Original Papers | Reviews + Book Chapters | Collaborations
816 views | +1 today
Follow
 
Scooped by ulcriv
onto Original Papers | Reviews + Book Chapters | Collaborations
Scoop.it!

Review in Int J Mol Sci • Torkamaneh Collaboration 2021 • Advances and Perspectives in Tissue Culture and Genetic Engineering of Cannabis

Review in Int J Mol Sci • Torkamaneh Collaboration 2021 • Advances and Perspectives in Tissue Culture and Genetic Engineering of Cannabis | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
For a long time, Cannabis sativa has been used for therapeutic and industrial purposes. Due to its increasing demand in medicine, recreation, and industry, there is a dire need to apply new biotechnological tools to introduce new genotypes with desirable traits and enhanced secondary metabolite production. Micropropagation, conservation, cell suspension culture, hairy root culture, polyploidy manipulation, and Agrobacterium-mediated gene transformation have been studied and used in cannabis. However, some obstacles such as the low rate of transgenic plant regeneration and low efficiency of secondary metabolite production in hairy root culture and cell suspension culture have restricted the application of these approaches in cannabis. In the current review, in vitro culture and genetic engineering methods in cannabis along with other promising techniques such as morphogenic genes, new computational approaches, clustered regularly interspaced short palindromic repeats (CRISPR), CRISPR/Cas9-equipped Agrobacterium-mediated genome editing, and hairy root culture, that can help improve gene transformation and plant regeneration, as well as enhance secondary metabolite production, have been highlighted and discussed.
No comment yet.
Your new post is loading...
Your new post is loading...
Scooped by ulcriv
Scoop.it!

Preprint in bioRxiv • Pérez-López Lab 2021 • Plasmodiophora brassicae in Mexico, from anecdote to fact 

Preprint in bioRxiv • Pérez-López Lab 2021 • Plasmodiophora brassicae in Mexico, from anecdote to fact  | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

For years, the presence of clubroot disease and its causal agent, Plasmodiophora brassicae, in Mexico has been given by granted. However, after a long search in the scientific literature in English and Spanish, as well as grey literature including thesis and government reports, we were not able to find any information regarding the actual detection of the pathogen, hosts affected, areas with the disease, or any real information about clubroot (‘hernia de la col’, in Mexico). To confirm if P. brassicae was indeed in Mexico, we started a true detective adventure. First, we identified agricultural communities in south-east Mexico known to grow cruciferous crops. Second, we asked to the growers if they have ever seen clubroot symptoms, showing them during the inquires pictures of the characteristic galls that might have been present in their crops. Third, we collected soil from two of the communities with positive response and grew an array of cruciferous in the soil as baits to “fish” the clubroot pathogen. We detected the presence of galls in the roots of 32 plants and observed the presence of resting spores. Through a P. brassicae specific PCR assay, we were able to confirm the presence of the clubroot pathogen in the samples and in Mexico for the very first time. This study is the first report and identification of P. brassicae in Mexico, opening the doors to understand the genetic diversity of this elusive and devastating plant pathogen.

No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Sci Rep • Pérez-López Collaboration 2021 • Detection of blueberry stunt phytoplasma in Eastern Canada using cpn60-based molecular diagnostic assays

Original Paper in Sci Rep • Pérez-López Collaboration 2021 • Detection of blueberry stunt phytoplasma in Eastern Canada using cpn60-based molecular diagnostic assays | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Blueberry stunt phytoplasma (BBSP; ‘Candidatus Phytoplasma asteris’) is an insect-vectored plant pathogen that causes severe yield losses in blueberry (Vaccinium corymbosum), which is the most valuable fruit crop in Canada. Rapid, field-based diagnostic assays are desirable tools for the control of BBSP, as part of an integrated, proactive approach to production management termed biovigilance. We designed and validated a chaperonin-60 (cpn60)-targeted LAMP assay for detection of BBSP, providing a rapid, low cost, field-deployable diagnostic option. Our validation demonstrates that the assay is reproducible, with high analytical specificity and improved sensitivity when compared with 16S rRNA nested PCR. We applied the validated LAMP assay to nearly 2000 blueberry samples from Québec and Nova Scotia over three growing seasons (2016–2018). Our surveys revealed that BBSP is present in most sites across both provinces, though detection of the pathogen in individual plants varied in different tissues across sampling dates and across years, and evidence of spread between plants was limited. To quantify pathogen load in select plants, we designed additional qPCR and ddPCR assays, also based on cpn60. We found that pathogen load fluctuates in individual plants, both within and between growing seasons. Finally, we designed an interactive map to visualize the results of our surveys. These results provide a validated diagnostic assay that can be used as part of a biovigilance strategy for detecting and controlling infections caused by BBSP.
No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in J Dairy Sci • Halde Collaboration 2021 • Milk production and efficiency of utilization of nitrogen, metabolizable protein, and amino acids are affected by protein and energy suppl...

