Three main diseases are hampering the effort to intensify rice cultivation in Africa: rice blast (due to pathogenic fungus Magnaporthe oryzae), bacterial blight (caused by Xanthomonas oryzae pv. oryzae) and rice yellow mottle disease (initiated by a Sobemovirus).
Rice yellow mottle virus (RYMV) was first observed in Kenya in the late 1960s. It is now a major disease of rice in the irrigated and lowland ecologies in almost all rice-producing countries in Africa, causing yield losses of 25–100% (depending on the rice variety grown).
For a long time, breeders had access to only one gene for RYMV resistance (rymv1), albeit in four versions — one (rymv1-2) available in an indica variety (Gigante) originating from Mozambique and the others (rymv1-3, rymv1-4 and rymv1-5) in Oryza glaberrima landraces (TOG5681, TOG 5672 and TOG5674, respectively).
These O. glaberrima genes are in several of the Lowland NERICA varieties. Subsequently, a second gene for RYMV resistance was found in O. glaberrima (RYMV2). Unfortunately, there are natural resistance-breaking isolates of the virus. This means that if we release a variety with one of the resistance genes into a hotspot area, the resistance-breaking viruses will survive and multiply, so that the final state is no better than the first!
As an insurance policy against this happening, the AfricaRice breeding strategy is to combine two resistance genes in varieties for release in hotspot areas. This work is being done in collaboration with Institut de recherche pour le développement (IRD).
In addition, since it has been shown that the occurrence of resistance-breaking strains is correlated with high disease inoculum, AfricaRice is seeking ways to reduce the disease pressure as a component of an integrated management system to reinforce the durability of the resistance.
Screening for RYMV resistance is conducted in a screenhouse in Cotonou, Benin. The screenhouse is designed to prevent the disease from escaping into the ‘wild’. Segregating populations (the offspring of crosses that are not yet true-breeding) are mechanically inoculated with the virus, and the disease is allowed to run its course.
In addition to visible symptoms, we now have access to three molecular markers for RYMV resistance, which can be detected in the laboratory to show the presence or absence of the resistance gene (or genes) in any particular plant.
Blast disease affects (particularly upland) rice in most parts of the world, inflicting yield losses of 70–80% under disease-favorable conditions. Bacterial blight (BB) has been known in Africa since the late 1970s in the irrigated ecology of the savannah and Sahel regions — yield losses attributable to BB are in the range of 20 to 78% in Southeast Asia and India.
There are several known major resistance genes for each of these diseases (blast resistance: Pi1, Pi2, Pia; BB resistance: Xa1, Xa2, … Xa26), but these are not durable, so new pathogens can emerge and ‘break’ the resistance conferred by these genes. The aim of the AfricaRice breeding program is to combine (pyramid) two or more of these non-durable resistance genes into varieties for farmers.
In addition, some major genes that induce partial durable resistance to blast in Asia (e.g. Pi40) will be tested under African conditions to see if they can be used to protect African rice varieties against blast disease.
The plant pathology laboratory is working in collaboration with the Japan International Research Center for Agricultural Science (JIRCAS) and the Green Super Rice project to determine which resistance genes are best for which populations of the disease — this will indicate the best candidates for pyramiding.
For both diseases, artificial screening of breeding and introduced material will soon be conducted in a climate-controlled greenhouse (expected to be operational in mid-2012).