Casiana Vera Cruz

Using Genetic Diversity to Achieve Sustainable Rice Disease Management

Host plant resistance is an important tool for rice disease control and has played a key role in sustaining rice productivity, especially in tropical Asia. Deploying resistant varieties as a means of disease control is attractive because it requires no additional cost to farmers and is environmentally safe (62). Furthermore, resistant varieties can be easily disseminated as seeds, leading to wide adoption (12). These are important considerations, because for resource-poor rice farmers in developing countries, the options for managing diseases are few. For example, during the 1970s and 1980s, when epidemics of rice tungro were frequent in the Philippines and Indonesia, farmers expressed more confidence in using resistant varieties than in other control measures. Disease control using chemicals is more common in the temperate or subtropical production environments where farmers apply fungicides for controlling blast (caused by Pyricularia grisea) and sheath blight (caused by Rhizoctonia solani). Despite regional differences in control measures, planting resistant varieties is considered most effective by rice farmers. Hence, breeding for disease resistance has been a major objective in rice improvement programs conducted at international agricultural research centers, such as the International Rice Research Institute (IRRI), and at the national agricultural research systems (NARS) of developing countries. There are limitations, however, in using resistant varieties alone to manage rice diseases. Most varieties are resistant only to a few major diseases that are the subjects of intensive breeding efforts. The rice production environments, particularly in the tropics, are habitats of many rice pathogens causing varying degrees of damage. Even the “minor” diseases collectively could pose a significant threat to production (63). Thus, pathologists and breeders have to deal with yield loss caused by diseases of epidemic and endemic nature. Epidemic loss is dramatic but less frequent, whereas endemic loss is less obvious but pervasive in each cropping season. Recent surveys indicated that an estimated annual yield loss from 1 to 10% was due to a combination of different diseases (80). Thus, resistance against a few targeted diseases offers only a partial solution to rice disease problems. To those diseases caused by nonspecialized pathogens, such as sheath blight and false smut (caused by Ustilaginoidea virens), no useful source of resistance has been identified to improve the resistance of rice varieties. To achieve sustainability of rice production in Asia, we need a rice production system built upon effective resistant varieties with broad resilience to a range of diseases and insect pests. Broad-spectrum resistance at the genotypic level and sustainability at the cropping systems level are therefore complementary approaches in managing rice diseases. Although considerable progress has been made over the past decades, much more can be done to integrate these two approaches to achieve results in farmers’ fields. Modern agricultural development has transformed the diverse, traditional rice production system into a monoculture system that relies only on a few fertilizer-responsive and high-yielding varieties. Farmers’ preference to high yield has led to wide adoption of modern rice varieties cultivated in millions of hectares of rice land. Although most modern varieties have built-in resistance against multiple diseases, genetic uniformity inevitably predisposes the system to disease epidemics, and under certain circumstances can lead to serious yield loss caused by diseases and insect pests (43). Varieties carrying a few resistance genes in a uniform genetic background are vulnerable to rapid adaptation of pathogens and pose uncertainty to farmers. For instance, emergence of new pathogen races caused several blast epidemics in Korea in the 1970s, leading to yield losses of 30 to 40% (38). In the 1980s, other disease outbreaks on a regional scale included epidemics of bacterial blight in northern India and Southeast Asia, tungro in Southeast Asia, and bacterial blight and blast in Japan (38,61,89). Another impact of the monoculture system is the gradual decline in the diversity of varieties grown by farmers. As modern high-yielding varieties expand to millions of hectares, they also replace the traditional varieties. Although useful genes from these traditional varieties are being used in breeding for modern varieties, many unique attributes and gene combinations resulting from years of selection are difficult to reconstitute. To achieve the productivity needed, it is not possible to revert to planting diverse traditional varieties that are poor yielding. However, it is within our capacity to work toward disease management methods that sustain productivity yet maintain adequate diversity and resilience in the production systems. In the past two decades, IRRI has moved toward increasing genetic diversity of modern rice varieties through resistance breeding (12,39,43) and deployment of different resistance genes based on an unCorresponding author: Twng Wah Mew, Entomology and Plant Pathology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines; E-mail: T.Mew@cgiar.org

Rice Molecular Breeding Laboratories in the Genomics Era: Current Status and Future Considerations

Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information—coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools—provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to “bridge the application gap” between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs.

Looking Ahead in Rice Disease Research and Management

Rice production is subject to increasing environmental and social constraints. Agricultural labor and water, which are key resources for rice production, illustrate this point. Nearly all rice-producing countries face reduced availability of agricultural water and shortage of farm labor. Plant pathologists should be concerned with such large-scale evolutions because these global drivers have an impact on not only the rice production system but also on the individual field and single-rice-plant levels. These concerns are closely associated with the long-term sustainability and environmental consequences of the intensification of agricultural systems brought about by problems of feeding a rapidly growing human population. Furthermore, genetic diversity in rice production has been reduced, thus inducing frequent disease epidemics and pest outbreaks. Looking ahead, we need to realize the need to maintain the diversity and yet retain the high productivity of the system. Natural resources, including genetic resources, are not infinitely abundant. We have to be efficient in utilizing genetic resources to develop durable resistance to rice diseases. Developing resistance is an important first step in tackling the disease problem, but it is not the only step available to achieve durability. Deployment of resistance must be considered in conjunction with development of host plant resistance. To attain durability, we need a better understanding of the coevolution process between the pathogen and the host resistance gene. Our target is an integrated gene management approach for better disease control and more effective utilization of genetic resources. Plant pathology, as an applied science, derives its strengths from various disciplines. To do the job right, we need a better understanding of the pathosystems, the epidemiology, and the coevolution process between the pathogen and the host resistance gene. The challenge, as pointed out by pioneers in our profession, is to prove the usefulness and the relevance of our research. Thus, we need to strike a balance between mission-oriented and fundamental research and make sure that our profession is (still) useful in the information technology and genomic era. We believe that a gene-based and a resource-based disease management approach should allow us to incorporate these new scientific developments. However, we do need to incorporate the new science for fundamental research to solve practical problems of rice production.

