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Beating blast

Farmer observing rice crop protected by blast resistance genes (© IRRI)
Farmer observing rice crop protected by blast resistance genes
© IRRI

The rice fungal disease, rice blast (caused by Magnaporthe oryzae), is a scourge to farmers across the world. Found in about 85 countries, it is highly destructive in lowland rice in temperate and subtropical Asia, and upland rice in Asia, Latin America and Africa. It has been estimated that, each year, the disease kills enough rice to feed 60 million people. Known as 'rice fever' in Chinese literature, the disease has been known to rice farmers for hundreds of years. But modern intensive agriculture (large areas of intensive rice production, dense cropping in space and time, and increased nitrogen fertiliser use) has contributed to spread of the disease.

Some farmers in China, Europe, Japan, Korea, and the US use fungicides for control. But most countries have relied upon plant breeding to develop blast-resistant varieties. Traditionally, breeders relied on 'single gene' resistance which works, but only for a short time: due to the variation of the pathogen, single resistance usually loses its effectiveness when the virulent strain dominates the pathogen population. To effectively combat blast, the International Rice Research Institute (IRRI) has been working to combine different race-specific genes and genes conferring general resistance to all races.

Breeding for better varieties

Advances in molecular biology and sequencing technologies have offered new opportunities to out-smart the pathogen. Through an international collaboration effort, scientists found a resistance gene called Pi9 (derived from a wild rice species Oryza minuta) that is effective over broad areas in South East Asia and China. Through detailed molecular analysis, IRRI scientists recently isolated the corresponding 'avirulence' gene, AvrPi9, in the pathogen. The resistance gene Pi9 recognises AvrPi9 so when the two genes encounter each other, resistance is triggered. A high correlation between the effectiveness of Pi9 resistance and the presence of AvrPi9 was observed by assessing different isolates (pathogens collected from diseased rice leaves or panicles) from the Philippines and Yunnan Province in China. "This illustrates the potential of pathogen surveillance for finding smart genes in breeding," explains IRRI scientist Dr Hei Leung.

Inter-planting of rice varieties (© IRRI)
Inter-planting of rice varieties
© IRRI

IRRI scientists together with scientists at Yunnan Agricultural University also introduced the practice of interplanting resistant and susceptible glutinous rice varieties with blast-resistant hybrid varieties in Yunnan province, China. Blast caused significant yield loss in traditional glutinous rice varieties and farmers were spraying fungicides multiple times in a cropping season. Interplanting helps change the micro-climate in the crop, resulting in less pathogen infection relative to that in a pure stand of glutinous rice. In interplanted plots, disease was reduced by 94 per cent, compared to monoculture plots, and this practice was adopted on over 1 million hectares*. Interplanting, while not necessarily applicable to all rice production systems, has raised awareness of the importance of plant diversity for managing diseases.

Despite some successes, however, the extremely high pathogenic variability and adaptability of the blast pathogen remains the most challenging problem in managing blast in large rice production areas. Most varieties currently have good resistance due to active breeding programmes, reflected by relatively few episodes of variety collapse, but there are still many vulnerable areas. "Without significant investment in pathogen monitoring and upgrading resistance in rice varieties, we are seeing a gradual erosion of resistance," Leung reveals. He gives the example of the 'mega variety' IR64, which was released in the mid-1980s and carried five blast-resistant genes. Susceptibility began to be seen in Indonesia in the early 2000s; more recently high susceptibility has been observed in the Philippines, with an outbreak of blast in IR64 in 2013.

Arms race

According to Leung, the monitoring of blast resistance in varieties and the effectiveness of resistant genes is essential to staying ahead of the pathogen. Using smart combinations of resistance genes to stabilise the pathogen requires surveillance over large areas and an understanding of how the pathogen changes. International collaboration is needed to collect and characterise pathogen populations in different countries. "Understanding the pathogen population dynamics should facilitate the development of a sustainable scheme for managing blast disease," IRRI scientist Bo Zhou adds.

Outbreak of rice blast disease in IR64 (© IRRI)
Outbreak of rice blast disease in IR64
© IRRI

Leung also highlights the need to tap into the diversity of rice by using low-cost genome sequencing to fully explore and deploy rice diversity. IRRI has around 120,000 accessions of rice germplasm maintained in the International Rice Gene Bank but only about five per cent has been actively used in breeding programmes. "We have recently launched an ambitious project to sequence ten per cent of the accessions," he explains. "So far we have obtained sequence information from 3,000 rice genomes. This will enable us to use the DNA-fingerprints of the rice accessions to select those with good potential for resistance breeding, and for improving other traits as well."

With growing concern about the use of excess chemicals, IRRI expects that building better blast resistance into rice varieties will be the primary crop protection strategy in the future. But with an unusually high capacity to change and adapt, breeding for blast resistance will be a never-ending process: "Developing blast resistance varieties is an 'arms race' between rapid pathogen evolution and rice breeders," Leung states.

* Zhu Y, Chen H, Fan J, Wang Y, Li Y, Chen J, Fan J, Yang S, Hu L., Leung H, Mew TM, Teng PS, Wang Z, Mundt CC. 2000. Genetic diversity and disease control in rice. Nature. 406:718-722.

With contributions from: Hei Leung and Bo Zhou, IRRI

Date published: January 2014

 

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