Harrow Research and Development Centre

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.

Abstract Inhibitors are widely considered an efficient tool for reducing nitrogen (N) loss and improving N use efficiency, but their effectiveness is highly variable across agroecosystems. In this study, we synthesized 182 studies (222 sites) worldwide to evaluate the impacts of inhibitors (urease inhibitors [UI], nitrification inhibitors [NI] and combined inhibitors) on crop yields and gaseous N loss (ammonia [NH 3 ] and nitrous oxide [N 2 O] emissions) and explored their responses to different management and environmental factors including inhibitor application timing, fertilization regime, cropping system, water management, soil properties and climatic conditions using subgroup meta‐analysis, meta‐regression and multivariate analyses. The UI were most effective in enhancing crop yields (by 5%) and reducing NH 3 volatilization (by 51%), whereas NI were most effective at reducing N 2 O emissions (by 49%). The application of UI mitigates NH 3 loss and increases crop yields especially in high NH 3 ‐N loss scenarios, whereas NI application would minimize the net N 2 O emissions and the resultant environmental impacts especially in low NH 3 ‐N loss scenarios. Alternatively, the combined application of UI and NI enables producers to balance crop production and environmental conservation goals without pollution tradeoffs. The inhibitor efficacy for decreasing gaseous N loss was dependent upon soil and climatic conditions and management practices. Notably, both meta‐regression and multivariate analyses suggest that inhibitors provide a greater opportunity for reducing fertilizer N inputs in high‐N‐surplus systems and presumably favor crop yield enhancement under soil N deficiency situations. The pursuit of an improved understanding of the interactions between plant‐soil‐climate‐management systems and different types of inhibitors should continue to optimize the effectiveness of inhibitors for reducing environmental losses while increasing productivity.

Abstract Diversifying agriculture by rotating a greater number of crop species in sequence is a promising practice to reduce negative impacts of crop production on the environment and maintain yields. However, it is unclear to what extent cereal yields change with crop rotation diversity and external nitrogen fertilization level over time, and which functional groups of crops provide the most yield benefit. Here, using grain yield data of small grain cereals and maize from 32 long-term (10–63 years) experiments across Europe and North America, we show that crop rotational diversity, measured as crop species diversity and functional richness, enhanced grain yields. This yield benefit increased over time. Only the yields of winter-sown small grain cereals showed a decline at the highest level of species diversity. Diversification was beneficial to all cereals with a low external nitrogen input, particularly maize, enabling a lower dependence on nitrogen fertilisers and ultimately reducing greenhouse gas emissions and nitrogen pollution. The results suggest that increasing crop functional richness rather than species diversity can be a strategy for supporting grain yields across many environments.

BACKGROUND: The occurrence of herbicide-resistant weed biotypes is increasing and this report of an acetyl-CoA carboxylase (ACCase) inhibitor-resistant Digitaria sanguinalis L. Scop. from southwestern Ontario is another example. The identified weed escaped control in an onion and carrot rotation in which graminicides were used for several consecutive years. Our goal was to characterize the level and mechanism of resistance of the biotype. RESULTS: The biotype was resistant to all five ACCase inhibitor herbicides tested. Gene-expression profiling was performed because none of the mutations known to confer resistance in the ACCase gene were detected. RNASeq and quantitative reverse-transcriptase PCR (qRT-PCR) results indicated that transcription of ACCase was 3.4-9.3 times higher in the resistant biotype than the susceptible biotype. ACCase gene copy number was determined by qPCR to be five to seven times higher in the resistant compared with the susceptible biotype. ACCase gene overexpression was directly related to the increase of the ACCase gene copy number. CONCLUSION: Our results are consistent with the hypothesis that overexpression of the herbicide target gene ACCase confers resistance to the herbicide. This is the first reported case of target gene duplication conferring resistance to a herbicide other than glyphosate. © 2017 Society of Chemical Industry See related Article.

