CRP 2020 Reviews: WHEAT

In 2020 the CGIAR CAS Secretariat is conducting independent reviews of the 12 CGIAR Research Programs (CRPs), including this one of WHEAT. The reviews will provide information on quality of science and effectiveness in each CRP. This review covers the Phase II years of 2017 through 2019, with a view to identifying lessons for future research modalities

Multi-contrast imaging and digital refocusing on a mobile microscope with a domed LED array

We demonstrate the design and application of an add-on device for improving the diagnostic and research capabilities of CellScope--a low-cost, smartphone-based point-of-care microscope. We replace the single LED illumination of the original CellScope with a programmable domed LED array. By leveraging recent advances in computational illumination, this new device enables simultaneous multi-contrast imaging with brightfield, darkfield, and phase imaging modes. Further, we scan through illumination angles to capture lightfield datasets, which can be used to recover 3D intensity and phase images without any hardware changes. This digital refocusing procedure can be used for either 3D imaging or software-only focus correction, reducing the need for precise mechanical focusing during field experiments. All acquisition and processing is performed on the mobile phone and controlled through a smartphone application, making the computational microscope compact and portable. Using multiple samples and different objective magnifications, we demonstrate that the performance of our device is comparable to that of a commercial microscope. This unique device platform extends the field imaging capabilities of CellScope, opening up new clinical and research possibilities

Exploration of data for analysis using boundary line methodology

The boundary line model has been proposed for interpretation of the plot of a biological response (such as crop yield) against a potentially-limiting variable from observations in a large set of scenarios across which other factors show uncontrolled variation. Under this model the upper bound of the distribution of data represents the limiting effect of the potential factor on the response. Methods have been proposed to fit this model, but we propose that an initial exploratory data analysis step is needed to evaluate evidence that (i) the model is plausible and (ii) that any limiting upper bound is exhibited by the data set (which could, in principle, not include any cases where the factor is limiting). We propose a statistic based on the density of observations in upper sections of early convex hull peels of the data plot. We evaluate this approach using various data sets, some of which have been used for boundary line analysis in previous studies

Hypoxia in grape berries: the role of seed respiration and lenticels on the berry pedicel and the possible link to cell death

Advance Access publication 6 March 2018Mesocarp cell death (CD) during ripening is common in berries of seeded Vitis vinifera L wine cultivars. We examined if hypoxia within berries is linked to CD. Internal oxygen concentration ([O₂]) across the mesocarp was measured in berries from Chardonnay and Shiraz, both seeded, and Ruby Seedless, using an oxygen micro-sensor. Steep [O₂] gradients were observed across the skin and [O₂] decreased toward the middle of the mesocarp. As ripening progressed the minimum [O₂] approached zero in the seeded cultivars and correlated to the profile of CD across the mesocarp. Seed respiration declined during ripening, from a large proportion of total berry respiration early to negligible at latter stages. [O₂] increased towards the central axis corresponding to the presence of air spaces visualised using x-ray micro-CT. These air spaces connect to the pedicel where lenticels are located that are critical for berry O₂ uptake as a function of temperature, and when blocked caused hypoxia in Chardonnay berries, ethanol accumulation and CD. The implications of hypoxia in grape berries are discussed in terms of its role in CD, ripening and berry water relations.Zeyu Xiao, Suzy Y. Rogiers, Victor O. Sadras and Stephen D. Tyerma

Food Security and Climate Change in the Asia-Pacific Region: Evaluating Mismatch between Crop Development and Water Availability

Phenological development is the single most important attribute of crop adaptation to shifting climates. Climate change may alter the rate of phenological development and the amount and distribution of rainfall during the growing season. These changes may in turn result in mismatch between water demand by crops and water availability from rainfall. This paper illustrates how an understanding of the impact of climate shifts on key crops will enable the Asia-Pacific farmers, community workers and policy agencies to better prepare and adapt to climate change. Strategies include changes to existing policy and practices, for example, timing of planting, managing rainwater resources, use of new varieties, disease management protocols, alternate crops and shift in geographic distribution of crops. An international project is described which combines a new analysis of realized changes in meteorological parameters, and use of estimates from published work on future climates to assess temporal shifts in crop phenology, likely shifts in the pattern of rain and water availability, mismatch between crop phenology and water availability, and the expected consequences of this mismatch for food security

