Friday, June 5, 2015

Improving predictive model for rice in arid environments

Projections of the likely impacts of climate change in the future are based on complex computer simulation models. A major emphasis in climate simulation modeling is determining the likely impact of climate change on agriculture.

The Africa Rice Center (AfricaRice) has long been involved with models that simulate crop development and predict planting dates to avoid the worst of seasonal stresses. In the mid- 1990s, AfricaRice researchers helped develop the model ORYZA_S by combining two existing models: ORYZA1, a rice crop model developed by Wageningen University and the International Rice Research Institute (IRRI) for irrigated conditions in Asia, and RIDEV, a much simpler model developed by AfricaRice simulating phenology of rice and sterility due to heat or cold stress under irrigated conditions in the Sahel.

An improved version, ORZYA2000, was released in 2001 by IRRI, followed by progressive revisions until 2009, but it was based on ORYZA1 and therefore fails to accurately simulate yield under Sahelian conditions.

“We chose to proceed with the 2009 version of ORYZA2000,” says Pepijn van Oort, crop modeler at AfricaRice, “because we hope that any improvement in the main model will also be useful under different conditions from those we tested, such as with water or nitrogen limitation, or in crop rotations. With ORYZA_S such applications were not possible.”

This meant that 20 years on, there was a need to take a fresh look at phenology and cold and heat stress in the Sahel. Developing new subroutines and other refinements to obtain a better predictive model for rice in the Sahel — in a changed climate with respect to the 1990s — became the new challenge for AfricaRice.

Computer-based models create simplified versions of reality and so should never be considered perfect. “Perfect prediction is suspect, may be caused by over-parameterization on a limited dataset, and runs a risk of adjusting parameter values without sound eco-physiological justification,” says van Oort. “We have tried to avoid this by using a large dataset, by making only modifications substantiated by solid experimental research, and by keeping calibration to a minimum.”

The large data set was obtained by Michiel de Vries, then AfricaRice irrigated-rice agronomist, from monthly sowings of variety IR64 at two sites in the Senegal River valley over 15 months in 2006–2007, a total of 29 treatments.

The modifications made, chosen on the basis of previous research, comprised: (i) so-called ‘cardinal’ temperatures for development; (ii) cardinal temperatures for early leaf growth; (iii) spikelet-formation process; and (iv) heat- and cold-induced sterility.

The model was specifically calibrated only for developmental characters. Moreover, to test the new heat- and cold-induced sterility subroutines, validation simulations were run to predict yield, first using observed development and number of spikelets, and second with simulated development and number of spikelets.

“The first thing we needed to adjust for IR64 grown in the Sahel was the cardinal temperatures,” says van Oort. “In particular, IR64 has a much higher base temperature than the default setting in ORYZA2000 (14°C cf. 8°C), a slightly higher optimum temperature (31°C cf. 30°C), and apparently experiences no delay in development at temperatures above the optimum (i.e. there is no maximum temperature, at least not under the conditions tested).” With these parameters corrected, the model gave improved simulation of rice development and therefore yield.

“We started with the situation in which ORYZA2000 over-estimated heat-induced sterility and underestimated cold-induced sterility,” says van Oort. “The new heat and cold subroutines give much better simulation of the two sterilities and, consequently, final yield.” The keys to improving heat-induced sterility simulation were transpirational cooling and flowering time, while the key to improved cold-induced sterility was using minimum daily temperature rather than average daily temperature.  

“These modifications are all logical if we think about where we’re working,” says van Oort. “ORYZA2000 was developed in and for Southeast Asia which, for the most part, is a humid tropical environment. In comparison, arid regions like the Sahel experience much lower humidity and much greater ranges in daily temperature.”

In a dry environment, the relative humidity (RH) is much lower than in a humid one. Thus, the ability of a plant to cool itself through transpiration is much greater in the arid zone (just like humans can sweat to cool themselves in a dry environment, while sweating in a humid environment just makes one wet!).

According to the subroutines developed by van Oort, at 35°C and 30% RH (typical of the Sahel), a plant can cool by 6°C relative to the air temperature via transpiration, while at 30°C and 90% RH (typical of humid tropical Southeast Asia), there is zero ability to cool via transpiration.

Flowering earlier in the morning means the rice plants are exposed to a lower temperature, which reduces the risk of heat sterility. In general, rice plants flower earlier during the day in hotter environments, but this characteristic is also genetically controlled and so varies with genotype. “Putting flowering time into the model now allows us to simulate how much yield gain can be obtained from breeding for earlier-flowering varieties,” says van Oort.