OBJECTIVE: Soybean seeds are an important source of vegetable proteins for both food and industry worldwide. Conglycinins (7S) and glycinins (11S), which are two major families of storage proteins encoded by a small family of genes, account for about 70% of total soy seed protein. Mutant alleles of these genes are often necessary in certain breeding programs, as the relative abundance of these protein subunits affect amino acid composition and soy food properties. In this study, we set out to test the efficiency of the CRISPR/Cas9 system in editing soybean storage protein genes using Agrobacterium rhizogenes-mediated hairy root transformation system. RESULTS: We designed and tested sgRNAs to target nine different major storage protein genes and detected DNA mutations in three storage protein genes in soybean hairy roots, at a ratio ranging from 3.8 to 43.7%. Our work provides a useful resource for future soybean breeders to engineer/develop varieties with mutations in seed storage proteins.

Abstract Ensuring sufficient fertilizer nitrogen (N) for crops while minimizing N losses requires best management practices optimized for climate, crop, soil, and root zone hydrology. In Ontario, pre‐plant N fertilization of corn ( Zea mays L.) is common; however, this practice extends the time between application and significant root interception of N by the plant, potentially increasing the risk of N loss through soil nitrous oxide emissions, ammonia (NH 3 ) volatilization, and nitrate leaching. These losses contribute to greenhouse gas emissions, affect air quality (NH 3 ), and are a substantial financial loss. This study compared three N placement methods (broadcast urea [BrUrea], broadcast incorporated urea [BrIncUrea], and injected urea ammonium nitrate [InjUAN]) and the presence or absence of N metabolite inhibitors (urease inhibitor [UI], urease plus nitrification inhibitor [UI+NI]). Fertilizer N was applied immediately before planting (150 kg N ha −1 ) to all treatments except for the control. Averaged over 3 yr (2015–2017), NH 3 losses were reduced by 34% from BrIncUrea, by 42–55% from BrUrea+UI+NI and BrIncUrea+UI+NI, and by 99% from InjUAN relative to BrUrea (21 kg N ha −1 ). On average, N application increased corn grain yields by 83% relative to the control (6 t ha −1 ). There were no annual yield differences among N placement methods. It was concluded that incorporation or injection of N in soil and use of urease and nitrification inhibitors reduced NH 3 emissions when N fertilizer was applied pre‐plant.

Abstract Currently accepted pedotransfer functions show negligible effect of management‐induced changes to soil organic carbon (SOC) on plant available water holding capacity (θ AWHC ), while some studies show the ability to substantially increase θ AWHC through management. The Soil Health Institute's North America Project to Evaluate Soil Health Measurements measured water content at field capacity using intact soil cores across 124 long‐term research sites that contained increases in SOC as a result of management treatments such as reduced tillage and cover cropping. Pedotransfer functions were created for volumetric water content at field capacity (θ FC ) and permanent wilting point (θ PWP ). New pedotransfer functions had predictions of θ AWHC that were similarly accurate compared with Saxton and Rawls when tested on samples from the National Soil Characterization database. Further, the new pedotransfer functions showed substantial effects of soil calcareousness and SOC on θ AWHC . For an increase in SOC of 10 g kg –1 (1%) in noncalcareous soils, an average increase in θ AWHC of 3.0 mm 100 mm –1 soil (0.03 m 3 m –3 ) on average across all soil texture classes was found. This SOC related increase in θ AWHC is about double previous estimates. Calcareous soils had an increase in θ AWHC of 1.2 mm 100 mm –1 soil associated with a 10 g kg –1 increase in SOC, across all soil texture classes. New equations can aid in quantifying benefits of soil management practices that increase SOC and can be used to model the effect of changes in management on drought resilience.

Abstract Farmers, scientists, and other soil health stakeholders require interpretable indicators of soil hydraulic function. Determining which indicators to use has been difficult because of measurement disconformity, spatial and temporal variability, recently established treatments, and the effect of site characteristics on management practice differences. The North American Project to Evaluate Soil Health Measurements includes 124 sites uniformly sampled across a range of soil health management practices in North America in 2019. We compare and recommend indicators of hydraulic function that best characterize soil health. We assessed the relationship of each indicator to a suite of soil inherent properties and climate variables, the response of each indicator to soil health management practices, the effect that soil inherent properties (clay content, sand content, and pH) and climatic variables (10‐yr mean annual precipitation and temperature) had on response to management practices, and the relationship among the responses of the indicators to soil health management practices. Field capacity measured on intact cores (θ FC_INTACT ) was the best measure of soil hydraulic function, because it responded to management, represents a direct measure of soil hydraulic function, is proximal to stakeholder values, and its response to management was not significantly influenced by inherent and climatic variables. Other suitable indicators are bulk density, soil organic carbon (SOC), and aggregate stability, which are not direct measures of soil hydraulic function but do respond to management and may be practical in situations in which measuring θ FC_INTACT is not. This study informs selection of soil health indicators to measure soil hydraulic function.

