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

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

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

Modelling long-term effects of cropping intensification reveals increased water and radiation productivity in the South-eastern Pampas

Wheat/soybean double crop provides a reliable platform for cropping intensification in many subtropical and temperate areas, even in those with a short growing season as the South-eastern Pampas of Argentina. However, the long-term impact of double cropping as part of feasible cropping sequences on resource productivity and the whole sequence performance is unknown. We propose that cropping intensification, based on wheat/soybean double cropping would (i) improve the annual water and radiation capture and productivity, and (ii) reduce unproductive water losses estimated on an annual basis. We tested these hypotheses through long term simulations (30 years), using DSSAT models locally calibrated and tested for wheat (W) (Triticum aestivum L.), soybean (S) (Glycine max [L.] Merr.) and maize (M) (Zea mays L.). Intensification was quantified with the index ISI=number of crops in rotation/duration of rotation. Pairs of sequences with similar crop composition but different degree of intensification were compared, i.e. W–S (ISI=1yr−1) vs W/S double crop (ISI=2yr−1), W–S–M (ISI=1yr−1) vs W/S–M (ISI=1.5yr−1) and W–S–M–S (ISI=1yr−1) vs W/S–M–S (ISI=1.33yr−1). The study also included feasible or traditional rotations of our region. The increase in intensification improved annual resource capture and therefore water and radiation productivity. Proportion of maize in sequences, irrespective of ISI, additionally increased resource productivity by increasing both water use efficiency (WUE) and radiation use efficiency (RUE). Across sequences, WUE and RUE were strongly associated. This correlation was involved in the link between water and radiation productivity. The increase in water productivity was related (P<0.0001) to a reduction in water loss, mainly accounted by runoff. In the long term, sequences with high intensification (ISI≥1.5yr−1) had as high stability and productivity as traditional sequences of our region, based on wheat-summer crop with ISI=1yr−1. Overall, wheat conferred stability to the sequences whereas maize conferred productivity. Our study, accounting for the ability of whole cropping systems to capture resources on an annual basis, gives new tools to develop more efficient and sustainable cropping sequences.O.P. Caviglia, V.O. Sadras, F.H. Andrad