breeding. As genomes of diploid and less heterozygous progenitor species are increasingly available, we discuss the lack of complexity of these currently available reference genomes as they relate to polyploid crops. Finally, we review recent approaches of haplotyping by phasing and the impact of third generation technologies on polyploid plant genome assembly.
TL;DR: This mini-review summarizes recent development and perspectives of phages used as antimicrobial agents in plant and animal agriculture at the farm level and the main pathogens and their adjoining phage therapies are discussed.
Abstract: The ability of agriculture to continually provide food to a growing world population is of crucial importance. Bacterial diseases of plants and animals have continually reduced production since the advent of crop cultivation and animal husbandry practices. Antibiotics have been used extensively to mitigate these losses. The rise of antimicrobial resistant (AMR) bacteria, however, together with consumers’ calls for antibiotic-free products, presents problems that threaten sustainable agriculture. Bacteriophages (phages) are proposed as bacterial population control alternatives to antibiotics. Their unique properties make them highly promising but challenging antimicrobials. The use of phages in agriculture also presents a number of unique challenges. This mini-review summarizes recent development and perspectives of phages used as antimicrobial agents in plant and animal agriculture at the farm level. The main pathogens and their adjoining phage therapies are discussed.
TL;DR: In this article, the authors highlight the value that can be added to this industrial co-product to generate new pharmaceutical, medical, nutraceuticals or functional food products, which is the main byproduct from the coca industry constituting 67-76% of the cocoa fruit weight.
Abstract: Background Cocoa Pod Husk (CPH) is the main by-product from the coca industry constituting 67–76% of the cocoa fruit weight. This waste represents an important, and challenging, economic, environmental renewable opportunity, since ten tons of wet CPH are generated for each ton of dry cocoa beans. Scope and approach This review highlights the value that can be added to this industrial co-product to generate new pharmaceutical, medical, nutraceuticals or functional food products. Key findings and conclusions The quality and functionality of cocoa pod husk (CPH) has being improving through processing (fermentation, enzymatic hydrolysis, and combustion, among others), guiding to their use as source of volatile fragrance compounds, lipase extraction, skin whitening, skin hydration and sun screening, ruminants’ food, vegetable gum, organic potash, antibacterial and nanoparticles synthesis with antioxidant and larvicidal activities. However, their exploration to produce high-value-added products, specially for the food industry, is limited as well as their potential health benefits. Cocoa pod husk, the main by-product from cacao industry (up to 76%), is an abundant, inexpensive, and renewable source of bioactive compounds like dietary fiber, pectin, antioxidant compounds, minerals and theobromine, justifying their valorization. This review highlights the value addition that can be achieved with this valuable industrial co-product to generate new pharmaceutical, medical, nutraceuticals or functional food products.
TL;DR: Challenges and obstacles to producing silages under hot and cold conditions are identified and strategies for addressing these challenges are discussed.
TL;DR: It is reported that turnip mosaic virus infection activates autophagy in plants and that Beclin1 (ATG6), a core component of autophagic component, binds the viral polymerase and inhibits virus replication.
Abstract: Autophagy emerges as an essential immunity defense against intracellular pathogens. Here we report that turnip mosaic virus (TuMV) infection activates autophagy in plants and that Beclin1 (ATG6), a core component of autophagy, inhibits virus replication. Beclin1 interacts with NIb, the RNA-dependent RNA polymerase (RdRp) of TuMV, via the highly conserved GDD motif and the interaction complex is targeted for autophagic degradation likely through the adaptor protein ATG8a. Beclin1-mediated NIb degradation is inhibited by autophagy inhibitors. Deficiency of Beclin1 or ATG8a enhances NIb accumulation and promotes viral infection and vice versa. These data suggest that Beclin1 may be a selective autophagy receptor. Overexpression of a Beclin1 truncation mutant that binds to NIb but lacks the ability to mediate NIb degradation also inhibits virus replication. The Beclin1–RdRp interaction further extends to several RNA viruses. Thus Beclin1 restricts viral infection through suppression and also likely autophagic degradation of the viral RdRp. Plant DNA virus replication is inhibited by autophagy, but the interplay between plant RNA viruses and autophagy is less clear. Here, Li et al. show that turnip mosaic virus infection activates autophagy and that Beclin1, a core autophagy component, binds the viral polymerase and inhibits virus replication.
TL;DR: It is concluded that soil biota may be a neglected factor determining ecosystem stability through their direct and indirect effects on plant diversity, the net productivity of an ecosystem, and compensatory dynamics among plant species, and via altering ecosystem resistance and resilience.
TL;DR: This analysis validates previous observations about effector functions, and also highlights some interesting features regarding effector specificity as well as functional diversification of phytopathogen virulence strategies.