Arid environments also have much larger temperature differences during the day. “On one day in January, temperature increased from 8°C to 33°C. According to ORYZA2000, the cold-sterility risk was small, because average temperature was ‘safe’, but it was clear that the minimum of 8°C caused severe cold sterility. We therefore changed the subroutine to use minimum rather than average temperature.”

“Model calibration can be a tricky enterprise,” says van Oort. “At a certain point we found that the model was overestimating biomass production and therefore also yield. An effective trick to increase accuracy for yield was to modify the parameter that determines that number of spikelets formed per unit of biomass. But this led to unrealistic parameter values, because the real problem was that the model was overestimating total biomass. So we kept focused on the real causes of errors and played no artificial tricks with parameters.”

At the end of the day, van Oort and the team were able to modify the ORYZA2000 model to better predict IR64 rice development and yield in the arid Sahel of the Senegal River valley. Moreover, it did a better job of these predictions than the benchmark ORYZA_S that was developed for the same environment and optimized for IR64 in 1999.

“It is important to remember that this work was not done in isolation,” says van Oort. “It would not have been possible without the work done in the 1990s by Michael Dingkuhn (formerly with AfricaRice) and his co-workers in developing ORYZA_S and RIDEV.” In fact, the Sahel-adapted ORYZA2000 of van Oort and partners uses several equations and parameters derived from ORYZA_S and RIDEV.

“Our results indicate a need for further research into the components we identified, and to re-assess the climate risk to rice in arid regions,” concludes van Oort. “Our discoveries about the importance of cardinal temperatures, heat tolerance and heat avoidance also provide a basis for variety selection, as these three critical characteristics are genetically controlled and vary across cultivars.”

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Monday, June 1, 2015

AfricaRice recognized as an important partner of Madagascar

“We are immensely gratified that AfricaRice has been recognized as an important partner of the government of Madagascar to help realize its vision of becoming the rice granary of the Indian Ocean,” said Africa Rice Center (AfricaRice) Director General Dr Harold Roy-Macauley during his recent visit to the country. “AfricaRice is best placed to contribute to this goal.”

Madagascar and AfricaRice have forged close ties since 2010, when the country joined AfricaRice. Dr Lala Razafinjara, Director General of FOFIFA – the main component of the national agricultural research system in Madagascar – is heading the Program Committee of the AfricaRice Board of Trustees.

The AfricaRice delegation led by Dr Roy-Macauley was received in audience by the President of Madagascar and had discussions with the Honorable Minister of Agriculture of Madagascar Mr Roland Ravatomanga and the FOFIFA rice team.

The delegation also met with representatives of the African Development Bank, the Government of Japan, the Food andAgriculture Organization of the United Nations (FAO) and the Centre de coopération internationale en recherche agronomique pour le développement (CIRAD) of France.  

Dr Roy-Macauley participated in an official ceremony chaired by the Honorable Minister of Agriculture in Antsirabe on 22 May 2015, where two new cold-tolerant rice varieties – named FOFIFA 183 and FOFIFA 184 – were released. These varieties were developed in collaboration with FOFIFA, as part of the ‘Stress-Tolerant Rice for Africa and South Asia’ (STRASA) project, supported by the Bill &Melinda Gates Foundation.

The ceremony also provided an opportunity to AfricaRice to present a range of agricultural equipment for the Rice Hubs of Ambohibary and Ankazomiriotra in the Vakinankaratra region of Madagascar as part of the collaborative project on the Support to Agricultural Research for Development of Strategic Crops in Africa (SARD-SC), funded by the African Development Bank (AfDB).

Rice is both the main crop and the staple food of the majority of the population of Madagascar. Per capita rice consumption is about 138 kg per year in the villages and about 118 kg in cities. Once self-sufficient, the country has been a net-importer of rice since 1980. Major constraints to rice production include lack of access to agricultural equipment, good quality seed, mineral fertilizers and a range of biotic and abiotic stresses, such as low temperature or cold.

AfricaRice scientists based in Madagascar are closely working with FOFIFA scientists to address these challenges. Madagascar is increasingly benefitting from collaborative R4D activities carried out by AfricaRice and its partners with support from several donors, including the AfDB, Japan, the Bill & Melinda Gates Foundation, and the CGIAR Research Program on Rice known as the Global Rice Science Partnership (GRiSP).

FOFIFA is involved in the Africa-wide Rice Task Forces convened by AfricaRice, particularly focused on rice breeding and agronomy, in line with its priorities. It has welcomed the approach of the Rice Sector Development Hubs to achieve greater coherence and impact.

Thanking the Minister of Agriculture and the Director General of FOFIFA as well as all the partners supporting the rice sector in Madagascar, Dr Roy-Macauley said that AfricaRice sees Madagascar as the regional center for rice research and development for the countries of the Indian Ocean.