Original Paper in J Dairy Sci • Halde Collaboration 2021 • Milk production and efficiency of utilization of nitrogen, metabolizable protein, and amino acids are affected by protein and energy suppl... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Alfalfa has a lower fiber digestibility and a greater concentration of degradable protein than grasses. Dairy cows could benefit from an increased digestibility of alfalfa fibers, or from a better match between nitrogen and energy supplies in the rumen. Alfalfa cultivars with improved fiber digestibility represent an opportunity to increase milk production, but no independent studies have tested these cultivars under the agroclimatic conditions of Canada. Moreover, decreasing metabolizable protein (MP) supply could increase N use efficiency while decreasing environmental impact, but it is often associated with a decrease in milk protein yield, possibly caused by a reduced supply of essential AA. This study evaluated the performance of dairy cows fed diets based on a regular or a reduced-lignin alfalfa cultivar and measured the effect of energy levels at low MP supply when digestible His (dHis), Lys (dLys), and Met (dMet) requirements were met. Eight Holstein cows were used in a double 4 × 4 Latin square design, each square representing an alfalfa cultivar. Within each square, 4 diets were tested: the control diet was formulated for an adequate supply of MP and energy (AMP_AE), whereas the 3 other diets were formulated to be deficient in MP (DMP; formulated to meet 90% of the MP requirement) with deficient (94% of requirement: DMP_DE), adequate (99% of requirement: DMP_AE), or excess energy supply (104% of requirement; DMP_EE). Alfalfa cultivars had no significant effect on all measured parameters. As compared with cows receiving AMP_AE, the dry matter intake of cows fed DMP_AE and DMP_EE was not significantly different but decreased for cows fed DMP_DE. The AMP_AE diet provided 103% of MP and 108% of NEL requirements whereas DMP_DE, DMP_AE, and DMP_EE diets provided 84, 87, and 87% of MP and 94, 101, and 107% of NEL requirements, respectively. In contrast to design, feeding DMP_EE resulted in a similar energy supply compared with AMP_AE, although MP supply has been effectively reduced. This resulted in a maintained milk and milk component yields and improved the efficiency of utilization of N, MP, and essential AA. The DMP diets decreased total N excretion, whereas DMP_AE and DMP_EE diets also decreased milk urea-N concentration. Reducing MP supply without negative effects on dairy cow performance is possible when energy, dHis, dLys, and dMet requirements are met. This could reduce N excretion and decrease the environmental impact of milk production.
No comment yet.
Scooped by ulcriv
Scoop.it!

New Disease report • Pérez-López Lab 2021 • First evidence of the occurrence of a putative new subgroup of ‘Candidatus Phytoplasma asteris’ (16SrI) associated with strawberry green petal disease in...

New Disease report • Pérez-López Lab 2021 • First evidence of the occurrence of a putative new subgroup of ‘Candidatus Phytoplasma asteris’ (16SrI) associated with strawberry green petal disease in... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

In Canada, Quebec is the main strawberry (Fragaria × ananassa) producing region and in 2018 more than 15,000 tonnes of fruit worth 66 million Canadian dollars was produced (Gouvernement du Québec, 2021). In recent years, an increasing number of leafhoppers in strawberry fields in Quebec, may have led to a rise in the number of plants affected by strawberry green petal disease (SbGP). This disease is known to be associated with phytoplasmas (‘Candidatus Phytoplasma’ sp.) (Brochu et al., 2021). Although SbGP was reported in Quebec in 1961 (Chiykowsky, 1962), the phytoplasma pathogen associated with the disease has not yet been identified.

No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Agric Ecosyst Environ • Halde Lab 2021 • Pea-based cover crop mixtures have greater plant belowground biomass, but lower plant aboveground biomass than a pure stand of pea

Original Paper in Agric Ecosyst Environ • Halde Lab 2021 • Pea-based cover crop mixtures have greater plant belowground biomass, but lower plant aboveground biomass than a pure stand of pea | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

In eastern Canada, organic grain producers have a rising interest in using cover crop mixtures instead of pure stands to maximize ecosystem services. Yield stability and belowground biomass of cover crop mixtures have however received limited attention in the scientific literature, although they do affect ecosystem services. The aims of this study were to evaluate the aboveground and belowground biomass and yield stability of pea-based cover crop mixtures, and to assess species-specific contributions to aboveground biomass. In a field experiment conducted at three site-years in Quebec, Canada, a pure stand of field pea (Pisum sativum L.) and cover crop mixtures of 2, 6, and 12 species, all including field pea, were compared to a weedy control (without cover crop). The mixtures were seeded according to a substitutive unbalanced design. The proportion of field pea ranged from 45% to 93% of the aboveground plant biomass within all mixtures. Among all site-years, pure stand of field pea provided the highest aboveground biomass (2636 kg ha1), followed by the 2-species mixture (2320 kg ha1) and both multi-species cover crop mixtures (mean of 1849 kg ha1). Aboveground biomass was inversely correlated to cover crop diversity (Pearson coefficient of 0.73), and inversely correlated to weed biomass (Pearson coefficient of 0.54). Pure stand of field pea had the lowest belowground biomass and stability (693 kg ha1, CV of 28%) when compared to mixtures (886 kg ha1, CV of 14% on average). This study confirms that the value of pea-based mixtures, compared to a pure stand of field pea, lies mainly below the soil surface rather than above it. This could likely enhance many soil-related ecosystem services.

No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Virulence • Pérez-López Lab 2021 • A clubroot pathogen effector targets cruciferous cysteine proteases to suppress plant immunity

Original Paper in Virulence • Pérez-López Lab 2021 • A clubroot pathogen effector targets cruciferous cysteine proteases to suppress plant immunity | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Plant pathogen effector proteins are key to pathogen virulence. In susceptible host Brassicas, the clubroot pathogen, Plasmodiophora brassicae, induces the production of nutrient-sink root galls, at the site of infection. Among a list of 32 P. brassiae effector candidates previously reported by our group, we identified SSPbP53 as a putative apoplastic cystatin-like protein highly expressed during the secondary infection. Here we found that SSPbP53 encoding gene is conserved among several P. brassicae pathotypes and that SSPbP53 is an apoplastic protein able to directly interact with and inhibit cruciferous papain-like cysteine proteases (PLCPs), specifically Arabidopsis XYLEM CYSTEINE PEPTIDASE 1 (AtXCP1). The severity of clubroot disease is greatly reduced in the Arabidopsis xcp1 null mutant (AtΔxcp1) after infection with P. brassicae resting spores, indicating that the interaction of P. brassicae SSPbP53 with XCP1 is important to clubroot susceptibility. SSPbP53 is the first cystatin-like effector identified and characterized for a plant pathogenic protist.

