Improvement of broad-spectrum disease resistance in rice: how a comprehensive study of natural rice diversity can help to reduce crop losses in developing countries

Repeated crop failure caused by plant diseases is one of the major reasons for food insecurity, hunger and poverty. Rice is the most important cereal crop, providing a daily food source for more than half of the human population, particularly in developing countries of Asia and Africa. Some countries in these regions show the highest population growth and rice production will therefore play a pivotal role in ensuring global food security in the coming decades. The planting of rice varieties with broad-spectrum disease resistance is the most sustainable strategy to protect rice from diseases and to ensure stable rice production. The term broad-spectrum refers to resistance mechanisms that are effective against all or most strains of a pathogen. It has been shown that this type of resistance is of particular durability in the field. Despite the potential benefit of broad-spectrum resistance for breeding and agriculture, the genetic and molecular basis of this resistance type is poorly characterized. Only few broad-spectrum resistance genes have been identified in cereals so far and even less are widely used in breeding. Modern rice cultivars only capture a small fraction of the diversity that exists among wild rice and landraces. This is because only a limited number of landraces and wild rice lines gave rise to today’s rice cultivars during domestication and breeding. As a consequence, a wealth of genes and gene variants of potential agricultural value can be found in landraces and wild rice that have not yet been incorporated into modern rice cultivars. Genebanks play an important role in preserving this diversity by collecting, storing and maintaining thousands of plant accessions. For example, the International Rice Genebank Collection located at the International Rice Research Institute (IRRI) in the Philippines contains more than hundred thousand different rice accessions from all over the world. Harnessing this diversity will be one of the greatest opportunities for crop improvement in the future. However, a systematic screening of these large collections for new and agronomically useful genes remains technically challenging. Variation in a particular trait (phenotype) between different plant lines is caused by polymorphisms on the genetic (DNA) level. Genome wide association studies (GWAS) use sophisticated statistical approaches to link phenotypic variation in natural populations to genetic polymorphisms. GWAS became the method of choice to unlock the enormous diversity stored in genebanks and to discover new genes and gene variants in large and diverse collections. The major obstacle for GWAS in cereals was the lack of adequate information on genome architecture and genome variation. However, recent advances in high-throughput genome sequencing made it possible to detect millions of single nucleotide polymorphisms (SNPs) simultaneously. This technical progress paved the way for the discovery of new trait-marker associations in large collections of diverse rice accessions.

The objective of this work is to identify new broad-spectrum disease resistance genes in rice landraces against the two most devastating diseases of rice, rice blast and bacterial blight (BLB), and to start their introgression into modern rice cultivars through marker-assisted forward breeding. We will make use of the recent resequencing of 3,000 rice genomes from the International Rice Genebank Collection (IRGC). This project provided the high-density molecular information about genome architecture that is required to identify broad-spectrum resistance genes through genome-wide association study (GWAS). We plan to screen a sub-selection of the 3,000 rice genomes project for broad-spectrum resistance against 10 rice blast and BLB races, respectively. GWAS will then be used to identify genetic regions and molecular markers linked to broad-spectrum disease resistance. The molecular marker information will serve as the basis to introgress these broad-spectrum resistance loci from the respective donor line into elite rice cultivars. In addition, we will validate candidate rice blast resistance genes. This approach aims to identify the specific genetic locations, genes and gene variants that control the broad-spectrum disease resistance. Identification of these genetic locations in combination with marker-assisted forward breeding will enable the precise transfer of broad-spectrum disease resistance genes from landraces into elite cultivars.

The transfer of agronomically important traits from landraces into modern cultivars is often hindered by the fact that most landraces show lower yield and are associated with other unwanted traits. In this project, we established a unique collaboration between rice research and breeding. Our approach will allow us to separate the desired broad-spectrum resistance from unwanted traits and to specifically transfer the genes of interest into modern rice cultivars by using marker-assisted breeding. Our research will result in the release and adoption of rice cultivars with improved broad-spectrum disease resistance. Planting of these varieties will ensure higher and more stable rice harvests and reduce the use of fungicides. This will result in an economic and environmental benefit for rice farmers and consumers in developing countries. IRRI is the largest and most experienced rice breeding institution in the world. The collaboration with IRRI will ensure that the research results generated during this project can be optimally disseminated to farmers.

• Rice growing countries in East Asia and Africa

• Link to project on SNSF research database P3