Yield gap analysis of field crops: Methods and case studies

The challenges of global agriculture have been analysed exhaustively and the need has been established for sustainable improvement in agricultural production aimed at food security in a context of increasing pressure on natural resources. Whereas the importance of R&D investment in agriculture is increasingly recognised, better allocation of limited funding is essential to improve food production. In this context, the common and often large gap between actual and attainable yield is a critical target. Realistic solutions are required to close yield gaps in both small and large scale cropping systems worldwide; to make progress in this direction, we need (1) definitions and techniques to measure and model yield at different levels (actual, attainable, potential) and different scales in space (field, farm, region, global) and time (short, long term); (2) identification of the causes of gaps between yield levels; (3) management options to reduce the gaps where feasible and (4) policies to favour adoption of gap-closing technologies. The aim of this publication is to review the methods for yield gap analysis, and to use case studies to illustrate different approaches, hence addressing the first of these four requirements. Theoretical, potential, water-limited, and actual yield are defined. Yield gap is the difference between two levels of yield in this series. Depending on the objectives of the study, different yield gaps are relevant. The exploitable yield gap accounts for both the unlikely alignment of all factors required for achievement of potential or water limited yield and the economic, management and environmental constraints that preclude, for example, the use of fertiliser rates that maximise yield, when growers’ aim is often a compromise between maximising profit and minimising risk at the whole-farm scale, rather than maximising yield of individual crops. The gap between potential and water limited yield is an indication of yield gap that can be removed with irrigation. Spatial and temporal scales for the determination of yield gaps are discussed. Spatially, yield gaps have been quantified at levels of field, region, national or mega-environment and globally. Remote sensing techniques describes the spatial variability of crop yield, even up to individual plots. Time scales can be defined in order to either remove or capture the dynamic components of the environment (soil, climate, biotic components of ecosystems) and technology. Criteria to define scales in both space and time need to be made explicit, and should be consistent with the objectives of the analysis. Satellite measurements can complement in situ measurements. The accuracy of estimating yield gaps is determined by the weakest link, which in many cases is good quality, sub-national scale data on actual yields that farmers achieve. In addition, calculation and interpretation of yield gaps requires reliable weather data, additional agronomic information and transparent assumptions. The main types of methods used in yield benchmarking and gap analysis are outlined using selected case studies. The diversity of benchmarking methods outlined in this publication reflects the diversity of spatial and temporal scales, the questions asked, and the resources available to answer them. We grouped methods in four broad approaches. Approach 1 compares actual yield with the best yield achieved in comparable environmental conditions, e.g. between neighbours with similar topography and soils. Comparisons of this type are spatially constrained by definition, and are an approximation to the gap between actual and attainable yield. With minimum input and greatest simplicity, this allows for limited but useful benchmarks; yield gaps can be primarily attributed to differences in management. This approach can be biased, however, where best management practices are not feasible; modelled yields provide more relevant benchmarks in these cases. Approach 2 is a variation of approach 1, i.e. it is based on comparisons of actual yield, but instead of a single yield benchmark, yield is expressed as a function of one or few environmental drivers in simple models. In common with Approach 1, these methods do not necessarily capture best management practices. The French and Schultz model is the archetype in this approach; this method plots actual yield against seasonal water use, fits a boundary function representing the best yield for a given water use, and calculates yield gaps as the departure between actual yields and the boundary function. A boundary model fitted to the data provides a scaled benchmark, thus partially accounting for seasonal conditions. Boundary functions can be estimated with different statistical methods but it is recommended that the shape and parameters of boundary functions are also assessed on the basis of their biophysical meaning. Variants of this approach use nitrogen uptake or soil properties instead of water. Approach 3 is based on modelling which may range from simple climatic indices to models of intermediate (e.g. AquaCrop) or high complexity (e.g. CERES-type models). More complex models are valuable agronomically because they capture some genetic features of the specific cultivar, and the critical interaction between water and nitrogen. On the other hand, more complex models have requirements of parameters and inputs that are not always available. “Best practice” approaches to model yield in gap analysis are outlined. Importantly, models to estimate potential yield require parameters that capture the physiology of unstressed crops. Approach 4 benchmarking involves a range of approaches combining actual data, remote sensing, GIS and models of varying complexity. This approach is important for benchmarking at and above the regional scale. At these large scales, particular attention needs to be paid to weather data used in modelling yield because significant bias can accrue from inappropriate data sources. Studies that have used gridded weather databases to simulate potential and water-limited yields for a grid are rarely validated against simulated yields based on actual weather station data from locations within the same grid. This should be standard practice, particularly where global scale yield gaps are used for policy decisions or investment in R&D. Alternatively, point-based simulations of potential and water-limited yields, complemented with an appropriate up-scaling method, may be more appropriate for large scale yield gap analysis. Remote sensing applied to yield gap analysis has improved over the last years, mainly through pixel-based biomass production models. Site-specific yield validation, disaggregated in biomass radiation-use-efficiency and harvest index, remains necessary and need to be carried out every 5 to 10 years

