Exploiting genotype × management interactions to increase rainfed crop production: a case study from south-eastern Australia.

Crop yield must increase to keep pace with growing global demand. Past increases in crop production have rarely been attributable to an individual innovation but have occurred when technologies and practices combine to form improved farming systems. Inevitably this has involved synergy between genotypic and management improvements. We argue that research focused on developing synergistic systems that overcome clear production constraints will accelerate increases in yield. This offers the opportunity to better focus and multiply the impact of discipline-focused research. Here we use the rainfed grain production systems of south-eastern Australia as a case study of how transformational change in water productivity can be achieved with research focused on genotype × management synergies. In this region, rainfall is low and variable and has declined since 1990. Despite this, growers have maintained yields by implementing synergistic systems combining innovations in (i) soil water conservation, (ii) crop diversity, (iii) earlier sowing, and (iv) matching nitrogen fertilizer to water-limited demand. Further increases are emerging from synergies between genetic improvements to deliver flowering time stability, adjusted sowing times, and potential dual-purpose use. Collaboration between agronomists, physiologists, and crop breeders has led to development of commercial genotypes with stable flowering time that are in early phases of testing and adoption.

Digging roots is easier with AI.

The scale of root quantification in research is often limited by the time required for sampling, measurement, and processing samples. Recent developments in convolutional neural networks (CNNs) have made faster and more accurate plant image analysis possible, which may significantly reduce the time required for root measurement, but challenges remain in making these methods accessible to researchers without an in-depth knowledge of machine learning. We analyzed root images acquired from three destructive root samplings using the RootPainter CNN software that features an interface for corrective annotation for easier use. Root scans with and without non-root debris were used to test if training a model (i.e. learning from labeled examples) can effectively exclude the debris by comparing the end results with measurements from clean images. Root images acquired from soil profile walls and the cross-section of soil cores were also used for training, and the derived measurements were compared with manual measurements. After 200 min of training on each dataset, significant relationships between manual measurements and RootPainter-derived data were noted for monolith (R2=0.99), profile wall (R2=0.76), and core-break (R2=0.57). The rooting density derived from images with debris was not significantly different from that derived from clean images after processing with RootPainter. Rooting density was also successfully calculated from both profile wall and soil core images, and in each case the gradient of root density with depth was not significantly different from manual counts. Differences in root-length density (RLD) between crops with contrasting root systems were captured using automatic segmentation at soil profiles with high RLD (1-5 cm cm-3) as well with low RLD (0.1-0.3 cm cm-3). Our results demonstrate that the proposed approach using CNN can lead to substantial reductions in root sample processing workloads, increasing the potential scale of future root investigations.

Toward a Better Understanding of Genotype × Environment × Management Interactions-A Global Wheat Initiative Agronomic Research Strategy.

The Wheat Initiative (WI) and the WI Expert Working Group (EWG) for Agronomy (www.wheatinitiative.org) were formed with a collective goal to "coordinate global wheat research efforts to increase wheat production, quality, and sustainability to advance food security and safety under changing climate conditions." The Agronomy EWG is responsive to the WI's research need, "A knowledge exchange strategy to ensure uptake of innovations on farm and to update scientists on changing field realities." The Agronomy EWG aims to consolidate global expertise for agronomy with a focus on wheat production systems. The overarching approach is to develop and adopt a systems-agronomy framework relevant to any wheat production system. It first establishes the scale of current yield gaps, identifies defensible benchmarks, and takes a holistic approach to understand and overcome exploitable yield gaps to complement genetic increases in potential yield. New opportunities to increase productivity will be sought by exploiting future Genotype × Environment × Management synergies in different wheat systems. To identify research gaps and opportunities for collaboration among different wheat producing regions, the EWG compiled a comprehensive database of currently funded wheat agronomy research (n = 782) in countries representing a large proportion of the wheat grown in the world. The yield gap analysis and research database positions the EWG to influence priorities for wheat agronomy research in member countries that would facilitate collaborations, minimize duplication, and maximize the global impact on wheat production systems. This paper outlines a vision for a global WI agronomic research strategy and discusses activities to date. The focus of the WI-EWG is to transform the agronomic research approach in wheat cropping systems, which will be applicable to other crop species.

Deep Soil Water-Use Determines the Yield Benefit of Long-Cycle Wheat.