No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Int J Food Microbiol • Goulet Collaboration 2021 • Effect of two thermoresistant non-starter lactic acid bacteria strains on volatilome profile during Cheddar ripening simulation

Original Paper in Int J Food Microbiol • Goulet Collaboration 2021 • Effect of two thermoresistant non-starter lactic acid bacteria strains on volatilome profile during Cheddar ripening simulation | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Dairy farm management practices can modify milk microbiota and therefore modulate non-starter lactic acid bacteria (NSLAB) found in cheese. These NSLAB can cause organoleptic defects. This study aimed to investigate the impact of two potential NSLAB in Cheddar cheesemaking: Lactiplantibacillus plantarum RKG 2–212 a strain isolated both in corn silage and raw milk, and Lactobacillus delbrueckii RKG R10, a strain isolated after pasteurisation of milk from a farm using grass and legume silage, and corn silage. The whole genome of these two lactobacilli was first sequenced. Then, the thermoresistance was evaluated after treatment at 60 °C for 5 min and compared to reference strains. Both lactobacilli were highly thermoresistant compared to other three lactic acid bacteria which are Lactococcus lactis subsp. cremoris ATCC 19257 and SK11, and L. plantarum ATCC 14917 (P < 0.0001). They lost less than 1 log cfu/mL (Δlog) and their genome contained a great number of copy number of genes coding for heat shock protein. During a Pearce test activity simulating Cheddar cheesemaking, the two lactobacilli did not show interaction with the starter Lcc. lactis subsp. cremoris SK11, and their population remained stable. During a ripening simulation, L. delbrueckii RKG R10 had a slight loss in viability in cheese slurry samples incubated at 30 °C for 12 d. However, L. plantarum RKG 2–212 had considerable growth, from 6.51 to 8.3 log cfu/g. This growth was associated with the acidification of the slurries (P < 0.0001). The presence of the lactobacilli modified the profile of volatile compounds evaluated by gas chromatography–mass spectrometry, accounting for 10.7% of the variation. The strain L. plantarum RKG 2–212 produced volatile compounds in greater quantity that could be associated with organoleptic defects such as acetic acid and 2-methylbutyraldehyde. Therefore, silage can be a vector of thermoresistant lactic acid bacteria for milk which can lead to flavor defects in cheese.

No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Front Plant Sci • Torkamaneh Collaboration 2021 • Genome-Wide Association Study of Seed Folate Content in Common Bean

Original Paper in Front Plant Sci • Torkamaneh Collaboration 2021 • Genome-Wide Association Study of Seed Folate Content in Common Bean | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Plant-derived folates (Vitamin B9) are essential components of the human diet. They provide one-carbon units that are required for the synthesis of nucleic acids and proteins, and folate deficiency is associated with numerous adverse health conditions. The development of high-folate cultivars of common bean (Phaseolus vulgaris L.) and other staple crops is an important tool to combat folate deficiency. A population of 96 P. vulgaris accessions, representing major North American market classes, was grown in 2 years in Ontario, Canada. The population was genotyped for 5,361 molecular markers with an Illumina Infinium platform. Total folate was extracted from mature seeds using the tri-enzyme extraction method and quantified based on a microbiological assay with Lactobacillus rhamnosus. Significant genetic diversity for folate content was observed among the population in both years of study, and folate content had a range 113–222 μg per 100 g of seeds. Quantitative trait loci (QTL) for seed folate content were identified based on a genome-wide association study (GWAS). Six QTL were identified on Chr. 4, 6, 8, and 11, with three in each year of field trials. Both QTL on Chr. 11 occurred in genomic regions that were syntenic to seed folate QTL detected in previous work with P. vulgaris, Z. mays, and O. sativa. Candidate genes were identified for these QTL that might be targets for the development of molecular markers for selecting P. vulgaris cultivars with improved seed folate content. This work reports the largest survey of genetic diversity for seed folate content in P. vulgaris and identified several genotypes, including SCN4, Bat 93, OAC Redstar, and Pompadour 1014, that would be useful for breeding beans with higher than average folate levels.

No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Int J Mol Sci • Torkamaneh Collaboration 2021 • Transcriptomics of Improved Fruit Retention by Hexanal in ‘Honeycrisp’ Reveals Hormonal Crosstalk and Reduced Cell Wall Degradation...

Original Paper in	Int J Mol Sci • Torkamaneh Collaboration 2021 • Transcriptomics of Improved Fruit Retention by Hexanal in ‘Honeycrisp’ Reveals Hormonal Crosstalk and Reduced Cell Wall Degradation... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Apples (Malus domestica Borkh) are prone to preharvest fruit drop, which is more pronounced in ‘Honeycrisp’. Hexanal is known to improve fruit retention in several economically important crops. The effects of hexanal on the fruit retention of ‘Honeycrisp’ apples were assessed using physiological, biochemical, and transcriptomic approaches. Fruit retention and fruit firmness were significantly improved by hexanal, while sugars and fresh weight did not show a significant change in response to hexanal treatment. At commercial maturity, abscisic acid and melatonin levels were significantly lower in the treated fruit abscission zone (FAZ) compared to control. At this stage, a total of 726 differentially expressed genes (DEGs) were identified between treated and control FAZ. Functional classification of the DEGs showed that hexanal downregulated ethylene biosynthesis genes, such as S-adenosylmethionine synthase (SAM2) and 1-aminocyclopropane-1-carboxylic acid oxidases (ACO3, ACO4, and ACO4-like), while it upregulated the receptor genes ETR2 and ERS1. Genes related to ABA biosynthesis (FDPS and CLE25) were also downregulated. On the contrary, key genes involved in gibberellic acid biosynthesis (GA20OX-like and KO) were upregulated. Further, hexanal downregulated the expression of genes related to cell wall degrading enzymes, such as polygalacturonase (PG1), glucanases (endo-β-1,4-glucanase), and expansins (EXPA1-like, EXPA6, EXPA8, EXPA10-like, EXPA16-like). Our findings reveal that hexanal reduced the sensitivity of FAZ cells to ethylene and ABA. Simultaneously, hexanal maintained the cell wall integrity of FAZ cells by regulating genes involved in cell wall modifications. Thus, delayed fruit abscission by hexanal is most likely achieved by minimizing ABA through an ethylene-dependent mechanism.
No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in J Agric Food Res • Desgagné-Penix Lab 2021 • Black spruce extracts reveal antimicrobial and sprout suppressive potentials to prevent potato (Solanum tuberosum L.) losses during st...