Metabolic effects of elevated temperature on organic acid degradation in ripening <em>Vitis vinifera</em> fruit

First published online: September 1, 2014Berries of the cultivated grapevine Vitis vinifera are notably responsive to temperature, which can influence fruit quality and hence the future compatibility of varieties with their current growing regions. Organic acids represent a key component of fruit organoleptic quality and their content is significantly influenced by temperature. The objectives of this study were to (i) manipulate thermal regimes to realistically capture warming-driven reduction of malate content in Shiraz berries, and (ii) investigate the mechanisms behind temperature-sensitive malate loss and the potential downstream effects on berry metabolism. In the field we compared untreated controls at ambient temperature with longer and milder warming (2-4 °C differential for three weeks; Experiment 1) or shorter and more severe warming (4-6 °C differential for 11 days; Experiment 2). We complemented field trials with control (25/15 °C) and elevated (35/20 °C) day/night temperature controlled-environment trials using potted vines (Experiment 3). Elevating maximum temperatures (4-10 °C above controls) during pre-véraison stages led to higher malate content, particularly with warmer nights. Heating at véraison and ripening stages reduced malate content, consistent with effects typically seen in warm vintages. However, when minimum temperatures were also raised by 4-6 °C, malate content was not reduced, suggesting that the regulation of malate metabolism differs during the day and night. Increased NAD-dependent malic enzyme activity and decreased phosphoenolpyruvate carboxylase and pyruvate kinase activities, as well as the accumulation of various amino acids and γ-aminobutyric acid, suggest enhanced anaplerotic capacity of the TCA cycle and a need for coping with decreased cytosolic pH in heated fruit.C. Sweetman, V. O. Sadras, R. D. Hancock, K. L. Soole and C. M. For

Compared to conventional, ecological intensive management promotes beneficial proteolytic soil microbial communities for agro-ecosystem functioning under climate change-induced rain regimes

Projected climate change and rainfall variability will affect soil microbial communities, biogeochemical cycling and agriculture. Nitrogen (N) is the most limiting nutrient in agroecosystems and its cycling and availability is highly dependent on microbial driven processes. In agroecosystems, hydrolysis of organic nitrogen (N) is an important step in controlling soil N availability. We analyzed the effect of management (ecological intensive vs. conventional intensive) on N-cycling processes and involved microbial communities under climate change-induced rain regimes. Terrestrial model ecosystems originating from agroecosystems across Europe were subjected to four different rain regimes for 263 days. Using structural equation modelling we identified direct impacts of rain regimes on N-cycling processes, whereas N-related microbial communities were more resistant. In addition to rain regimes, management indirectly affected N-cycling processes via modifications of N-related microbial community composition. Ecological intensive management promoted a beneficial N-related microbial community composition involved in N-cycling processes under climate change-induced rain regimes. Exploratory analyses identified phosphorus-associated litter properties as possible drivers for the observed management effects on N-related microbial community composition. This work provides novel insights into mechanisms controlling agro-ecosystem functioning under climate change