Wheat production in southern Australia is reliant on autumn (April-May) rainfall to germinate seeds and allow timely establishment. Reliance on autumn rainfall can be removed by sowing earlier than currently practiced and using late summer and early autumn rainfall to establish crops, but this requires slower developing cultivars to match life-cycle to seasonal conditions. While slow-developing wheat cultivars sown early in the sowing window (long-cycle), have in some cases increased yield in comparison to the more commonly grown fast-developing cultivars sown later (short-cycle), the yield response is variable between environments. In irrigated wheat in the sub-tropics, the variable response has been linked to ability to withstand water stress, but the mechanism behind this is unknown. We compared short- vs. long-cycle cultivars × time of sowing combinations over four seasons (2011, 2012, 2015, and 2016) at Temora, NSW, Australia. Two seasons (2011 and 2012) had above average summer fallow (December-March) rain, and two seasons had below average summer fallow rain (2015 and 2016). Initial plant available water in each season was 104, 91, 28, and 27 mm, respectively. Rainfall in the 30 days prior to flowering (approximating the critical period for yield determination) in each year was 8, 6, 14, and 190 mm, respectively. We only observed a yield benefit in long-cycle treatments in 2011 and 2012 seasons where there was (i) soil water stored at depth (ii) little rain during the critical period. The higher yield of long-cycle treatments could be attributed to greater deep soil water extraction (<1.0 m), dry-matter production and grain number. In 2015, there was little rain during the critical period, no water stored at depth and no difference between treatments. In 2016, high in-crop rainfall filled the soil profile, but high rainfall during the critical period removed crop reliance on deep water, and yields were equivalent. A simulation study extended our findings to demonstrate a median yield benefit in long-cycle treatments when the volume of starting soil water was increased. This work reveals environmental conditions that can be used to quantify the frequency of circumstances where long-cycle wheat will provide a yield advantage over current practice.

Interactions of Spring Cereal Genotypic Attributes and Recovery of Grain Yield After Defoliation.

Dual-purpose crops are grazed during their vegetative phase and allowed to regrow to produce grain. Grazing slow-developing winter cereals (wheat, barley, and triticale) is common, but there is also potential to graze faster-developing spring cereals used in regions with shorter-growing seasons. Defoliation in faster-developing genotypes has risks of larger yield penalties, however, little is known about genotypic characteristics that may improve recovery after grazing. Four experiments examined 7 spring wheat and 2 barley cultivars with differing physiological attributes (phenological development rate, putative capacity to accumulate soluble carbohydrates, and tillering capacity) that may influence the capacity of spring wheat to recover after defoliation. Defoliated and undefoliated crops were compared to assess physiological differences between cultivars including recovery of biomass, leaf area and radiation interception at anthesis, and subsequent crop grain yield and yield components. All genotypes had similar responses to defoliation treatments indicating that the physiological attributes studied played little part in mitigating yield penalties after defoliation. Despite some differences in yield components amongst cultivars, defoliation did not adversely affect cultivars with different yield component combinations under non-water limited conditions. Later and intense defoliation (around GS30/31) resulted in large yield penalties (40%) which reduced both grain number and kernel mass. However, earlier defoliation (before GS28) induced small or insignificant yield penalties. Defoliation often reduced canopy radiation interception and crop biomass at anthesis but this rarely translated into large yield penalties. These studies further demonstrate that shorter season spring cereals can provide valuable forage (up to 1.2 t DM/ha) for grazing during early vegetative growth without inducing large yield penalties. This study suggests that beyond appropriate phenology, there were no other specific characteristics of cultivars that improved the recovery after grazing. Hence farmers don't need specific dual-purpose cultivars and can still focus on those that optimize grain yield potential for a particular environment and sowing date. The timing and intensity of defoliation appear to be larger drivers of yield recovery in spring cereals and better understanding of these relationships are needed to provide grazing management guidelines that mitigate risk of yield penalties in dual-purpose cereal crops.

Inorganic Nutrients Increase Humification Efficiency and C-Sequestration in an Annually Cropped Soil.

