Showing papers by "Agriculture and Agri-Food Canada published in 2022"

Subsoiling and conversion to conservation tillage enriched nitrogen cycling bacterial communities in sandy soils under long-term maize monoculture

Abstract: Desertification degrades soil health and severely reduces crop productivity. Conventional tillage practices can amplify these problems in arid and semi-arid regions. For semi-arid regions in Inner Mongolia, China, the effects of introducing different tillage practices such as subsoiling (SS), straw mulching (SM), and no-tillage (NT) on otherwise long-term conventional tilled maize monoculture systems, were examined in the context of sandy soil bacterial and archaeal community diversity. Results showed that after three to four years of introduction, subsoiling and conversion to conservation tillage practices had no immediate effect on the alpha-diversity of the soil microbial communities. The beta-diversity of the soil microbial communities was less affected by the introduced tillage practices than by the growing season conditions, soil moisture, total nitrogen, soil macro-aggregate, and organic matter. Importantly, the introduced tillage practices had a notable effect on soil microbial communities associated with nitrogen (N) cycling processes, especially N fixation, nitrate reduction, nitrification, and denitrification. In particular, several years of tillage change from long-term conventional tillage enhanced the abundance of KEGG orthologs (KOs) associated with N fixation function involving species in Rhodoplanes, Nitrospira, Skermanella, and Rhizobium according to PICURSt prediction. Rhodoplanes spp. are involved in nitrate reduction and denitrification processes, and Nitrospira spp. associated with nitrite oxidization. We conclude that, for maize monoculture systems in semi-arid sandy soils, the soil bacterial and archaeal communities associated with many beneficial N cycling processes can be significantly impacted by only three to four years of introduced conservation and subsoiling tillage practices.

Two independent approaches converge to the cloning of a new <i>Leptosphaeria maculans</i> avirulence effector gene, <i>AvrLmS‐Lep2</i>

Abstract: Brassica napus (oilseed rape, canola) seedling resistance to Leptosphaeria maculans, the causal agent of blackleg (stem canker) disease, follows a gene-for-gene relationship. The avirulence genes AvrLmS and AvrLep2 were described to be perceived by the resistance genes RlmS and LepR2, respectively, present in B. napus 'Surpass 400'. Here we report cloning of AvrLmS and AvrLep2 using two independent methods. AvrLmS was cloned using combined in vitro crossing between avirulent and virulent isolates with sequencing of DNA bulks from avirulent or virulent progeny (bulked segregant sequencing). AvrLep2 was cloned using a biparental cross of avirulent and virulent L. maculans isolates and a classical map-based cloning approach. Taking these two approaches independently, we found that AvrLmS and AvrLep2 are the same gene. Complementation of virulent isolates with this gene confirmed its role in inducing resistance on Surpass 400, Topas-LepR2, and an RlmS-line. The gene, renamed AvrLmS-Lep2, encodes a small cysteine-rich protein of unknown function with an N-terminal secretory signal peptide, which is a common feature of the majority of effectors from extracellular fungal plant pathogens. The AvrLmS-Lep2/LepR2 interaction phenotype was found to vary from a typical hypersensitive response through intermediate resistance sometimes towards susceptibility, depending on the inoculation conditions. AvrLmS-Lep2 was nevertheless sufficient to significantly slow the systemic growth of the pathogen and reduce the stem lesion size on plant genotypes with LepR2, indicating the potential efficiency of this resistance to control the disease in the field.

Health Benefits of Cereal Grain- and Pulse-Derived Proteins

Abstract: Pulses and whole grains are considered staple foods that provide a significant amount of calories, fibre and protein, making them key food sources in a nutritionally balanced diet. Additionally, pulses and whole grains contain many bioactive compounds such as dietary fibre, resistant starch, phenolic compounds and mono- and polyunsaturated fatty acids that are known to combat chronic disease. Notably, recent research has demonstrated that protein derived from pulse and whole grain sources contains bioactive peptides that also possess disease-fighting properties. Mechanisms of action include inhibition or alteration of enzyme activities, vasodilatation, modulation of lipid metabolism and gut microbiome and oxidative stress reduction. Consumer demand for plant-based proteins has skyrocketed primarily based on the perceived health benefits and lower carbon footprint of consuming foods from plant sources versus animal. Therefore, more research should be invested in discovering the health-promoting effects that pulse and whole grain proteins have to offer.

