Data Pre-processing for Agricultural Simulations

The process of agricultural simulation using APSIM requires input meteorological data to be prepared in a specific format and the simulation setting file to be ready before the simulation processing starts. Because of possible time savings when conducting large number of simulations at once, it is preferable to create all the input and settings files for all the simulations beforehand and process the simulations in batches as large as possible. This article specifically deals with the data acquisition, transformation and preparation process. It also outlines initial testing and computing time estimations and discusses scheduling, parallel processing and other possible simulation optimization methods

Water extraction under terminal drought explains the genotypic differences in yield, not the anti-oxidants changes in leaves of pearl millet (Pennisetum glaucum (L.) R. Br.)

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a resilient crop suiting the harshest conditions of the semi-arid tropics, in which we assessed possible relationships between crop tolerance, anti-oxidative enzyme activity, and plant / soil water status. Biochemical acclimation and cell homeostasis traits have indeed been proposed as critical for the drought tolerance of crops, but their limited practical application in breeding so far suggests that the role of biochemical acclimation for drought tolerance is still unclear. A possible limitation of previous research may be in not having approached biochemical acclimation from the angle of plant water relations. Four pearl millet genotypes, contrasting for terminal drought tolerance, were evaluated (sensitive H77/833-2, tolerant PRLT2/89-33, and two near isogenic lines carrying a terminal drought tolerance quantitative trait locus) under water stress (WS) and well-watered (WW) conditions in a lysimetric system that simulates field-like conditions. We assessed the genotypic variation and relationship between photosynthetic pigments (chlorophylls a, b, carotenoids), antioxidative isoenzymatic spectrum (superoxide dismutase, ascorbate peroxidase, catalase), physiological traits (soil moisture available, normalized transpiration, stay-green, water extraction), biomass and yield. Investigated biochemical traits were tightly related among each other under WS conditions but not under WW conditions. Two major ascorbate peroxidase isoforms (APX6&7), whose variation in both water regimes reflected the presence/absence of the drought tolerance quantitative trait locus, were identified, but these did not relate to yield. Both, yield and biochemical traits under terminal drought stress were closely related to the traits linked to soil-plant water status (soil moisture available, normalized transpiration, stay-green, water extraction), while yield and the biochemical indicators were not correlated, except for one. It is concluded that there is no direct effect of biochemical traits on yield parameters since both are consequences of soil-plant water status and their putative relation appear to be secondary â through soil-plant water status

Understanding crop physiological processes for climate resilience

As everybody knows, the climate is changing and over the next decade will be putting an increasing strain on agriculture production. This paper aims at putting some focus on what can really be addressed (the change in temperature) from what really cannot be predicted and dealt with (rainfall). But even the effect of one factor like temperature triggers a complex myriad of effects and the paper structures what needs to be done in relation to temperature, and focuses on recently discovered mechanism to adapt to a change in temperature. The paper then briefly reviews its biological basis, the mean to phenotype for it at a high rate and precision, and how the use of crop simulation can help us predict the effect of this trait on yield..

Small temporal differences in water uptake among varities of pearl millet (Pennisetum glaucum (L.) R. Br.) are critical for grain yield under terminal drought.

Intuitively, access to water from the soil at key phenological stages is important for adaptation to drought. This study aimed to assess the temporal pattern of water extraction under terminal drought stress.

Coping with drought: Resilience versus risk. Targeting the most suitable G*E*M options by crop simulation modeling*

Crop production is axiomatically related to water consumption of transpiring leaves. Crop adaptation to water limitation then becomes an exercise of matching water supply and demand in away that the crop has enough water to complete its cropping cycle. Weather conditions vary greatly across years within environments while both weather and soil conditions vary across locations, which means that drought scenario are extremely variable and these need to be properly characterized as a pre-requisite to undertake drought research. Once the weather scenarios are defined, traits contributing to the crop adaptation to any of these scenarios need to be identified.We believe that much of these traits revolve around the need to optimize plant water use and make it efficient, together with the need to maximize water capture from the soil.Optimization of plant water use consist in identifying traits that will ensure maximum crop growth while keeping sufficient water for the grain filling period, and it deals with controlling water losses, and minimizing leaf canopy development. While tapping more water is surely important, the timing of water extraction to critical crop stages, e.g. the grain filling stage, is even more critical. It depends in great part on the way water has been managed by the plant at earlier stages, in particular to the capacity to develop a smaller crop canopy, or the capacity to restrict plant transpiration, especially under high evaporative demand. Clearly, the development of cultivars capable of better performance under water limited conditions is the result of many possible characteristics that interact with one another andwith the environment, and it is difficult to experimentally determinewhich among these traits has a predominant effect on yield in a given situation. Crop simulation modeling comes in to help to navigate biological complexity by allowing to test the effect of traits on yield acrossmany years of weather andmany locations. It also helps combining both agronomic and genetic options to maximize crop production at the plot level

Autopsy examination in sudden cardiac death: a current perspective on behalf of the Association for European Cardiovascular Pathology.