Original Paper in J Agric Food Res • Desgagné-Penix Lab 2021 • Black spruce extracts reveal antimicrobial and sprout suppressive potentials to prevent potato (Solanum tuberosum L.) losses during st... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Canadian forest residues, such as bark, are an abundant and accessible biomass currently burned to produce energy, therefore neglecting their great potential for various applications owing to their multiple biological properties. Potato storage constitutes a challenge for potato producers because of disease propagation and potato sprouting. Barks appear to be promising candidates in the research of greener alternatives to synthetic chemicals presently used to limit these problems. Hence, this study aimed to develop a bio-based ingredient from bark residues to prevent diseases and sprouting of potatoes during storage. First, forest extracts were produced from the bark of black spruce (Picea mariana Mill.), balsam fir (Abies balsamea L. Mill.) and yellow birch (Betula alleghaniensis Britton) by three different methods: water extraction, ethyl acetate fractionation of the water extract, and acid-base extraction. Then, in vitro screening of extracts and commercial essential oils was performed to determine their ability to inhibit potato soft and dry rot and potato sprouting. More specifically, Fusarium oxysporum, Fusarium graminearum, Fusarium sambucinum, Pectobacterium atrosepticum, Pectobacterium carotovorum, and Dickeya dianthicola were selected for antimicrobial assays. Two black spruce extracts, ethyl acetate extract and essential oil, showed promising antimicrobial and anti-sprouting properties. The black spruce ethyl acetate extract inhibited microorganism growth with minimum concentrations ranging from 1.37 × 10–3 to 3.00% (w/w) depending on the strain. Black spruce essential oil completely prevented potato sprouting in Colomba cv. at a minimal concentration of 25% (w/w). Furthermore, when mixed, both properties were maintained, and even showed a synergistic effect. Indeed, in antimicrobial assays, the fractional inhibitory concentration index obtained was lower than 0.50. Therefore, these two black spruce extracts can be formulated into one product with broad properties aimed at controlling potato post-harvest losses due to rot and sprouting.

No comment yet.
Scooped by ulcriv
Scoop.it!

Review in Crit Rev Plant Sci • Belzile Collaboration 2021 • Omics advances and integrative approaches for the simultaneous improvement of seed oil and protein content in soybean (Glycine max L.)

Review in Crit Rev Plant Sci • Belzile Collaboration 2021 • Omics advances and integrative approaches for the simultaneous improvement of seed oil and protein content in soybean (Glycine max L.) | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Genetic improvement of soybean, one of the major crops providing edible oil and protein-rich food, is important to ensure balanced nutrition for the growing world population. To make soybean cultivation more rewarding, an increase in seed oil and protein content is most desirable. Here, a critical review of the efforts employed over a half-century to accomplish the improvement of soybean oil and protein content has been presented. Many studies have used diverse parental lines to map and characterize quantitative trait loci (QTL)/genes regulating these two essential traits. Here, we highlighted such genomic loci that were consistently identified with different mapping approaches, like QTL mapping, genome-wide association studies (GWAS), and meta-QTL analysis. In addition, the information generated through efforts utilizing omics approaches, such as genomics, transcriptomics, and proteomics has also been compiled to anticipate the molecular mechanism. Several innovative approaches like multi-parental mapping, induced mutagenesis, genomic selection, transgenics, and genome-editing have been discussed in terms of effective utilization of technological advances to improve the oil and protein content in soybean. Information provided here will be helpful for better understanding and designing an effective strategy for simultaneous improvement in seed oil and protein content in soybean.

No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Restor Ecol • Rochefort Collaboration 2021 • Restoration of Boreal Peatland Impacted by an In-Situ Oil Sands Well-Pad: 1. Vegetation Response

Original Paper in Restor Ecol • Rochefort Collaboration 2021 • Restoration of Boreal Peatland Impacted by an In-Situ Oil Sands Well-Pad: 1. Vegetation Response | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
In this study, our goal was to adapt the Moss Layer Transfer Technique (MLTT), first developed to restore degraded Sphagnum-dominated peatland explicitly with a bryophyte layer, to a former in-situ oil sands well-pad constructed with nearby mineral fill in northwestern Alberta, Canada. Mineral fill was either completely removed or partially removed with residual fill buried under excavated and decompacted peat, followed by the transfer of donor moss collected from nearby linear features with different plant communities in peatlands. Three years after MLTT, peatland vegetation covers 63% of the site. Carex spp. dominate with 36% coverage, followed by mosses at 12%, including 3% Sphagnum spp. and 8% fen mosses, and shrubs at 8%. Different substrate adjustment treatments and types of donor moss had negligible impact on vegetation development although areas without MLTT remained devoid of mosses and had the lowest peatland species cover. Instead, surface elevation, moisture conditions, and substrate chemistry played important roles in shaping the vegetation communities. The prompt introduction and establishment of peatland donor species through MLTT was crucial to the overall re-establishment of peatland vegetation. This is the first full pad scale study to prove that a flat, moist peat surface created by the removal and/or burial of mineral fill can support peatland vegetation development, particularly ground layer bryophytes. Overall, the reclaimed well-pad appears to be on trajectory towards becoming a functional peatland and our approaches should be considered and tested in future well-pad reclamation trials.
No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Agron J • Halde Collaboration 2021 • Root recovery and elemental composition in a perennial grass as affected by soaking conditions