Dual-target inhibitors of poly (ADP-ribose) polymerase-1 for cancer therapy: Advances, challenges, and opportunities

Abstract: PARP1 plays a crucial role in DNA damage repair, making it an essential target for cancer therapy. PARP1 inhibitors are widely used to treat BRCA-deficient malignancies, and six PARP inhibitors have been approved for clinical use. However, excluding the great clinical success of PARP inhibitors, the concomitant toxicity, drug resistance, and limited scope of application restrict their clinical efficacy. To find solutions to these problems, dual-target inhibitors have shown great potential. In recent years, several studies have linked PAPR1 to other primary cancer targets. Many dual-target inhibitors have been developed using structural fusion, linkage, or library construction methods, overcoming the defects of many single-target inhibitors of PARP1 and achieving great success in clinical cancer therapy. This review summarizes the advance of dual-target PARP1 inhibitors in recent years, focusing on their structural optimization process, structure-activity relationships (SARs), and in vitro or in vivo analysis results.

Minimizing cosecant-squared pattern side lobe level of linear array antenna by genetic algorithm and optimizing feed network

Abstract: This paper designs and synthesizes a 12-element linear array of microstrip patch antenna with cosecant-squared pattern for radar applications at the frequency 9.6 GHz. The antenna array consists of three microstrip sublayers including two lower sublayers designed for feed network, and radiating patches located on the upper sublayer which are excited through a slot in the ground plate. One of the most important advantages of this antenna array is the cross-polarization discrimination of less than −50 dB which is the result of removing undesirable and unwanted radiations caused by feed network. The Genetic Algorithm (GA) optimization method has been used to synthesize cosecant-squared pattern with considering the mutual coupling effect of array elements. In this method, the amplitude and phase of each element in the far field has been calculated by taking into account the mutual coupling effect, and applied in the optimization process. Finally, the feed network has been designed according to the amplitudes and phases obtained from the GA. The simulation results confirm the validity of all design and synthesis stages.

Processing Technologies to Produce Plant Protein Concentrates and Isolates

Abstract: The demand for new healthy food ingredients and products is on the rise. The global plant-based protein market is projected to grow from US$10.3 billion in 2020 to US$14.5 billion by 2025, recording a compound annual growth rate of 7.1% during the forecast period. Plant protein ingredients, namely concentrate (65–90% w/w protein dry basis) and isolate (90%+ w/w protein dry basis), are increasingly finding their way into a broad range of food products, not only due to their nutritional value but also given that such ingredients interact well with other food ingredients. However, their functional properties differ depending on the protein source and on the way the ingredients are processed and/or extracted. Key functional properties include solubility, water- and fat-adsorption capacities, emulsifying properties, foam-forming capacity and stability, and gelling properties. The main plant protein sources are oilseeds (soybean, canola, flax, etc.), pulses (pea, chickpea, bean, lentil, etc.), and cereals (wheat, corn, barley, etc.), with soybean, wheat, pea and corn being the current key players in the plant-based foods market. However, new alternative sources are finding their way into the market, including barley, bean, camelina, canola, chickpea, flax, hemp, lentil, mustard, peanut, pea, quinoa, rice, sesame, sorghum, and sunflower. Plant proteins can be extracted directly from the oilseeds, pulses and cereals moreover, several sources of plant proteins are from different agro-industrial waste materials. The redirection of by-products, which are usually used as animal feed livestock, to human consumption helps to preserve the environment, ensure food security and support the sustainability of food systems. Many technologies are involved in the production of plant protein concentrates and isolates, including milling to obtain flour, and drying to dry the protein extracts into a powder when wet extraction is carried out. However, the core of the process is protein extraction and separation. Protein extraction and separation processes can be classified into two main categories: dry fractionation and wet extraction processes. Wet extraction processes are the most common methods used to produce plant protein ingredients and include conventional processes such as alkaline extraction–isoelectric precipitation (AE-IP), salt extraction–dialysis (SED), and micellar precipitation (MP). They also include emerging processes such as enzyme-assisted extraction, ultrasound-assisted extraction, microwave-assisted extraction, and membrane technologies. The selection of the most appropriate plant protein extraction/separation process depends on many factors, such as the composition of the oilseeds, pulses, and cereals (fiber-rich content, polysaccharides, and fat), the part that is used, the targeted level of proteins in the ingredients, and so on. This chapter provides a review of the processing technologies used to produce plant protein concentrates and isolates, and discusses their impact on the main plant protein sources.