Removing carbon dioxide (CO2) from the atmosphere and storing the carbon (C) in resistant soil organic matter (SOM) is a global priority to restore soil fertility and help mitigate climate change. Although it is widely assumed that retaining rather than removing or burning crop residues will increase SOM levels, many studies have failed to demonstrate this. We hypothesised that the microbial nature of resistant SOM provides a predictable nutrient stoichiometry (C:nitrogen, C:phosphorus and C:sulphur-C:N:P:S) to target using supplementary nutrients when incorporating C-rich crop residues into soil. An improvement in the humification efficiency of the soil microbiome as a whole, and thereby C-sequestration, was predicted. In a field study over 5 years, soil organic-C (SOC) stocks to 1.6 m soil depth were increased by 5.5 t C ha-1 where supplementary nutrients were applied with incorporated crop residues, but were reduced by 3.2 t C ha-1 without nutrient addition, with 2.9 t C ha-1 being lost from the 0-10 cm layer. A net difference of 8.7 t C ha-1 was thus achieved in a cropping soil over a 5 year period, despite the same level of C addition. Despite shallow incorporation (0.15 m), more than 50% of the SOC increase occurred below 0.3 m, and as predicted by the stoichiometry, increases in resistant SOC were accompanied by increases in soil NPS at all depths. Interestingly the C:N, C:P and C:S ratios decreased significantly with depth possibly as a consequence of differences in fungi to bacteria ratio. Our results demonstrate that irrespective of the C-input, it is essential to balance the nutrient stoichiometry of added C to better match that of resistant SOM to increase SOC sequestration. This has implications for global practices and policies aimed at increasing SOC sequestration and specifically highlight the need to consider the hidden cost and availability of associated nutrients in building soil-C.

Farming system context drives the value of deep wheat roots in semi-arid environments.

The capture of subsoil water by wheat roots can make a valuable contribution to grain yield on deep soils. More extensive root systems can capture more water, but leave the soil in a drier state, potentially limiting water availability to subsequent crops. To evaluate the importance of these legacy effects, a long-term simulation analysis at eight sites in the semi-arid environment of Australia compared the yield of standard wheat cultivars with cultivars that were (i) modified to have root systems which extract more water at depth and/or (ii) sown earlier to increase the duration of the vegetative period and hence rooting depth. We compared simulations with and without annual resetting of soil water to investigate the legacy effects of drier subsoils related to modified root systems. Simulated mean yield benefits from modified root systems declined from 0.1-0.6 t ha(-1) when annually reset, to 0-0.2 t ha(-1) in the continuous simulation due to a legacy of drier soils (mean 0-32mm) at subsequent crop sowing. For continuous simulations, predicted yield benefits of >0.2 t ha(-1) from more extensive root systems were rare (3-10% of years) at sites with shallow soils (<1.0 m), but occurred in 14-44% of years at sites with deeper soils (1.6-2.5 m). Earlier sowing had a larger impact than modified root systems on water uptake (14-31 vs 2-17mm) and mean yield increase (up to 0.7 vs 0-0.2 t ha(-1)) and the benefits occurred on deep and shallow soils and in more years (9-79 vs 3-44%). Increasing the proportion of crops in the sequence which dry the subsoil extensively has implications for the farming system productivity, and the crop sequence must be managed tactically to optimize overall system benefits.

Evolution of bacterial communities in the wheat crop rhizosphere.

The gap between current average global wheat yields and that achievable through best agronomic management and crop genetics is large. This is notable in intensive wheat rotations which are widely used. Expectations are that this gap can be reduced by manipulating soil processes, especially those that involve microbial ecology. Cross-year analysis of the soil microbiome in an intensive wheat cropping system revealed that rhizosphere bacteria changed much more than the bulk soil community. Dominant factors influencing populations included binding to roots, plant age, site and planting sequence. We demonstrated evolution of bacterial communities within the field rhizosphere. Early in the season, communities tightly bound to the root were simplest. These increased in diversity with plant age and senescence. Loosely bound communities also increased in diversity from vegetative to reproductive plant stages but were more stable than those tightly bound to roots. Planting sequence and, to a lesser extent, wheat genotype also significantly affected rhizosphere bacteria. Plasticity in the rhizosphere generated from crop root system management and genetics offers promise for manipulating the soil ecology of intense cereal systems. Analyses of soil microbiomes for the purpose of developing agronomic benefit should include roots as well as soil loosely adhered to the roots, and the bulk soil.

The distribution and abundance of wheat roots in a dense, structured subsoil--implications for water uptake.