Abstract Various soil health indicators that measure a chemically defined fraction of nitrogen (N) or a process related to N cycling have been proposed to quantify the potential to supply N to crops, a key soil function. We evaluated five N indicators (total soil N, autoclavable citrate extractable N, water‐extractable organic N, potentially mineralizable N, and N ‐acetyl‐β‐ D ‐glucosaminidase activity) at 124 sites with long‐term experiments across North America evaluating a variety of managements. We found that 59%–81% of the variation in N indicators was among sites, with indicator values decreasing with temperature and increasing with precipitation and clay content. The N indicators increased from 6%–39% in response to decreasing tillage, cover cropping, retaining residue, and applying organic sources of nutrients. Overall, increasing the quantity of organic inputs, whether from increased residue retention, cover cropping, or rotations with higher biomass, resulted in higher values of the N indicators. Although N indicators responded to management in similar ways, the analysis cost and availability of testing laboratories is highly variable. Further, given the strong relationships of the N indicators with carbon (C) indicators, measuring soil organic C along with 24‐h potential C mineralization could be used as a proxy for N supply instead of measuring potentially mineralizable N or any other N indicator directly.

The common bean is generally regarded as a relatively inefficient fixer of nitrogen. Information on the relative importance of host cultivar and rhizobium strain would be useful in guiding a breeding program to improve nitrogen fixation in common bean. Seventeen cultivars of common bean (15 of Meso-American and 2 of Andean origin, differing in nodulation potential, maturity, growth habit and market class) were investigated for symbiotic compatibility with 10 genetically diverse strains of bean rhizobia. In a greenhouse (27/22 °C), five sets of 170 pots were replicated over time: three sets were harvested after 30 d for determination of acetylene reduction activity, plant dry weights, and nitrogen content; two replications were grown to maturity for determination of seed dry weight and nitrogen content. There were highly significant effects of both strain and cultivar on most measured characteristics, but there was no interaction between cultivar and strain. Italian Barlotti produced the greatest plant weight after 30 d, but its final seed yield did not differ significantly from that of the highest yielding cv. BAT271. The strain TAL182 was associated with the greatest plant weight at 30 d, but the final seed yield associated with it was less than that of the most productive strain USDA9001. Strain USDA 2667 was characterized as type I by determination of its 16S rRNA gene nucleotide sequence. The nodules of plants in symbiosis with strains of type IIB had high levels (8.1%) of nitrogen and high levels (227 µmol g −1 h −1 ) of acetylene reduction activity (ARR). Nodules occupied by strains of type IIA and the type I USDA2667 had intermediate levels of nitrogen (6.9%) and ARR (166 µmol g −1 h −1 ), while nodules occupied by type 1 strains had low levels of nitrogen (5.2%) and ARR (144 µmol g −1 h −1 ). Screening of lines, parents and other breeding materials for improved N-fixation may be achieved with any effective strain since no host × strain interaction was detected. Key words: Common bean, Phaseolus vulgaris, nodulation, nitrogen fixation, rhizobium strains, cultivar × strain interaction

SPT6 is a conserved elongation factor that is associated with phosphorylated RNA polymerase II (RNAPII) during transcription. Recent transcriptome analysis in yeast mutants revealed its potential role in the control of transcription initiation at genic promoters. However, the mechanism by which this is achieved and how this is linked to elongation remains to be elucidated. Here, we present the genome-wide occupancy of Arabidopsis SPT6-like (SPT6L) and demonstrate its conserved role in facilitating RNAPII occupancy across transcribed genes. We also further demonstrate that SPT6L enrichment is unexpectedly shifted, from gene body to transcription start site (TSS), when its association with RNAPII is disrupted. Protein domains, required for proper function and enrichment of SPT6L on chromatin, are subsequently identified. Finally, our results suggest that recruitment of SPT6L at TSS is indispensable for its spreading along the gene body during transcription. These findings provide new insights into the mechanisms underlying SPT6L recruitment in transcription and shed light on the coordination between transcription initiation and elongation.