Abstract: Phytopathogens translocate effector proteins into plant cells where they sabotage the host cellular machinery to promote infection. An individual pathogen can translocate numerous distinct effectors during the infection process to target an array of host macromolecules (proteins, metabolites, DNA, etc.) and manipulate them using a variety of enzymatic activities. In this review, we have surveyed the literature for effector targets and curated them to convey the range of functions carried out by phytopathogenic proteins inside host cells. In particular, we have curated the locations of effector targets, as well as their biological and molecular functions and compared these properties across diverse phytopathogens. This analysis validates previous observations about effector functions (e.g. immunosuppression), and also highlights some interesting features regarding effector specificity as well as functional diversification of phytopathogen virulence strategies.
TL;DR: Evidence is presented suggesting that the loss of RNAi and cytosine DNA methylation triggered transposon attrition, which resulted in shortening of centromere length during evolution.
Abstract: The centromere DNA locus on a eukaryotic chromosome facilitates faithful chromosome segregation. Despite performing such a conserved function, centromere DNA sequence as well as the organization of sequence elements is rapidly evolving in all forms of eukaryotes. The driving force that facilitates centromere evolution remains an enigma. Here, we studied the evolution of centromeres in closely related species in the fungal phylum of Basidiomycota. Using ChIP-seq analysis of conserved inner kinetochore proteins, we identified centromeres in three closely related Cryptococcus species: two of which are RNAi-proficient, while the other lost functional RNAi. We find that the centromeres in the RNAi-deficient species are significantly shorter than those of the two RNAi-proficient species. While centromeres are LTR retrotransposon-rich in all cases, the RNAi-deficient species lost all full-length retroelements from its centromeres. In addition, centromeres in RNAi-proficient species are associated with a significantly higher level of cytosine DNA modifications compared with those of RNAi-deficient species. Furthermore, when an RNAi-proficient Cryptococcus species and its RNAi-deficient mutants were passaged under similar conditions, the centromere length was found to be occasionally shortened in RNAi mutants. In silico analysis of predicted centromeres in a group of closely related Ustilago species, also belonging to the Basidiomycota, were found to have undergone a similar transition in the centromere length in an RNAi-dependent fashion. Based on the correlation found in two independent basidiomycetous species complexes, we present evidence suggesting that the loss of RNAi and cytosine DNA methylation triggered transposon attrition, which resulted in shortening of centromere length during evolution.
TL;DR: Overall the SOCsp for French soils appears to be very large when compared to previous total SOC stocks estimates, and might thus be very sensitive to land use change.
TL;DR: The combined anti-cancer effects of CGA with its major colonic microbial metabolites, caffeic acid (CA), 3-phenylpropionic acid (3-PPA) and benzoic Acid (BA), needs elucidation as they occur together in colonic digesta.
Abstract: Chlorogenic acid (CGA) decreases colon cancer-cell proliferation but the combined anti-cancer effects of CGA with its major colonic microbial metabolites, caffeic acid (CA), 3-phenylpropionic acid (3-PPA) and benzoic acid (BA), needs elucidation as they occur together in colonic digesta. Caco-2 cancer cells were treated for 24 h with the four compounds individually (50–1000 µM) and as an equimolar ratio (1:1:1:1; MIX). The effective concentration to decrease cell proliferation by 50% (EC50) was lower for MIX (431 ± 51.84 µM) and CA (460 ± 21.88) versus CGA (758 ± 19.09 µM). The EC50 for cytotoxicity measured by lactate dehydrogenase release in MIX (527 ± 75.34 µM) showed more potency than CA (740 ± 38.68 µM). Cell proliferation was decreased by 3-PPA and BA at 1000 µM with no cytotoxicity. Cell-cycle arrest was induced at the S-phase by CA (100 µM), MIX (100 µM), CGA (250 µM) and 3-PPA (500 µM) with activation of caspase-3 by CGA, CA, MIX (500 and 1000 µM). Mitochondrial DNA content was reduced by 3-PPA (1000 µM). The anti-cancer effects occurred at markedly lower concentrations of each compound within MIX than when provided singly, indicating that they function together to enhance anti-colon cancer activities.
TL;DR: Knowing the mode of action and tissue distribution of HS will provide a better perspective for defining the cues and signaling crosstalk of HS that mediate various metabolic and hormonal networks operating in plant systems.
Abstract: Humic substances (HSs) have considerable effects on soil fertility and crop productivity owing to their unique physiochemical and biochemical properties, and play a vital role in establishing biotic and abiotic interactions within the plant rhizosphere. A comprehensive understanding of the mode of action and tissue distribution of HS is, however, required, as this knowledge could be useful for devising advanced rhizospheric management practices. These substances trigger various molecular processes in plant cells, and can strengthen the plant's tolerance to various kinds of abiotic stresses. HS manifest their effects in cells through genetic, post-transcriptional, and post-translational modifications of signaling entities that trigger different molecular, biochemical, and physiological processes. Understanding of such fundamental mechanisms will provide a better perspective for defining the cues and signaling crosstalk of HS that mediate various metabolic and hormonal networks operating in plant systems. Various regulatory activities and distribution strategies of HS have been discussed in this review.