Original Paper in Agron J • Halde Collaboration 2021 • Root recovery and elemental composition in a perennial grass as affected by soaking conditions | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Roots of perennial grasses, with their fibrous architecture, are difficult to separate from the surrounding soil. We assessed the effect of five soaking solutions [sodium bicarbonate, sodium chloride, disodium ethylenediamine tetraacetic acid (disodium EDTA), distilled water, and sodium hexametaphosphate] and three soaking durations (15 min, 2 h, and 16 h) on root recovery and root elemental composition, with and without a mathematical correction for residual soil adhering to roots. Roots were collected by soil coring in a timothy (Phleum pratense L.) sward on a loam soil. After soaking, roots were washed, digitized, and analyzed for elemental composition. Soaking duration did not affect root mass and length, but the 16-h duration resulted in the lowest ash concentration [136.7 vs. 146.4 g kg–1 dry matter (DM) on average across shorter durations], indicating a lower contamination by soil. The greatest root recovery was obtained with sodium bicarbonate (0.118 vs. 0.101 g DM core–1 on average across other solutions). Sodium hexametaphosphate led to the lowest root ash and element concentrations, but left a P residue on the roots. Distilled water did not impair root cell integrity and led to a similar root recovery as sodium chloride, sodium EDTA, and sodium hexametaphosphate. A mathematical correction improved the estimates of (i) root mass for all soaking solutions, and (ii) root elemental composition for elements with higher concentrations in soils than in roots. Soaking solutions should be chosen as a function of the study objectives because of the trade-off between root recovery and contamination by adhering soil.

No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in FEBS J • Michaud/Goulet Collaboration 2021 • Harnessing the functional diversity of plant cystatins to design inhibitor variants highly active against herbivorous arthropod digest...

Original Paper in FEBS J • Michaud/Goulet Collaboration 2021 • Harnessing the functional diversity of plant cystatins to design inhibitor variants highly active against herbivorous arthropod digest... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Protein engineering approaches have been proposed to improve the inhibitory properties of plant cystatins against herbivorous arthropod digestive proteases, generally involving the site-directed mutagenesis of functionally relevant amino acids or the selection of improved inhibitor variants by phage display approaches. Here, we propose a novel approach where the function-related structural elements of a cystatin are substituted by the corresponding elements of an alternative cystatin. Inhibitory assays were first performed with 20 representative plant cystatins and model Cys proteases, including arthropod proteases, to appreciate the extent of functional variability among the plant cystatin family. The most, and less, potent of these cystatins were then used as ‘donors’ of structural elements to create hybrids of tomato cystatin SlCYS8 used as a model ‘recipient’ inhibitor. In brief, inhibitory activities against Cys proteases strongly differed from one plant cystatin to another, with Ki (papain) values diverging by more than 30-fold and inhibitory rates against arthropod proteases varying by up to 50-fold depending on the enzymes assessed. In line with theoretical assumptions from docking models generated for different Cys protease–cystatin combinations, structural element substitutions had a strong impact on the activity of recipient cystatin SlCYS8, positive or negative depending on the basic inhibitory potency of the donor cystatin. Our data confirm the wide variety of cystatin inhibitory profiles among plant taxa. They also demonstrate the usefulness of these proteins as a pool of discrete structural elements for the design of cystatin variants with improved potency against herbivorous pest digestive Cys proteases.

No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Agronomy • Dorais Lab 2021 • Blueberry Yield and Soil Mineral Nitrogen Response to Nitrogen Fertilizer and Nitrification Inhibitors under Drip-Fertigation Systems

Original Paper in Agronomy • Dorais Lab 2021 • Blueberry Yield and Soil Mineral Nitrogen Response to Nitrogen Fertilizer and Nitrification Inhibitors under Drip-Fertigation Systems | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
In blueberry plantings, nitrification can result in losses of mineral nitrogen (N) through leaching because blueberries prefer ammonium (NH4+) over nitrate (NO3−). The objective of this study was to assess the effects of two rates of N fertilizer, mixed or not with nitrification inhibitors (NI) and applied through two fertigation systems, on berry yield and the concentrations of NH4+-N and NO3−-N along the soil profile. Thus, nine combinations of treatments including two N fertilizer rates (60 and 120 kg N ha−1), two NI (with DCD + Nitra-pyrin or without) and two fertigation application methods (buried and suspended drip lines) and a control (0 kg N ha−1) were tested over three years (2016–2018) in a long-term blueberry planting. Berry yield was on average 47.32 Mg ha−1 in 2016 and 26.86 Mg ha−1 in 2018. In 2017, berry yield varied between 8.60 Mg ha−1 under the control and 11.66 Mg ha−1 with 120 kg N ha−1 applied through suspended drip lines. Low berry yield in 2017 was due to a heavy pruning to rejuvenate the plants. In 2016, the concentration of NH4+-N in the sawdust mulch layer varied between 13.1 and 27.1 mg kg−1 in the spring, 11.4 and 32.1 mg kg−1 in the summer, and 7.9 and 72.9 mg kg−1 in the fall; the concentration of high NH4+-N along the soil profile did not exceed 5 mg kg−1. High concentrations of NH4+-N in the sawdust mulch layer were associated with NI, but did not translate to high berry yields. The concentration of NO3−-N in the soil profile reached 42.6 mg kg−1 in the summer and 39.0 mg kg−1 in the fall and these high concentrations were associated with NI. In 2017 and 2018, there was no effect of NI on NH4+-N concentrations even in the layer of sawdust mulch which was not consistent with the results obtained in 2016. High concentrations of NO3−-N were measured beneath the sawdust mulch layer with treatments including N fertilizer alone or mixed with NI. It is possible that NH4+ retained in the layer of sawdust mulch and not taken up by plant roots was subsequently oxidized to NO3− at the end of the residence time of NI in the soil. Our results showed that high concentrations of NO3−-N along the soil profile occurred mainly during the summer which could be explained by irrigation water driving NO3− leaching.
No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Scientific Reports • Belzile/Torkamaneh Collaboration 2021 • GWAS identifies an ortholog of the rice D11 gene as a candidate gene for grain size in an international collection of ...