Crop yield prediction which provides critical information for management decision-making is of significant importance in precision agriculture. Traditional manual inspection and calculation are often laborious and time-consuming. For yield prediction using high-resolution images, existing methods, e.g., convolutional neural network, are challenging to model long range multi-level dependencies across image regions. This paper proposes a transformer-based approach for yield prediction using early-stage images and seed information. First, each original image is segmented into plant and soil categories. Two vision transformer (ViT) modules are designed to extract features from each category. Then a transformer module is established to deal with the time-series features. Finally, the image features and seed features are combined to estimate the yield. A case study has been conducted using a dataset that was collected during the 2020 soybean-growing seasons in Canadian fields. Compared with other baseline models, the proposed method can reduce the prediction error by more than 40%. The impact of seed information on predictions is studied both between models and within a single model. The results show that the influence of seed information varies among different plots but it is particularly important for the prediction of low yields.

Cytochrome P450 monooxygenases (P450) participate in the catalytic conversion of biological compounds in a plethora of metabolic pathways, such as the biosynthesis of alkaloids, terpenoids, phenylpropanoids, and hormones in plants. Plants utilize these metabolites for growth and defense against biotic and abiotic stress. In this study, we identified 346 P450 (GmP450) enzymes encoded by 317 genes in soybean where 26 GmP450 genes produced splice variants. The genome-wide comparison of both A-type and non-A-type GmP450s for their motifs composition, gene structure, tissue-specific expression, and their chromosomal distribution were determined. Even though conserved P450 signature motifs were found in all GmP450 families, larger variation within a specific motif was observed in the non-A-type GmP450s as compared with the A-type. Here, we report that the length of variable region between two conserved motifs is exact in the members of the same family in majority of the A-type GmP450. Analyses of the transcriptomic datasets from soybean- Phytophthora sojae interaction studies, quantitative trait loci (QTL) associated with P. sojae resistance, and co-expression analysis identified some GmP450s that may be, in part, play an important role in partial resistance against P. sojae. The findings of our CYPome study provides novel insights into the functions of GmP450s and their involvements in metabolic pathways in soybean. Further experiments will elucidate their roles in general and legume-specific function.

Commercial sweet corn ( Zea mays L.) production requires significant quantities of fertilizer N, leading to inefficient N use and negative environmental impact. A field experiment was conducted for 4 yr (2001–2004) in Ottawa, Canada, to assess and compare presidedress soil nitrate test (PSNT) with some crop‐based measurements (canopy reflectance, leaf chlorophyll and plant total N) for improved N management. A fresh market sweet corn (FMSC, hybrid ‘Temptation’) grown from 2001 to 2003, and a processing sweet corn (PSC, hybrid ‘Hollywood’) from 2002 to 2004, both received five fertilizer N rates (0, 50, 100, 150, and 200 kg N ha −1 ). Soil samples taken from the V4 to V8 growth stages were analyzed for NO 3 − –N. Leaf chlorophyll content (SPAD) and canopy reflectance were also measured for FMSC at the same time. All N treatments affected the number of marketable ears, kernel dry weight and total biomass production. However, in most cases, there was no difference between N treatments from 100 to 200 kg ha −1 . The PSNT NO 3 − –N increased linearly with the fertilizer N rates, and there were significant positive correlations between PSNT at V4 to V6 and the number of marketable ears. It was evident that PSNT, plant N concentration at V6, SPAD and canopy reflectance all differentiated sweet corn N response similarly, and they were highly correlated with one another. We concluded that PSNT at V4 to V6 was effective in predicting sweet corn N requirement in this cool and short‐growing region.

