Thursday, May 5, 2016

Climate-proofing East Africa’s rice sector

For rice as for other crops, the distribution and behavior of diseases is expected to change under the influence of climate change. In fact, it is already doing so. In rice-disease hot spots in Tanzania, 92% of rice farmers with 15–30 years of experience have observed increased temperatures and changing rainfall patterns in terms of timing and amounts — effects they associate with climate change and with changes in both the incidence and the severity of diseases.

Some 91% of farmers are familiar with the symptoms of rice diseases, but few, if any, regularly practise any form of disease control. It has long been known that the most effective way to help farmers overcome diseases is to provide them with rice cultivars that are resistant to those diseases. In East Africa, the commonest rice diseases are bacterial blight, blast (a fungal disease) and Rice yellow mottle virus.

In response to this challenge, Germany’s Federal Ministry for Economic Cooperation and Development (BMZ) funded a 3-year project, ‘Mitigating the impact of climate change on rice disease resistance in East Africa’ (MICCORDEA) carried out by the Africa Rice Center (AfricaRice). The project focused on bacterial blight and blast in Rwanda, Tanzania and Uganda.

“Perhaps the most important outcome of the project is that we have a number of national scientists qualified at master’s and doctoral levels in the three countries,” says Drissa Silué, AfricaRice plant pathologist. “This means that there are now scientists in place in the national programs who can carry out research on rice diseases in general and on these two diseases in particular.”

An immediate upshot of this has been the mapping of the distribution and severity of bacterial blight and blast across the three countries. “This is the first time that we have had detailed maps of the distribution of these diseases in East Africa, which will help target breeding efforts,” says Silué. This work has also established baseline data for measuring changes in disease patterns as climate change takes hold over the coming decades.

The causal organisms of both diseases are highly variable. The variability of blast pathogens is demonstrated by the gene-for-gene theory of genetic resistance — specific resistance genes in rice prevent infection by specific virulence genes of the pathogen. Over 70 major resistance genes have been documented for blast in rice worldwide. Meanwhile, over 30 resistance genes for bacterial blight are known, some of them in native African rice species such as Oryza barthii, O. glaberima and O. longistaminata.

In the MICCORDEA project, rice germplasm known to be carrying resistance genes was screened at disease hot spots in each of the three countries. This is a quick and cheap way of identifying material resistant to local strains of the pathogens and, in the case of blast, the pathotypes prevalent in each hot spot.

Bacterial blight

From the work conducted by Rwanda Agricultural Research Institute (ISAR), Rwanda seems to have the most complex distribution of variation in the two diseases, with both registering considerable diversity across sites. For bacterial blight, two of the sites registered three pathotypes/resistance groups each, but the third site registered uniform moderate resistance across rice lines.

No candidate resistant varieties for use in a bacterial blight-resistance breeding program emerged from this work. However, in a separate experiment conducted by the Rwanda Agriculture Board (RAB), five cultivars proved resistant to all bacterial blight isolates.

In Tanzania, researchers at the Agricultural Research Institute in Uyole found two lines resistant to bacterial blight that show promise for inclusion in the country’s bacterial blight-resistance breeding program. Research testing rice genotypes against five strains from bacterial blight hot spots across the country revealed large variations across seasons and sites, suggesting the worrying prospect of genetic shifts in pathogen populations.

However, six genotypes were resistant to four of the site-specific strains of the disease. In Uganda, the National Agricultural Research Organisation (NARO) and National Crops Resources Research Institute (NaCRRI) found no lines completely resistant to bacterial blight, and just two lines showing moderate resistance. However, in a test of five cultivars against the three most aggressive isolates, AfricaRice’s WITA 9 and NERICA 4 performed best.

In parallel with the fieldwork in East Africa, Georg- August University of Göttingen, Germany, conducted diversity, virulence and toxin production studies on bacterial blight. A major result from the diversity studies was the diagnosis of bacterial blight isolate Ug12 from Uganda.

Meanwhile, the virulence studies identified two genes that conferred broad resistance to bacterial blight — one providing strong resistance and the other moderate resistance. The research also confirmed that African strains of the blight bacterium are distinct from those found in Asia. The toxin production study led the research team to speculate that a low-molecular-weight toxin may be present but not playing a major role in bacterial blight virulence.  


The results of ISAR’s blast screening were more promising than those of its bacterial blight screening, with at least two and up to seven genotypes (each with between one and four resistance genes) showing promise for disease control at each of the three hotspot sites. An inoculation test using the five most virulent isolates of blast against recently released cultivars showed that Rumbuka has broad resistance to all five isolates, while Mpembuke is resistant to two of them. This information should help the extension service target areas for promotion of these new cultivars. 

The upland site of Kyela in southern Tanzania has a particularly diverse and aggressive blast population, which destroyed up to 75% of the rice lines tested, the disease being at its worst early in the rainy season. However, even here, the screening revealed 10 resistant lines (9 with monogenic resistance, 1 with a four-gene combination). These 10 lines have been recommended for use in a breeding program to ‘pyramid’ (i.e. combine) the resistance genes in popular local varieties that are susceptible to the disease.

Five rice lines showed stable resistance to blast across four hotspot sites in Uganda (4 monogenic, 1 with a combination of two genes). Moreover, five accessions (i.e. varieties or landraces originally collected in the field rather than from breeders) also performed well in these hot spots. These accessions include the well-known varieties IR24 and AfricaRice’s own NERICA 1. All these materials were recommended for inclusion in the effort to pyramid resistance genes.