Diversifying crop rotations enhances agroecosystem services and resilience

Abstract: A significant challenge in our time is to produce sufficient agricultural products on limited farmable land to meet the needs for food, feed, fiber, and industrial uses in the face of a changing climate. Conventional cropping systems mostly rely on inputs, such as fertilizers and pesticides, to boost crop yields. However, excessive inputs increase production costs and entail more direct and indirect emissions of greenhouse gases to the atmosphere that negatively impact the environment. Finding sustainable ways to increase crop productivity with little or no impact on the environment is the primary goal of modern agriculture. This review reveals that temporal-spatial diversification of crop rotations is critically needed to advance toward this goal sustainably. We find that (i) intensified crop rotations enhance carbon conversion from atmospheric CO2 into plant biomass and thus sequester more carbon into soil; (ii) diversified crop mixtures improve system resilience, i.e., increased resistance to pest/disease incidence and weed infestation, and faster recovery after removal of the abiotic or biotic stress; (iii) diversifying crop rotations increases crop yields at the system level with improved water and fertilizer use efficiencies; (iv) legume-based crop rotations reduce the need for synthetic nitrogen fertilizers thus lowering N2O and CO2 emissions to the atmosphere; (v) crop diversity leads to soil microbiome diversity that optimizes soil microenvironment, improving soil health. We believe that developing and adopting of diversified cropping systems are key factors for agricultural policy setting and a top priority for on-farm decision-making to increase crop productivity and enhance soil health, while reducing negative environmental impacts.

Mechanistic insights into the digestion of complex dietary fibre by the rumen microbiota using combinatorial high-resolution glycomics and transcriptomic analyses

Abstract: There is a knowledge gap regarding the factors that impede the ruminal digestion of plant cell walls or if rumen microbiota possess the functional activities to overcome these constraints. Innovative experimental methods were adopted to provide a high-resolution understanding of plant cell wall chemistries, identify higher-order structures that resist microbial digestion, and determine how they interact with the functional activities of the rumen microbiota. We characterized the total tract indigestible residue (TTIR) from cattle fed a low-quality straw diet using two comparative glycomic approaches: ELISA-based glycome profiling and total cell wall glycosidic linkage analysis. We successfully detected numerous and diverse cell wall glycan epitopes in barley straw (BS) and TTIR and determined their relative abundance pre- and post-total tract digestion. Of these, xyloglucans and heteroxylans were of higher abundance in TTIR. To determine if the rumen microbiota can further saccharify the residual plant polysaccharides within TTIR, rumen microbiota from cattle fed a diet containing BS were incubated with BS and TTIR ex vivo in batch cultures. Transcripts coding for carbohydrate-active enzymes (CAZymes) were identified and characterized for their contribution to cell wall digestion based on glycomic analyses, comparative gene expression profiles, and associated CAZyme families. High-resolution phylogenetic fingerprinting of these sequences encoded CAZymes with activities predicted to cleave the primary linkages within heteroxylan and arabinan. This experimental platform provides unprecedented precision in the understanding of forage structure and digestibility, which can be extended to other feed-host systems and inform next-generation solutions to improve the performance of ruminants fed low-quality forages.