We analysed the abundance, spatial distribution and soil contact of wheat roots in dense, structured subsoil to determine whether incomplete extraction of subsoil water was due to root system limitations. Intact soil cores were collected to 1.6 m below wheat crops at maturity on a red Kandosol in southern Australia. Wheat roots, remnant roots, soil pores and root-soil contact were quantified at fresh breaks in the soil cores. In surface soil layers (<0.6 m) 30-40% of roots were clumped within pores and cracks in the soil, increasing to 85-100% in the subsoil (>0.6 m), where 44% of roots were in pores with at least three other roots. Most pores contained no roots, with occupancy declining from 20% in surface layers to 5% in subsoil. Wheat roots clumped into pores contacted the surrounding soil via numerous root hairs, whereas roots in cracks were appressed to the soil surface and had very few root hairs. Calculations assuming good root-soil contact indicated that root density was sufficient to extract available subsoil water, suggesting that uptake is constrained at the root-soil interface. To increase extraction of subsoil water, genetic targets could include increasing root-soil contact with denser root hairs, and increasing root proliferation to utilize existing soil pores.

Distribution of glucosinolates and sulphur-rich cells in roots of field-grown canola (Brassica napus).

To investigate the role played by the distribution pattern of glucosinolates (GSLs) in root systems in the release of biocides to the rhizosphere, GSLs have been localized, for the first time, to specific regions and cells in field-grown roots. GSL concentrations in separated tissues of canola (Brassica napus) were determined by chemical analysis, and cell-specific concentrations by extrapolation from sulphur concentrations obtained by quantitative cryo-analytical scanning electron microscopy (SEM). In roots with secondary growth, GSL concentrations in the outer secondary tissues were up to 5x those of the inner core. The highest GSL concentrations (from sulphur measurements) were in two cell layers just under the outermost periderm layer, with up to 100x published concentrations for whole roots. Primary tissues had negligible GSL. Release and renewal of the peripheral GSLs is probably a normal developmental process as secondary thickening continues and surface cells senesce, accounting for published observations that intact roots release GSLs and their biocide hydrolosates to the rhizosphere. Absence of myrosin idioblasts close to the root surface suggests that GSLs released developmentally are hydrolysed by myrosinase in the rhizosphere, ensuring a continuous localized source of biotoxic hydrolysates which can deter soil-borne pests, and influence microbial populations associated with long-lived components of the root system.

Pathways of infection of Brassica napus roots by Leptosphaeria maculans.

Infection of Brassica napus cotyledons and leaves by germinating ascospores of Leptosphaeria maculans leads to production of leaf lesions followed by stem cankers (blackleg). Leptosphaeria maculans also causes root rot but the pathway of infection has not been described. An L. maculans isolate expressing green fluorescent protein (GFP) was applied to the petiole of B. napus plants. Hyphal growth was followed by fluorescence microscopy and by culturing of sections of plant tissue on growth media. Leptosphaeria maculans grew within stem and hypocotyl tissue during the vegetative stages of plant growth, and proliferated into the roots within xylem vessels at the onset of flowering. Hyphae grew in all tissues in the stem and hypocotyl, but were restricted mainly to xylem tissue in the root. Leptosphaeria maculans also infected intact roots when inoculum was applied directly to them and hyphae entered at sites of lateral root emergence. Hyphal entry may occur at other sites but the mechanism is uncertain as penetration structures were not observed. Infection of B. napus roots by L. maculans can occur via above- and below-ground sources of inoculum, but the relative importance of the infection pathways under field conditions is unknown.

MYC2 differentially modulates diverse jasmonate-dependent functions in Arabidopsis.

The Arabidopsis thaliana basic helix-loop-helix Leu zipper transcription factor (TF) MYC2/JIN1 differentially regulates jasmonate (JA)-responsive pathogen defense (e.g., PDF1.2) and wound response (e.g., VSP) genes. In this study, genome-wide transcriptional profiling of wild type and mutant myc2/jin1 plants followed by functional analyses has revealed new roles for MYC2 in the modulation of diverse JA functions. We found that MYC2 negatively regulates Trp and Trp-derived secondary metabolism such as indole glucosinolate biosynthesis during JA signaling. Furthermore, MYC2 positively regulates JA-mediated resistance to insect pests, such as Helicoverpa armigera, and tolerance to oxidative stress, possibly via enhanced ascorbate redox cycling and flavonoid biosynthesis. Analyses of MYC2 cis binding elements and expression of MYC2-regulated genes in T-DNA insertion lines of a subset of MYC2-regulated TFs suggested that MYC2 might modulate JA responses via differential regulation of an intermediate spectrum of TFs with activating or repressing roles in JA signaling. MYC2 also negatively regulates its own expression, and this may be one of the mechanisms used in fine-tuning JA signaling. Overall, these results provide new insights into the function of MYC2 and the transcriptional coordination of the JA signaling pathway.