Original Paper in Scientific Reports • Belzile/Torkamaneh Collaboration 2021 • GWAS identifies an ortholog of the rice D11 gene as a candidate gene for grain size in an international collection of ... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Grain size is a key agronomic trait that contributes to grain yield in hexaploid wheat. Grain length and width were evaluated in an international collection of 157 wheat accessions. These accessions were genetically characterized using a genotyping-by-sequencing (GBS) protocol that produced 73,784 single nucleotide polymorphism (SNP) markers. GBS-derived genotype calls obtained on Chinese Spring proved extremely accurate when compared to the reference (> 99.9%) and showed > 95% agreement with calls made at SNP loci shared with the 90 K SNP array on a subset of 71 Canadian wheat accessions for which both types of data were available. This indicates that GBS can yield a large amount of highly accurate SNP data in hexaploid wheat. The genetic diversity analysis performed using this set of SNP markers revealed the presence of six distinct groups within this collection. A GWAS was conducted to uncover genomic regions controlling variation for grain length and width. In total, seven SNPs were found to be associated with one or both traits, identifying three quantitative trait loci (QTLs) located on chromosomes 1D, 2D and 4A. In the vicinity of the peak SNP on chromosome 2D, we found a promising candidate gene (TraesCS2D01G331100), whose rice ortholog (D11) had previously been reported to be involved in the regulation of grain size. These markers will be useful in breeding for enhanced wheat productivity.
No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Peer J • Gumiere Collaboration 2021 • Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields

Original Paper in Peer J • Gumiere Collaboration 2021 • Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Background The importance of organic farming has increased through the years to promote food security allied with minimal harm to the ecosystem. Besides the environmental benefits, a recurring problem associated with organic management is the unsatisfactory yield. A possible solution may rely on the soil microbiome, which presents a crucial role in the soil system. Here, we aimed to evaluate the soil bacterial community structure and composition under organic and conventional farming, considering the tropical climate and tropical soil. Methodology Our organic management treatments were composed by composted poultry manure and green manure with Bokashi. Both organic treatments were based on low nitrogen inputs. We evaluated the soil bacterial community composition by high-throughput sequencing of 16S rRNA genes, soil fertility, and soil enzyme activity in two organic farming systems, one conventional and the last transitional from conventional to organic. Results We observed that both organic systems evaluated in this study, have higher yield than the conventional treatment, even in a year with drought conditions. These yield results are highly correlated with changes in soil chemical properties and enzymatic activity. The attributes pH, Ca, P, alkaline phosphatase, and β- glucosidase activity are positively correlated with organic systems, while K and Al are correlated with conventional treatment. Also, our results show in the organic systems the changes in the soil bacteria community, being phyla Acidobacteria, Firmicutes, Nitrospirae, and Rokubacteria the most abundant. These phyla were correlated with soil biochemical changes in the organic systems, helping to increase crop yields. Conclusion Different organic management systems, (the so-called natural and organic management systems, which use distinct organic sources), shift the soil bacterial community composition, implying changes in their functionalities. Also, our results contributed to the identification of target bacterial groups and changes in soil chemical properties and enzymatic activity in a trophic organic farming system, which may contribute to higher crop yields.
No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Plant Dis • Bélanger Lab 2021 • New insights into the fungal diversity of cranberry fruit rot in Québec farms through a large-scale molecular analysis

Original Paper in Plant Dis • Bélanger Lab 2021 • New insights into the fungal diversity of cranberry fruit rot in Québec farms through a large-scale molecular analysis | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Cranberry fruit rot (CFR) pathogens are widely reported in the literature but performing large-scale analysis of their presence inside fruit has always been challenging. In this study, a new molecular diagnostic tool, capable of identifying simultaneously 12 potential fungal species causing CFR, was exploited to better define the impact of CFR across cranberry fields in Québec. For this purpose, 126 fields and 7,825 fruit were sampled in three cranberry farms distributed throughout the province and subjected to comparative analyses of fungal presence and abundance according to cultural practices, sampling times and cranberry cultivars. All 12 pathogens were detected throughout the study but, as a first major finding, the analyses revealed that four species, Godronia cassandrae, Colletotrichum fructivorum, Allantophomopsis cytisporea, and Coleophoma empetri were consistently predominant regardless of the parameters studied. Conventional productions versus organic ones showed a significant reduction in fungal richness and relative abundance. Interestingly, Monilinia oxycocci was found almost exclusively in organic productions indicating that fungicides had a strong and persistent effect on its population. Surprisingly, there were no significant differences in fungal relative abundance or species richness between fruit sampled at harvest or in storage, suggesting that there may not exist a clear distinction between field and storage rot, as it was previously thought. Comparative analysis of fungal species found on eight different cranberry cultivars indicated that they were all infected by the same fungi, but could not rule out differences in genetic resistance. This large-scale analysis allows us to draw an exhaustive picture of CFR in Québec and provides new information with respect to its management.
No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Biomolecules • Desgagné-Penix Collab 2021 • Isolation and Biological Characterization of Homoisoflavanoids and the Alkylamide N-p-Coumaroyltyramine from Crinum biflorum Rottb., an...