The use of contact sand to achieve good hydraulic connection between the tension infiltrometer (TI) membrane and the soil is known to introduce an offset between the pressure head set on the bubble tower ( h 0 ) and the pressure head applied to the soil surface ( h s ). The nature and importance of the offset are poorly understood, however. Hence, the objectives of this study were to characterize the offset and to demonstrate its impacts on TI determinations of near‐saturated hydraulic conductivity, K ( h ), sorptive number, α*( h ), flow‐weighted mean pore diameter, D ( h ), and number of flow‐weighted mean pores per unit area, N ( h ). The offset, Δ h = h s − h 0 , consists of a constant elevation component and a variable head‐loss component. The elevation component increases h s relative to h 0 , and comprises most of the offset for low TI flux density, q ( h 0 ), and large contact sand hydraulic conductivity, K cs The head‐loss component decreases h s relative to h 0 , and becomes more important as q ( h 0 ) increases or K cs decreases. The offset has little effect on the accuracy of K ( h ), α*( h ), D ( h ), and N ( h ) when these relationships are insensitive to changes in h 0 When the relationships are sensitive to changing h 0 , the offset can change the shapes of the relationships; cause systematic overestimates of the K ( h ), α*( h ), and D ( h ) values; and cause systematic underestimates of the N ( h ) values. The amount of overestimate and underestimate increases with increasing offset and should be corrected using a form of Darcy's law to prevent the introduction of systematic biases in TI results.

Infection of greenhouse pepper plants (Capsicum annuum L.) by Fusarium oxysporum was observed in two commercial operations in Ontario, causing plant death and yield losses. The pathogen was identified based on cultural, morphological and pathogenicity tests supplemented by PCR amplification of TEF primers. Following inoculation, symptoms of mild stunting occurred within 5–6 weeks, followed by more severe stunting later. Other symptoms, such as chlorosis, wilting and necrosis of the lower foliage, did not become readily evident until about 60 days after inoculation. At 77 days after inoculation, there was considerable brown-black discolouration and decay of crown tissue but little internal stem discolouration or damage beyond the crown portion was observed. Roots were dark brown to black, severely decayed, and easily separated from the surrounding rock wool medium. The fungus was not pathogenic to greenhouse tomato, cucumber or eggplant, nor to field crops such as bean, chickpea or zucchini squash. There were no significant differences in virulence among isolates but differences in resistance/susceptibility among pepper cultivars were observed. The fungicides Medallion® (fludioxonil) and Senator® (thiophanate-methyl) were as effective as bio-control products Mycostop® (Streptomyces griseoviridis) and Prestop® (Gliocladium catenulatum) in limiting Fusarium crown and root rot in greenhouse pepper. Aspects of an integrated disease management strategy are discussed.

Societal impact statement Plant biodiversity is fundamental to the future of food security and agriculture. Berries are the most economically important fruit crops in Canada. Within this article, we explore the nutritional, cultural, and botanical importance of berries, including crop wild relatives (plant species that are closely related to domesticated crops) and plants that are significant to Indigenous Peoples. Using berries as a case study, we explore opportunities for the conservation, use, and public engagement of crop wild relatives. Our objective is to lay the groundwork for future collaborative efforts across these diverse plants. Summary Conservation of plant biodiversity, in particular crop wild relatives including those tended and cultivated by Indigenous Peoples, is critical to food security and agriculture. Building on the 2019 road map for crop wild relatives, we examine berries as a case study for crop wild relative conservation, use, and public engagement. We focus on berries due not only to their economic, cultural, and nutritional importance but also because they are consumed fresh, providing a unique opportunity for individuals and communities to connect with plants. We outline health benefits, geographic distribution, and species at risk for Canadian berries. We describe practices, strategies, and approaches used by Indigenous Peoples to steward berries and emphasize the importance of traditional knowledge. We highlight opportunities for in situ and ex situ berry conservation and use of berries in plant breeding and Indigenous foodways. Our aim is to lay the groundwork for future collaborative efforts in these areas and to showcase berries as a useful case study for conservation of food plant biodiversity and public engagement.