In Germany, institutions at three universities — the Institute of Plant Pathology and Plant Protection, the Karlovsky lab and the Section for Tropical and Subtropical Agriculture and Forestry (SeTSAF) at the Georg-August University of Göttingen; the Institute of Plant Diseases and Plant Protection at Leibniz University, Hannover; and the University of Applied Sciences of Erfurt — investigated the population structure, pathogenicity and mating type of blast pathogens in preparation for further studies on the impact of climate change on disease incidence and severity.

Some 88 blast isolates were used to determine variation in virulence among isolates. The research into mating type revealed the possibility of recombination via sexual reproduction of the blast fungus in East Africa, though this has never been proved to occur in the field.

Resistance analysis in Germany identified two genes with potential for use in East Africa, while a study of cultivar reaction to blast strains demonstrated that NERICA 4 has broad-spectrum resistance to East African strains, though the genetic basis for this is as yet unknown. This makes NERICA 4 potentially doubly interesting, given the resistance to bacterial blight demonstrated in Rwanda.

How will climate change affect disease patterns?

A central aim of the project was to work toward mitigation of the impact of rice diseases as East Africa’s climate changes. The degree studies and short-course training provided for national scientists are a major component of this, as they will give rise to continuing activities over the coming years, enabling scientists to respond to farmers’ changing needs. However, the project also included a component of research to find out how the two diseases are likely to affect the East African rice crop as temperature increases and rainfall becomes more erratic.

The crop model RICEPEST, which determines rice losses to diseases under current climatic conditions, was an obvious place to start. To develop future scenarios, the climate model EPIRICE was used to generate data on projected climate to feed into RICEPEST. This was the first time these two models had been combined. For blast, the news for farmers is good: although it can be locally virulent, the disease currently has a relatively minor impact on rice yields in the region as a whole, and this is predicted not to change in the foreseeable future.

The combined model predicted a less than 2.5% probability of blast epidemic outbreak in Tanzania, with low yield losses (no more than 0.017 t/ha) due to blast up to 2050 (i.e. 35 years hence). However, the news is not so good regarding bacterial blight: this disease is predicted to reduce yields by between 0.47 and 0.67 t/ha by 2050. The implication is that, for East Africa, breeding efforts should focus far more on resistance to bacterial blight than to blast.

Georg-AugustUniversity tested six blast-resistance genes in two genetic backgrounds at two temperatures against a Tanzanian strain of blast. The research found that, in general, both temperature and genetic background tend to affect resistance. However, the good news is that two of the resistance genes were not affected by either temperature or genetic background, providing strong resistance in all cases. Parallel research showed that rice reactions to blast and temperature are both genetic.

A major stress under predicted future climate scenarios will be drought. If rainfall becomes more erratic, rainfed rice in particular is likely to suffer yield losses as it undergoes increasingly long and severe dry spells during the growing season. Drought resistance in rice is complex: there is no major drought-resistance gene, but rather a number of small-effect genes whose impact is cumulative, so that the more of these genes a plant has the more resistant it is. These genes are collectively known as ‘quantitative trait loci’ (QTLs). 

Project research demonstrated that rice plants with a selection of drought-resistant QTLs were more susceptible to bacterial blight than those without them. Moreover, rice lines with both the drought QTLs and a bacterial blight resistance gene suffered more severely from the disease under drought conditions than under ‘normal’ conditions.

This apparent breakdown in resistance would seem to be a major problem, until one looks at parallel research which showed that the effects depend very much on the gene-for-gene alignment of rice resistance with pathogen virulence. With the right bacterial blight-resistance gene combined with drought-resistance QTLs, rice plants displayed increased resistance to the disease under drought. 

The other major component of climate change is temperature. Over the coming decades, East African rice systems are likely to experience gradually increasing temperatures, especially night-time temperatures during the growing season. Two bacterial blight-resistance genes were studied: higher temperatures enhanced the resistance effects of one while reducing the effects of the other!

Clearly, climate-proofing rice against bacterial blight is going to be a complicated business. Another avenue is to tap the resistance genes of O. glaberrima, ensuring these enter the widely grown sativa cultivars. To this end, 18 O. glaberrima accessions were screened, including 9 that had demonstrated resistance to many Philippine strains of bacterial blight.

These accessions were screened against 14 strains of the blight bacterium at two temperatures. Four of the accessions showed broad-spectrum resistance at high temperature. One of these carries a known resistance gene, but the others are still being tested to see whether they carry known resistance genes or novel ones.

Project achievements

“I believe that the project has done what we wanted it to. It has made a significant contribution to preparing the rice production sector for future climate change,” says Silué. “We have a gene for bacterial blight resistance that currently stands up to most of the bacterial blight in East Africa. We also have a pair of genes for blast that not only show durable resistance today, but also seem to be effective at higher temperatures. This means we have the basic tools for climate-proofing existing and new varieties for East Africa.

“The other element of climate-proofing is having the skills on the ground to continue to study the diseases as they evolve over the coming years. This is what the master’s and doctoral training was all about.” All in all, then, a successful project, though there is no room for complacency. Much hard work both in the lab and in farmers’ fields remains to be done in future years to enable East Africa’s rice sector to cope effectively with the disease challenges associated with climate change.

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