Crop Water Deficit and Supplemental Irrigation Requirements for Potato Production in a Temperate Humid Region (Prince Edward Island, Canada)

Abstract: The global increase in potato production and yield is expected to lead to increased irrigation needs and this has prompted concerns with respect to the sustainability of irrigation water sources, such as groundwater. The magnitude, and inter- and intra-annual variation, of the crop water requirements and irrigation needs for potato production together with their impact on aquifer storage in a temperate humid region (Prince Edward Island, Canada) were estimated by using long-term (i.e., 2010–2019) daily soil water content (SWC). The amount of supplemental irrigation required for the minimal irrigation scenario (SWC = 70% of field capacity; 0.7 FC) was relatively small (i.e., 17.0 mm); however, this increased significantly, to 85.2 and 189.6 mm, for the moderate (SWC = 0.8 FC) and extensive (SWC = 0.9 FC) irrigation scenarios, respectively. The water supply requirement for the growing season (GS) increased to 154.9 and 344.7 mm for a moderately efficient irrigation system (55% efficiency) for the SWC = 0.8 FC and SWC = 0.9 FC irrigation scenarios, respectively. Depending on the efficiency and the areal extent of the irrigation system, the irrigation water supply requirement can approach or exceed both the GS and annual groundwater recharge. The methodology developed in this research has been translated into a free online tool (SWIB—Soil Water Stress, Irrigation Requirement and Water Balance), which can be applied to other areas or crops where an estimation of soil water deficit and irrigation requirement is sought.

Understanding the root rot and wilting complex of raspberry: current research advances and future perspectives

Abstract: Red raspberry (Rubus idaeus L.) is an important fruit crop in British Columbia, Canada, and the Pacific Northwest (PNW) region of the USA, as well as in other regions of the world. Root rot and wilting complex (RRWC), primarily caused by Phytophthora rubi, is the most important biotic constraint responsible for declining raspberry production in these regions, causing millions of dollars in losses. Other root-infecting fungal species and the root lesion nematode (Pratylenchus penetrans) may also be found associated with the disease complex. The average lifespan of raspberry plantings in the PNW is 10 to 12 years, which is reduced to 5 years by the disease complex. Phytophthora spp. play a predominant role in the RRWC complex due to the persistent nature of oospores, rapid dispersal of inoculum, and the polycyclic nature of infection, all of which increase disease severity. In this review, we discuss the current understanding of Phytophthora spp. and other pathogens associated with the RRWC, including pathogen biology and the disease cycle, the impact of infection on the plant, as well as current and potential cultural, biological, and chemical options for management. In addition, we discuss breeding efforts for disease resistance, including conventional and molecular approaches to identify sources of resistance, molecular markers linked to potential resistance genes, and their incorporation into elite breeding materials or cultivars. We also present the current gaps in knowledge, unique challenges, and future perspectives in sustainable disease management of this important disease complex.

Short-term germination of faba bean (Vicia faba L.) and the effect on selected chemical constituents

Abstract: Selected chemical compounds of five faba bean (FB) cultivars; Snowdrop (low tannin), Taboar (high tannin), Snowbird (low tannin), Fabelle (low vicine & convicine), and Malik (high tannin) that were grown in North America (3 production years) were determined. The effect of short-term germination (24 h, 48 h, and 72 h) on the levels of phytic acid, vicine/convicine (v/cv), oligosaccharides, and total phenolics were evaluated. On average, FB contained 2% phytic acid and there was no difference between the 5 cultivars. Fabelle presented the lowest level of v/cv of 1 and 0.4 mg/g, respectively while the others had 7.27–10.82 and 3.53–3.93 mg/g, respectively. No significant difference was found among cultivars for oligosaccharides content. Content of total phenolics differed significantly (p ≤ 0.05) between FB cultivars. Snowdrop and Snowbird had the highest total phenolic content of 48.4 and 48.3 mg/g, respectively, while Fabelle had the lowest level of 10.8 mg/g. All cultivars showed significantly (p ≤ 0.05) reduced contents of raffinose (100%), stachyose (60%), verbascose (80%) at 72 h. Germination had no significant effect on phytic acid, vicine (except Snowbird), and convicine levels. At 48-h, Snowdrop and Snowbird seeds only showed 17-18% reduction (p ≤ 0.05) in total phenolic content. Germination between 48 to 72 h is an option to produce FB seeds with very low levels of oligosaccharides.