Institut national de la recherche agronomique1, Queensland University of Technology2, AgResearch3, University of Aberdeen4, Michigan State University5, Indian Agricultural Research Institute6, University of Florence7, Counterintelligence Field Activity8, Colorado State University9, University of Sassari10, Universidade Federal de Santa Maria11, Agriculture and Agri-Food Canada12, Scotland's Rural College13, Landcare Research14, Université Paris-Saclay15, Agricultural Research Service16, Commonwealth Scientific and Industrial Research Organisation17, International Livestock Research Institute18, ETH Zurich19, Potsdam Institute for Climate Impact Research20, Plant & Food Research21, Rothamsted Research22, Chinese Academy of Sciences23
TL;DR: An international model comparison and benchmarking exercise, showing the potential of multi-model ensembles to predict productivity and nitrous oxide (N2 O) emissions for wheat, maize, rice and temperate grasslands.
Abstract: Simulation models are extensively used to predict agricultural productivity and greenhouse gas emissions. However, the uncertainties of (reduced) model ensemble simulations have not been assessed systematically for variables affecting food security and climate change mitigation, within multi-species agricultural contexts. We report an international model comparison and benchmarking exercise, showing the potential of multi-model ensembles to predict productivity and nitrous oxide (N2O) emissions for wheat, maize, rice and temperate grasslands. Using a multi-stage modelling protocol, from blind simulations (stage 1) to partial (stages 2 –4) and full calibration (stage 5), 24 process-based biogeochemical models were assessed individually or as an ensemble against long-term experimental data from four temperate grassland and five arable crop rotation sites spanning four continents.Comparisons were performed by reference to the experimental uncertainties of observed yields and N2O emissions. Results showed that across sites and crop/grassland types, 23%–40% of the uncalibrated individual models were within two standard deviations (SD) of observed yields, while 42 (rice) to 96% (grasslands) of the models were within 1 SD of observed N2O emissions. At stage 1, ensembles formed by the three lowest prediction model errors predicted both yields and N2O emissions within experimental uncertainties for 44% and 33% of the crop and grass-land growth cycles, respectively. Partial model calibration (stages 2–4) markedly reduced prediction errors of the full model ensemble E-median for crop grain yields (from 36% at stage 1 down to 4% on average) and grassland productivity (from 44%to 27%) and to a lesser and more variable extent for N2O emissions. Yield-scaled N2O emissions (N2O emissions divided by crop yields) were ranked accurately by three-model ensembles across crop species and field sites. The potential of using process-based model ensembles to predict jointly productivity and N2O emissions at field scale is discussed.
TL;DR: In this paper, the authors evaluated the response of Brassica napus L, from flowering to seed development, to two temperature and water treatments and a combination of these treatments, and found that the reduction in the net photosynthetic assimilation rate was caused by combinations of heat and drought (heat + drought) treatments, by drought alone, and, to a lesser extent, by heat alone.
Abstract: Photosynthetic assimilation is remarkably altered by heat and drought, and this depends on the individual or combined occurrence of stressors and their respective intensities and durations. Abiotic stressors may also alter the nutritional quality and economic value of crops. In this controlled greenhouse study, we evaluated the response of Brassica napus L., from flowering to seed development, to two temperature and water treatments and a combination of these treatments. The diffusional limitations of stomatal conductance and mesophyll conductance on photosynthesis, as well as resource-use efficiency (particularly water and nitrogen), were assessed. In addition, the effects of stressors on the seed fatty acid content and composition and the total protein content were examined. The results showed that the reduction in the net photosynthetic assimilation rate was caused by combinations of heat and drought (heat + drought) treatments, by drought alone, and, to a lesser extent, by heat alone. The stomatal conductance decreased under drought and heat + drought treatments but not under heat. Conversely, the mesophyll conductance was reduced significantly in the plants exposed to heat and heat + drought but not in the plants exposed to drought alone. The carboxylation efficiency rate and the electron transport rate were reduced under the heat treatment. The seed yield was reduced by 85.3% under the heat treatment and, to a lesser extent, under the drought treatment (31%). This emphasizes the devastating effects of hotter weather on seed formation and development. Seed oil content decreased by 52% in the plants exposed to heat, the protein content increased under all the stress treatments. Heat treatment had a more deleterious effect than drought on the seed oil composition, leading to enhanced levels of saturated fatty oils and, consequently, desaturation efficiency, a measure of oil frying ability. Overall, this study showed that except for the photosynthetic assimilation rate and stomatal conductance, heat, rather than drought, negatively affected the photosynthetic capacity, yield, and oil quality attributes when imposed during the flowering and silique-filling stages. This result highlights the necessity for a better understanding of heat tolerance mechanisms in crops to help to create germplasms that are adapted to rapid climate warming.