Abstract Many studies haveexamined soil‐borne nitrous oxide (N 2 O) emissions from crops, but little effort has gone into determining the N 2 O emissions from each phase of a crop rotation. A 4‐yr study on a long‐term field experiment compared growing season N 2 O emissions from continuous corn (CC; Zea mays L.) and a 4‐yr crop rotation involving corn (RC), oat (Avena Sativa L .) underseeded to alfalfa ( Medicago sativa L.) (RO), and 2 yr of alfalfa (RA1, RA2). Molecular microbial biomass (DNA yield), as well as N‐cycling functioning genes (mineralization, nitrification, and denitrification), were also evaluated. Although 4‐yr cumulative N 2 O emissions from RC (9.25 kg N ha –1 ) were significantly greater than from CC (7.94 kg N ha –1 ), cumulative emissions from the entire rotation were 54% lower (3.69 kg N ha –1 ) than CC because of low emissions from RO (3.1 kg N ha –1 ), RA1, and RA2 (1.11–1.27 kg N ha –1 ). Years that had substantial early‐season precipitation combined with high soil inorganic N from alfalfa plow‐down contributed to elevated N 2 O emissions from RC. Improved soil conditions and fertility under rotation increased RC grain yields by 35% (9.45 Mg ha –1 ) compared with CC (7.01 Mg ha –1 ). Microbial biomass was 73% greater in RC compared with CC. Nitrogen mineralization genes were 19% greater in RC but they were not correlated to N 2 O emissions, whereas bacterial nitrifiers were positively correlated. Denitrification was likely responsible for N 2 O emissions under CC, while nitrifier‐denitrification appeared to be the primary pathway under RC. The N 2 O emissions and microbial processes from all phases of a rotation should be considered for environmental modeling and policy decisions.

Abstract The pepper weevil (Anthonomus eugenii Cano) is a destructive insect pest of field and greenhouse pepper crops across North America. Its management remains challenging with significant implications for pepper production, despite a documented presence in Central America, Mexico, the United States, and the Caribbean for approximately a century, and recently in Canada. Currently, the main tools and methods applied to manage pepper weevil populations in greenhouse peppers are the implementation of strict biosecurity protocols, diligent monitoring, physical and cultural management techniques, and chemical insecticides when necessary. However, these tools can be costly, labor-intensive, and insufficient, particularly when new outbreaks go undetected for prolonged periods. Additionally, the use of available insecticides is limited due to significant nontarget effects these have on biological control agents used to manage other important greenhouse pepper pests. Recently, research efforts have focused on developing better tools for pepper weevil management to mitigate a rising incidence of insecticide resistance and the spread of weevils into temperate regions, however, multiple constraints remain. Here, we review the current state of knowledge of the pepper weevil and identify information gaps, which future research should address to improve the targeted management of this pest in greenhouse pepper production systems.

Benthic microbial communities contribute to nitrogen (N) cycling in coastal ecosystems through taxon-specific processes such as anammox, nitrification and N-fixation and community attributed pathways such as denitrification. By measuring the total (DNA-based) and active (RNA-based) surface sediment microbial community composition and the abundance and activity profiles of key N-cycling genes in a semi-enclosed embayment—Port Phillip Bay (PPB), Australia—we show that although the total relative abundance of N-cycling taxa is comparatively lower close to estuary inputs (Hobsons Bay [HB]), the capacity for this community to perform diverse Ncycling processes is comparatively higher than in sediments isolated from inputs (Central PPB [CPPB]). In HB, seasonal structuring of the sediment microbial community occurred between spring and summer, co-occurring with decreases in the activity profiles of anammox bacteria and organic carbon content. No changes were detected in the activity profiles of nitrifiers or the community-based pathway denitrification. Although no seasonal structuring of the sediment microbial community occurred in CPPB, the activity profiles of key N-cycling genes displayed comparatively higher within-site variability. These results show that despite N-cycling taxa representing a smaller fraction of the total community composition in estuary impacted sediments (HB) these microbial communities consistently engage in N-cycling processes and that seasonal instability in the composition of this community is not reflective of changes in its capacity to cycle N through coupled nitrification-denitrification but potentially via changes within the anammox community.