Effect of commercial slow-release urea product on in vitro rumen fermentation and ruminal microbial community using RUSITEC technique

Abstract: Abstract Background The objectives of this study were to determine the effect of commercial slow-release urea (SRU) on in vitro fermentation characteristics, nutrient digestibility, gas production, microbial protein synthesis and bacterial community using a rumen simulation technique (RUSITEC). The experiment was a completely randomized design with four treatments and four replications of each treatment. Treatments were: control diet (no SRU addition), control diet plus 0.28% SRU (U28), or plus 0.56% SRU (U56), and control diet that was modified substituting a part of soybean meal equivalent to 0.35% SRU (MU35; dry matter [DM] basis). The experiment consisted of 8 d of adaptation and 7 d of data and sample collection. Rumen inoculum was obtained from three ruminally fistulated Angus cows fed the same diet to the substrate incubated. Results Digestibility of DM, organic matter (OM), crude protein (CP), fibre and starch was not affected, but daily production of gas ( P < 0.07) and methane ( P < 0.05) was quadratically increased with increasing SRU supplementation. The increase of SRU addition did not affect fermentation pH and total volatile fatty acid (VFA) production, whereas linearly ( P < 0.01) decreased proportion of propionate, and linearly ( P < 0.01) increased acetate to propionate ratio and ammonia nitrogen (N) concentration. The microbial N efficiency was also linearly ( P < 0.03) improved with increasing supplementation of SRU. In comparison with control diet, the dietary substitution of SRU for part of soybean meal increased ( P < 0.05) the digestibility of DM, OM and CP and decreased ( P < 0.02) the total gas production. The total VFA production and acetate to propionate ratio did not differ between control and MU35, whereas the proportion of butyrate was lower ( P < 0.05) and that of branched-chain VFA was greater ( P < 0.05) with MU35 than control diet. Total and liquid-associated microbial N production as well as ammonia N concentration were greater ( P < 0.03) with MU35 than control diet. Observed operational taxonomic units (OTUs), Shannon diversity index, and beta diversity of the microbial community did not differ among treatments. Taxonomic analysis revealed no effect of adding SRU on the relative abundance of bacteria at the phylum level, while at the genus level, the beneficial impact of SRU on relative abundance of Rikenellaceae and Prevotellaceae in feed particle-associated bacteria, and the abundance of Roseburia in liquid associate bacteria was greater ( P < 0.05) with MU35. Conclusions Supplementation of a dairy cow diet with SRU showed potential of increase in ammonia N concentration and microbial protein production, and change fermentation pattern to more acetate production. Adding SRU in dairy cow diet also showed beneficial effect on improving digestibility of OM and fibre. The results suggest that SRU can partially substitute soybean meal in dairy cow diet to increase microbial protein production without impairing rumen fermentation.