In sudden cardiac death, an autopsy is an essential step in establishing a diagnosis of inherited cardiac disease and identifying families that require cardiac screening. To evaluate aspects of post-mortem practice in Europe, a questionnaire was designed and circulated to both clinical and forensic pathologists. There was a 48% response rate and information was obtained from 17 countries. The results showed a wide variety in the management of sudden cardiac death, with a general tendency towards a lack of thorough investigation. In up to 40% of cases, autopsies were not performed in subjects less than 50 years who may have died from cardiac disease. Reasons for this were lack of finance and lack of interest from police, legal authorities, and doctors. Only 50% of pathologists seem to follow a standard protocol for autopsy examination, apparently due to lack of expertise and/or training. When autopsies were performed, histology and toxicology were almost always taken, genetic studies were generally available and retention of the heart for specialist study was usually permitted. Our results suggest that although the standard of practice is appropriate in many centres, many more cases should have autopsies, especially in sudden deaths in subjects less than 50 years

Target Population Environments and Pest Distribution Modelling: An Approach towards Pest Prioritization and Preparedness

The transboundary crop pest and disease (P&D) outbreaks over large geographical regions jeopardizes the food security and have broad economic, social and environmental impacts. The upsurge of new crop P&D, such as fall armyworm; cassava mosaic and brown streak virus; banana fusarium wilt tropical race 4 and wheat stem rust Ug99 are having serious repercussions on agriculture. Climate change is, in part, responsible for food chain catastrophes arising from these transboundary P&D. However, there is clear evidence that climate change impacts are altering the distribution of crop P&D. Such accelerated events require more attention on a greater scale to strengthen food security and protect the livelihoods of poor and most vulnerable countries of the world. A well-defined P&D ranking and distribution will focus on supporting policy-making, integrated P&D management as well as tangible pre-emptive breeding strategies at large scale. Here, we have used chickpea homogenous systems units (HSUs) defined by mechanistic models and geo-bio-physical parameters; over which the P&D distribution and rankings were over-layered. The chickpea P&D severity, distributions, social impact and key drivers responsible for spread on these locations were identified by using meta-analysis. Further, in order to understand the possible risks and consequences of P&D population growth and geographical expansion, the CLIMEX package was used. We aim to compare the pest distribution generic models and prioritization methodologies for emerging regional specific P&D. These findings would support policy intrusions associated with long term transformative adaptation strategies for climate change

Maize, sorghum, and pearl millet have highly contrasting species strategies to adapt to water stress and climate change-like conditions

This study compared maize, sorghum and pearl-millet, leading C4 cereals, for the transpiration rate (TR) response to increasing atmospheric and soil water stress. The TR response to transiently increasing VPD (0.9–4.1kPa) and the transpiration and leaf areaexpansion response to progressive soildrying were measuredin controlled conditions at early vegetative stage in 10–16 genotypes of each species grown in moderate or high vapor pressure deficit (VPD) conditions. Maize grown under moderate VPD conditions restricted TR under high VPD, but not sorghum and pearl millet. By contrast, when grown under high VPD, all species increased TR upon increasing VPD, suggesting a loss of TR responsiveness. Sorghum and pearl-millet grown under high VPD reduced leaf area, but not maize. Upon progressive soil drying, maize reduced transpiration at higher soil moisture than sorghum and pearl millet, especially under high VPD, and leaf area expansion declined at similar or lower soil moisture than transpiration in maize and sorghum. It is concluded that maize conserves water by restricting transpiration upon increasing VPD and under higher soil moisture than sorghum and millet, giving maize significantly higher TE, whereas sorghum and pearl millet rely mostly on reduced leaf area and somewhat on transpiration restriction

An integrated research framework combining genomics, systems biology, physiology, modelling and breeding for legume improvement in response to elevated CO2 under climate change scenario

How unprecedented changes in climatic conditions will impact yield and productivity of some crops and their response to existing stresses, abiotic and biotic interactions is a key global concern. Climate change can also alter natural species’ abundance and distribution or favor invasive species, which in turn can modify ecosystem dynamics and the provisioning of ecosystem services. Basic anatomical differences in C3 and C4 plants lead to their varied responses to climate variations. In plants having a C3 pathway of photosynthesis, increased atmospheric carbon dioxide (CO2) positively regulates photosynthetic carbon (C) assimilation and depresses photorespiration. Legumes being C3 plants, they may be in a favorable position to increase biomass and yield through various strategies. This paper comprehensively presents recent progress made in the physiological and molecular attributes in plants with special emphasis on legumes under elevated CO2 conditions in a climate change scenario. A strategic research framework for future action integrating genomics, systems biology, physiology and crop modelling approaches to cope with changing climate is also discussed. Advances in sequencing and phenotyping methodologies make it possible to use vast genetic and genomic resources by deploying high resolution phenotyping coupled with high throughput multi-omics approaches for trait improvement. Integrated crop modelling studies focusing on farming systems design and management, prediction of climate impacts and disease forecasting may also help in planning adaptation. Hence, an integrated research framework combining genomics, plant molecular physiology, crop breeding, systems biology and integrated crop-soil-climate modelling will be very effective to cope with climate change