Original Paper in Biomolecules • Desgagné-Penix Collab 2021 • Isolation and Biological Characterization of Homoisoflavanoids and the Alkylamide N-p-Coumaroyltyramine from Crinum biflorum Rottb., an... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Crinum biflorum Rottb. (syn. Crinum distichum) is an Amaryllidaceae plant used in African traditional medicine but very few studies have been performed on this species from a chemical and applicative point of view. Bulbs of C. biflorum, collected in Senegal, were extracted with ethanol by Soxhlet and the corresponding organic extract was purified using chromatographic methods. The pure compounds were chemically characterized by spectroscopic techniques (1D and 2D 1H and 13C NMR, HR MS and ECD) and X-ray analysis. Four homoisoflavonoids (1–4) and one alkylamide (5) were isolated and characterized as 5,6,7-trimethoxy-3-(4-hydroxybenzyl)chroman-4-one (1), as 3-hydroxy-5,6,7-trimethoxy-3-(4-hydroxybenzyl)chroman-4-one (2), as 3-hydroxy-5,6,7-trimethoxy-3-(4-methoxybenzyl)chroman-4-one (3) and as 5,6,7-trimethoxy-3-(4-methoxybenzyl)chroman-4-one (4), and the alkylamide as (E)-N-(4-hydroxyphenethyl)-3-(4-hydroxyphenyl)acrylamide (5), commonly named N-p-coumaroyltyramine. The relative configuration of compound 1 was verified thanks to the X-ray analysis which also allowed us to confirm its racemic nature. The absolute configurations of compounds 2 and 3 were assigned by comparing their ECD spectra with those previously reported for urgineanins A and B. Flavanoids 1, 3 and 4 showed promising anticancer properties being cytotoxic at low micromolar concentrations towards HeLa and A431 human cancer cell lines. The N-p-coumaroyltyramine (5) was selectively toxic to A431 and HeLa cancer cells while it protected immortalized HaCaT cells against oxidative stress induced by hydrogen peroxide. Compounds 1–4 also inhibited acetylcholinesterase activity with compound 3 being the most potent. The anti-amylase and the strong anti-glucosidase activity of compound 5 were confirmed. Our results show that C. biflorum produces compounds of therapeutic interest with anti-diabetic, anti-tumoral and anti-acetylcholinesterase properties.
No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Restor Ecol • Rochefort Lab 2021 • The resistance and short‐term resilience of a restored extracted peatland ecosystems post‐fire: an opportunistic study after a wildfire 

Original Paper in Restor Ecol • Rochefort Lab 2021 • The resistance and short‐term resilience of a restored extracted peatland ecosystems post‐fire: an opportunistic study after a wildfire  | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Bogs are known to be relatively resistant and resilient to fire, due to the dominance of wet Sphagnum mosses. Indeed, Sphagnum mosses by holding water, ensure bog resistance, and by regenerating from any fragments left post-fire, ensure bog resilience. The return of several ecological attributes has been reported in the literature post-restoration. However, the resistance and resilience have not yet been evaluated in restored peatlands. A fire affecting an extracted peatland restored 10 years ago provided the opportunity to 1) evaluate the losses post-fire, in terms of phytobiomass and plant cover and 2) assess early vegetation recovery after one growing season post-fire. The fire response of the restored peatland, in terms of resistance and short-term resilience, differed between the main plant communities. Sphagnum Lawn communities (Sphagnum species from the Acutifolia subgenus and Eriophorum vaginatum) showed greater resistance to fire losing proportionally less phytobiomass (17%) than Wet Hollow communities (44%) (Sphagnum species from the Cuspidata subgenus and Scirpus cyperinus). Greater resistance of the Sphagnum Lawn likely comes from the Acutifolia Sphagnum species growing in dense carpets with good water retention, along with the E. vaginatum tussocks being able to retain humidity below the tussocks, whereas the looser growth habit of Cuspidata Sphagnum species do not have good capillary rise capacity and Scirpus produced litter that can produce a good fuel. This study reinforces the idea that a peatland restoration approach using reintroduction material dominated by Acutifolia Sphagnum species and tussock cottongrass provides a better resistance and short-term resilience of restored peatlands.

No comment yet.
Scooped by ulcriv
Scoop.it!

Preprint in bioRxiv • Belzile/Torkamaneh Collaboration 2021 • Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology 

Preprint in bioRxiv • Belzile/Torkamaneh Collaboration 2021 • Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology  | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Background. Structural variant (SV) discovery based on short reads is challenging due to their complex signatures and tendency to occur in repeated regions. The increasing availability of long-read technologies has greatly facilitated SV discovery, however these technologies remain too costly to apply routinely to population-level studies. Here, we combined short-read and long-read sequencing technologies to provide a comprehensive population-scale assessment of structural variation in a panel of Canadian soybean cultivars. 


Results. We used Oxford Nanopore sequencing data (∼12X mean coverage) for 17 samples to both benchmark SV calls made from the Illumina data and predict SVs that were subsequently genotyped in a population of 102 samples using Illumina data. Benchmarking results show that variants discovered using Oxford Nanopore can be accurately genotyped from the Illumina data. We first use the genotyped SVs for population structure analysis and show that results are comparable to those based on single-nucleotide variants. We observe that the population frequency and distribution within the genome of SVs are constrained by the location of genes. Gene Ontology and PFAM domain enrichment analyses also confirm previous reports that genes harboring high-frequency SVs are enriched for functions in defense response. Finally, we discover polymorphic transposable elements from the SVs and report evidence of the recent activity of a Stowaway MITE. 


Conclusions. Our results demonstrate that long-read and short-read sequencing technologies can be efficiently combined to enhance SV analysis in large populations, providing a reusable framework for their study in a wider range of samples and non-model species

No comment yet.
Scooped by ulcriv
Scoop.it!

Preprint in bioRxiv • Michaud/ Goulet Collaboration 2021 • Harnessing the functional diversity of plant cystatins to design inhibitor variants highly active against herbivorous arthropod digestive ...