Extraction and determination of glucosinolates from soil.

The use of glucosinolate-containing plants as soil-incorporated biofumigants for pest and disease control has raised questions regarding the fate of glucosinolates in soil; however, no method for routine analysis of glucosinolates in soil has been reported. A simple method to extract glucosinolates from soil with quantification as desulfoglucosinolates by HPLC is presented. The method involves two extractions with 70% methanol at room temperature, centrifugation, and filtration prior to the desulfation step. The desulfoglucosinolates are then quantified by HPLC using established protocols for plant tissue analysis. There were no significant interfering peaks from the soil extracts, and the method provided high extraction efficiencies (around 100%) for both aromatic (benzyl) and aliphatic (2-propenyl) glucosinolates when amended at a wide range of realistic field soil concentrations (1.6-120 nmol/g of soil). The method was equally effective in three diverse Australian soils that varied in organic matter, clay content, and pH. The method was effective in air-dried or field-moist soil, although evidence for rapid glucosinolate degradation in field-moist soil indicates that extraction of moist soils should be performed as soon as possible after sampling. The method is compatible with field soil sampling at remote sites and utilizes the same equipment and protocols already established for plant tissue analysis. Extraction of glucosinolates in the field following incorporation of Indian mustard (Brassica juncea) and rape (Brassica napus) green manure crops was also tested. Eight different glucosinolates contained in the plant tissues were identified and quantified in soil extracts at concentrations ranging from 0.11 to 21.7 nmol/g of soil.

A wheat genotype developed for rapid leaf growth copes well with the physical and biological constraints of unploughed soil.

Conventional wheat (Triticum aestivum L.) cultivars grow slowly in unploughed soil because of physical and biological constraints. Here a conventional cultivar (Janz) is compared with a novel experimental line (Vigour 18), bred for high leaf vigour, to explore the hypothesis that a vigorous wheat grows better in unploughed soil. Roots of both genotypes in unploughed soil were three times more distorted with 30% shorter apices and 60% shorter expansion zones than roots in ploughed soil, because of voids between blocky peds and packed sand particles that impeded root apices. More than half the root length contacted dead, remnant roots. Vigour 18 roots grew 39% faster, were thicker and distorted less than Janz roots in unploughed soil, but developed similarly in ploughed soil. Vigour 18 shoots grew 64% faster in unploughed soil, but 15% faster in ploughed soil. Fumigation of unploughed soil improved the growth of Janz only. We suggest that faster root growth, different exudates promoting a more beneficial rhizosphere microflora, or modified shoot responses are possible mechanisms to explain Vigour 18's superior growth. Vigorous genotypes may present a new opportunity for increased productivity with conservation farming.

Soil strength and rate of root elongation alter the accumulation of Pseudomonas spp. and other bacteria in the rhizosphere of wheat.

Results from a controlled environment system and the field showed that slow root elongation rate was associated with accumulation of Pseudomonas spp. in the rhizosphere; fast root elongation avoided accumulation. In the controlled environment system, total bacteria and bacteria belonging to the genus Pseudomonas were quantified along wheat (Triticum aestivum L. cv. Janz) seminal roots elongating at rates of 2.4 or 0.8 cm d-1 in loose and compacted field soil, respectively. Although total numbers of bacteria were similar for both rates of elongation, more Pseudomonas spp. accumulated on the slow-growing roots and their numbers were greatest 0.5-1 cm from the root tips. A reduced rate of root elongation in compacted soil accelerated the differentiation of root hairs, branch roots and adhesion of rhizosheath soil. Elongation rate and distance between the root tip and the zone of root hair development were positively correlated (r=0.9), providing a morphological indicator of root elongation rate in the field. Slow-growing roots from the field had 20 times more Pseudomonas spp. per unit root length than fast-growing field roots, while total bacteria were 8-fold higher; differences were greatest 0-1 cm from the tips. These results may explain how soil structure and Pseudomonas spp. interact in conservation farming. Rapid root elongation is identified as a desirable trait for avoiding accumulations of bacteria.