Main effect and epistatic QTL affecting spike shattering and association with plant height revealed in two spring wheat (Triticum aestivum L.) populations

Abstract: Abstract Key message A major QTL on chromosome arm 4BS was associated with reduced spike shattering and reduced plant height in coupling phase, and a second major QTL associated with reduced spike shattering was detected on chromosome arm 5AL in the same wheat variety Carberry. Abstract Spike shattering can cause severe grain yield loss in wheat. Development of cultivars with reduced shattering but having easy mechanical threshability is the target of wheat breeding programs. This study was conducted to determine quantitative trait loci (QTL) associated with shattering resistance, and epistasis among QTL in the populations Carberry/AC Cadillac and Carberry/Thatcher. Response of the populations to spike shattering was evaluated near Swift Current, SK, in four to five environments. Plant height data recorded in different locations and years were used to determine the relationship of the trait with spike shattering. Each population was genotyped and mapped with the wheat 90 K Illumina iSelect SNP array. Main effect QTL were analyzed by MapQTL 6, and epistatic interactions between main effect QTL were determined by QTLNetwork 2.0. Correlations between height and shattering ranged from 0.15 to 0.49. Carberry contributed two major QTL associated with spike shattering on chromosome arms 4BS and 5AL, detected in both populations. Carberry also contributed two minor QTL on 7AS and 7AL. AC Cadillac contributed five minor QTL on 1AL, 2DL, 3AL, 3DL and 7DS. Nine epistatic QTL interactions were identified, out of which the most consistent and synergistic interaction, that reduced the expression of shattering, occurred between 4BS and 5AL QTL. The 4BS QTL was consistently associated with reduced shattering and reduced plant height in the coupling phase. The present findings shed light on the inheritance of shattering resistance and provide genetic markers for manipulating the trait to develop wheat cultivars.

Development and application of multiplex targeted-sequencing approaches to identify Phytophthora species associated with root rot and wilting complex of red raspberry

Abstract: Phytophthora species are primary causal agents of raspberry root rot and wilting complex (RRWC), a disease complex that is of major concern to raspberry producers worldwide. Accurate identification of the causal agents is a first step for effective disease management. Advancements in molecular diagnostics can facilitate the detection of multiple pathogen species associated with this disease complex. We developed multiplex targeted-sequencing methods using degenerate primers for heat shock protein 90, elongation factor 1α and β-tubulin genes to identify Phytophthora species causing RRWC. One hundred and twenty-eight isolates recovered during 2018 to 2020 from diverse fields in major raspberry growing areas of British Columbia (BC) were sequenced and identified by comparing with known reference sequences of 142 Phytophthora species, 111 Pythium species, and nine Phytopythium species in the NCBI database. This multiplex targeted-sequencing method was highly specific and identified two species of Phytophthora associated with RRWC. These were P. rubi (85% of isolates) and P. gonapodyides (15% of isolates). Phytophthora rubi was predominantly isolated from the cultivars 'Chemainus' (51%), 'Rudi' (27%) and 'Meeker' (15%), whereas P. gonapodyides was predominately isolated from the moderately resistant cultivar 'Cascade Bounty'. Pathogenicity studies on intact plants and detached leaves confirmed that P. rubi and P. gonapodyides can cause symptoms of RRWC on raspberry, thus fulfilling Koch's postulates. To our knowledge, this is the first report of P. gonapodyides as a causal agent of RRWC on raspberry in BC. This study provides novel insights into the identification and species composition of Phytophthora associated with RRWC in raspberry production systems.

Applications of CPPs in Genome Editing of Plants

Abstract: Cell penetrating peptides (CPPs) are short peptides that are able to translocate themselves and their cargo into cells. The progressive and continuous application of CPPs in various fields of basic and applied research shows that they are efficient delivery vectors for an assortment of biomolecules, including nucleic acids and proteins. This feature makes CPPs an excellent tool for modification of plant genomes through transgenesis and genome editing. In this review, we present the progress during the last three decades in application of CPPs for delivery of DNA, RNA, and proteins into plant cells and tissues. Moreover, we highlight the exploiting of CPPs as advantageous and beneficial tool for plant genome editing via delivery of nuclease proteins, and provide a practical example of genome alternation through CPP-delivered nucleases. Finally, the current exploitation of peptides in organelle-specific DNA delivery and modification of organellar genomes is discussed.