Responses of grape berry anthocyanin and tritratable acidity to the projected climate change across the Western Australian wine regions

More than a century of observations has established that climate influences grape berry composition. Accordingly, the projected global climate change is expected to impact on grape berry composition although the magnitude and direction of impact at regional and subregional scales are not fully known. The aim of this study was to assess potential impacts of climate change on levels of berry anthocyanin and titratable acidity (TA) of the major grapevine varieties grown across all of the Western Australian (WA) wine regions. Grape berry anthocyanin and TA responses across all WA wine regions were projected for 2030, 2050 and 2070 by utilising empirical models that link these berry attributes and climate data downscaled (to ∼5 km resolution) from the csiro_mk3_5 and miroc3_2_medres global climate model outputs under IPCC SRES A2 emissions scenario. Due to the dependence of berry composition on maturity, climate impacts on anthocyanin and TA levels were assessed at a common maturity of 22 °Brix total soluble solids (TSS), which necessitated the determination of when this maturity will be reached for each variety, region and warming scenario, and future period.The results indicate that both anthocyanin and TA levels will be affected negatively by a warming climate, but the magnitude of the impacts will differ between varieties and wine regions. Compared to 1990 levels, median anthocyanins concentrations are projected to decrease, depending on global climate model, by up to 3–12 % and 9–33 % for the northern wine regions by 2030 and 2070, respectively while 2–18 % reductions are projected in the southern wine regions for the same time periods. Patterns of reductions in the median Shiraz berry anthocyanin concentrations are similar to that of Cabernet Sauvignon; however, the magnitude is lower (up to 9–18 % in southern and northern wine regions respectively by 2070). Similarly, uneven declines in TA levels are projected across the study regions. The largest reductions in median TA are likely to occur in the present day warmer wine regions, up to 40 % for Chardonnay followed by 15 % and 12 % for Shiraz and Cabernet Sauvignon, respectively, by 2070 under the high warming projection (csiro_mk3_5). It is concluded that, under existing management practices, some of the key grape attributes that are integral to premium wine production will be affected negatively by a warming climate, but the magnitudes of the impacts vary across the established wine regions, varieties, the magnitude of warming and future periods considered

Heritability of seed weight in Maritime pine, a relevant trait in the transmission of environmental maternal effects

Quantitative seed provisioning is an important life-history trait with strong effects on offspring phenotype and fitness. As for any other trait, heritability estimates are vital for understanding its evolutionary dynamics. However, being a trait in between two generations, estimating additive genetic variation of seed provisioning requires complex quantitative genetic approaches for distinguishing between true genetic and environmental maternal effects. Here, using Maritime pine as a long-lived plant model, we quantified additive genetic variation of cone and seed weight (SW) mean and SW within-individual variation. We used a powerful approach combining both half-sib analysis and parent-offspring regression using several common garden tests established in contrasting environments to separate G, E and G x E effects. Both cone weight and SW mean showed significant genetic variation but were also influenced by the maternal environment. Most of the large variation in SW mean was attributable to additive genetic effects (h(2) = 0.55-0.74). SW showed no apparent G x E interaction, particularly when accounting for cone weight covariation, suggesting that the maternal genotypes actively control the SW mean irrespective of the amount of resources allocated to cones. Within-individual variation in SW was low (12%) relative to between-individual variation (88%), and showed no genetic variation but was largely affected by the maternal environment, with greater variation in the less favourable sites for pine growth. In summary, results were very consistent between the parental and the offspring common garden tests, and clearly indicated heritable genetic variation for SW mean but not for within-individual variation in SW.This study was financed by the Spanish National Research Grants RTA2007-100 and AGL2012-40151 (FENOPIN), both co-financed by EU-FEDER. The progeny trials and the clonal seed orchards are part of the experimental set up of the Maritime pine breeding programme developed by the Centro de Investigacion Forestal de Lourizan, Xunta de Galicia.Spanish National Research Grant RTA2007-100Spanish National Research Grant AGL2012-40151 (FENOPIN)EU-FEDERPeer reviewe