Preprint in bioRxiv • Michaud/ Goulet Collaboration 2021 • Harnessing the functional diversity of plant cystatins to design inhibitor variants highly active against herbivorous arthropod digestive ... | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Protein engineering approaches have been proposed to improve the inhibitory properties of plant cystatins against herbivorous arthropod digestive proteases. These approachestypically involve the site-directed mutagenesis of functionally relevant amino acids, the production and selection of improved inhibitory variants by molecular phage display procedures, or the design of bi/multifunctional translational fusions integrating one or several cystatin inhibitory domains. Here, we propose a new approach where the function-related structural elements of a cystatin are substituted by the corresponding elements of an alternative cystatin. Cys protease inhibitory assays were first performed with 20 representative plant cystatins and model Cys proteases, including herbivorous arthropod digestive proteases, to appreciate the extent of functional variability among plant cystatin protein family members. The most, and less, potent of these cystatins were then used as ‘donors’ of structural elements to create hybrids of tomato cystatin SlCYS8 used as a model ‘recipient’ inhibitor. Our data confirm the wide variety of cystatin protease inhibitory profiles among plant taxa. They also demonstrate the usefulness of these proteins as a pool of discrete structural elements for the design of cystatin variants with improved potency against herbivorous pest digestive Cys proteases.

No comment yet.
Scooped by ulcriv
Scoop.it!

Perspective Article in Horticulturae • Pérez-López Lab 2021 • Digitalization of Clubroot Disease Index, a Long Overdue Task

Perspective Article in Horticulturae • Pérez-López Lab 2021 • Digitalization of Clubroot Disease Index, a Long Overdue Task | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it
Clubroot is a devastating disease caused by the protist Plasmodiophora brassicae Woronin. After root hair colonization, the clubroot pathogen induces clubs that block water uptake, leading to dehydration and death. The study of the severity of plant diseases is very important. It allows us to characterize the level of resistance of plant germplasm and to classify the virulence of pathogen strains or isolates. Lately, the use of learning machines and automatization has expanded to plant pathology. Fast, reliable and unbiased methods are always necessary, and with clubroot disease indexing this is not different. From this perspective, we discuss why this is the case and how we could achieve this long overdue task for clubroot disease.
No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in J Environ Qual • Grégoire Lab 2021 • Reducing nitrate leaching losses from turfgrass fertilization of residential lawns

Original Paper in J Environ Qual • Grégoire Lab 2021 • Reducing nitrate leaching losses from turfgrass fertilization of residential lawns | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Fertilizer applications on lawns have raised environmental concerns in many Canadian municipalities. In this greenhouse study, NO3 -N leaching losses from Kentucky Bluegrass (Poa pratensis. L) lawns were evaluated on two soils, a schist loam and a clay loam, and on a sand/peat moss rootzone mix (80% sand, 20% peat moss). Eight different fertilizer N sources (urea, Polyon® 8 and 12-week release, Duration® 45 and 90-d release, XCU® , corn gluten meal and UFLEXX® ) were assessed at five application rates (25 to 200 kg N ha-1 yr-1 ) and two application frequencies over two 8-week trials. Average NO3 -N concentration in leachate were measured at levels of 3.5, 7.4 and 1.4 mg L-1 from turf grown in loam, clay and sand respectively, but losses from loam and clay were mostly affected by N mineralization from organic matter. Turf fertilized with rates ≥ 100 kg N ha-1 generally resulted in acceptable visual quality on both soils, but coated-urea fertilizers were more efficient to reduce leaching. In sand, UFLEXX® and urea (150 and 200 kg N ha-1 ) as well as XCU® (200 kg N ha-1 ) resulted in higher NO3 -N losses varying from 8.5 to 23.7 mg L-1 , while losses from other N sources were consistently below 3 mg L-1 . Our results show that it is possible to maintain good quality turfgrass while keeping low NO3 -N leaching losses (i.e. < 4 mg L-1 ) in loam, clay and sand by selecting the ideal combination of N source, N rate and application frequency. This article is protected by copyright. All rights reserved.

No comment yet.
Scooped by ulcriv
Scoop.it!

Original Paper in Restor Ecol • Rochefort Collaboration 2021 • Restoration of a Boreal Peatland Impacted by an In‐Situ Oil Sands Well‐Pad 2. Greenhouse gas exchange dynamics

Original Paper in Restor Ecol • Rochefort Collaboration 2021 • Restoration of a Boreal Peatland Impacted by an In‐Situ Oil Sands Well‐Pad 2. Greenhouse gas exchange dynamics | Original Papers | Reviews + Book Chapters | Collaborations | Scoop.it

Across Canada's boreal forest, disturbances from in situ oil sands mining, including well-pads, significantly impact vast areas of the landscape. The creation of well-pads requires removal of vegetation and placement of mineral fill which essentially stops any carbon (C) sequestration on the once peatland ecosystem. It is important that, once no longer in use, these well-pads are restored as long-term C (peat) accumulation is what defines peatland ecosystem. However, little is known about the recovery of greenhouse gas exchange post-restoration of these features. We studied a decommissioned well-pad located in a treed poor fen that was restored using three soil adjustment treatments (SATs): 1) complete mineral fill removal (Peat-Dec), 2) partial pad removal and burial under peat (BUPL), and 3) mixing mineral and peat by inversion (Mixed-P-M). The recreated peat surface was revegetated with donor peatland species using the Moss Layer Transfer Technique (MLTT). The objectives of this paper were to 1) quantify plot-scale seasonal carbon dioxide (CO2) and methane (CH4) exchange of the SATs, two to four years post-restoration compared to reference sites, and 2) determine the influence of several environmental variables on CO2 and CH4 exchange. All SATs proved effective in recreating a soil surface needed to support peatland vegetation as shown by similar rates of net ecosystem exchange (NEE). Equally, both types of vegetation reintroduced led this site on a trajectory towards functioning as a net C sink.

No comment yet.