Genomics-Based Diagnostic Marker Development for Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola

A computational genomics pipeline was used to compare sequenced genomes of Xanthomonas spp. and to rapidly identify unique regions for development of highly specific diagnostic markers. A suite of diagnostic primers was selected to monitor diverse loci and to distinguish the rice bacterial blight and bacterial leaf streak pathogens, Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola, respectively. A subset of these primers was combined into a multiplex polymerase chain reaction set that accurately distinguished the two rice pathogens in a survey of a geographically diverse collection of X. oryzae pv. oryzae, X. oryzae pv. oryzicola, other xanthomonads, and several genera of plant-pathogenic and plant- or seed-associated bacteria. This computational approach for identification of unique loci through whole-genome comparisons is a powerful tool that can be applied to other plant pathogens to expedite development of diagnostic primers.

Controlling rice bacterial blight in Africa: Needs and prospects

Rice cultivation has drastically increased in Africa over the last decade. During this time, the region has also seen a rise in the incidence of rice bacterial blight caused by the pathogen Xanthomonas oryzae pv. oryzae. The disease is expanding to new rice production areas and threatens food security in the region. Yield losses caused by X. oryzae pv. oryzae range from 20 to 30% and can be as high as 50% in some areas. Employing resistant cultivars is the most economical and effective way to control this disease. To facilitate development and strategic deployment of rice cultivars with resistance to bacterial blight, biotechnology tools and approaches, including marker-assisted breeding, gene combinations for disease control, and multiplex-PCR for pathogen diagnosis, have been developed. Although these technologies are routinely used elsewhere, their application in Africa remains limited, usually due to high cost and advanced technical skills required. To combat this problem, developers of the technologies at research institutions need to work with farmers from an early stage to create and promote the integration of successful, low cost applications of research biotech products. Here, we review the current knowledge and biotechnologies available to improve bacterial blight control. We will also discuss how to facilitate their application in Africa and delivery to the field.

Phylogenomic Relationships of Rice Oxalate Oxidases to the Cupin Superfamily and Their Association with Disease Resistance QTL

Rice oxalate oxidase genes (OXO) may play a role in resistance to Magnaporthe oryzae. Genome analyses showed four tandemly duplicated OXO genes, OsOXO1–OsOXO4, which mapped to a blast resistance QTL in chromosome 3. These genes have >90% nucleotide and amino acid identity, but they have unique gene structures, conserved motifs, and phylogeny compared to the 70 other members of the cupin superfamily in the Nipponbare genome, which were divided into several classes. In resistant and susceptible Vandana/Moroberekan advanced backcross lines, only OsOXO4 was expressed during rice–M. oryzae interactions, and its expression increased earlier in resistant than susceptible lines. The earlier expression of OsOXO4 in resistant lines correlated with a 26-bp promoter insertion containing an additional copy of the bacterial responsive nodulation cis-element. Our results showed that OsOXO1–4 are in a separate class of rice cupin genes and supports a role for the promoter variant of OsOXO4 in resistance to M. oryzae.

Allele mining and enhanced genetic recombination for rice breeding

Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources.

Large scale germplasm screening for identification of novel rice blast resistance sources

Rice is a major cereal crop that contributes significantly to global food security. Biotic stresses, including the rice blast fungus, cause severe yield losses that significantly impair rice production worldwide. The rapid genetic evolution of the fungus often overcomes the resistance conferred by major genes after a few years of intensive agricultural use. Therefore, resistance breeding requires continuous efforts of enriching the reservoir of resistance genes/alleles to effectively tackle the disease. Seed banks represent a rich stock of genetic diversity, however, they are still under-explored for identifying novel genes and/or their functional alleles. We conducted a large-scale screen for new rice blast resistance sources in 4246 geographically diverse rice accessions originating from 13 major rice-growing countries. The accessions were selected from a total collection of over 120,000 accessions based on their annotated rice blast resistance information in the International Rice Genebank. A two-step resistance screening protocol was used involving natural infection in a rice uniform blast nursery and subsequent artificial infections with five single rice blast isolates. The nursery-resistant accessions showed varied disease responses when infected with single isolates, suggesting the presence of diverse resistance genes/alleles in this accession collection. In addition, 289 accessions showed broad-spectrum resistance against all five single rice blast isolates. The selected resistant accessions were genotyped for the presence of the Pi2 resistance gene, thereby identifying potential accessions for isolation of allelic variants of this blast resistance gene. Together, the accession collection with broad spectrum and isolate specific blast resistance represent the core material for isolation of previously unknown blast resistance genes and/or their allelic variants that can be deployed in rice breeding programs.

Update on Bacterial Blight of Rice: Fourth International Conference on Bacterial Blight

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Development of a Genomics-Based LAMP (Loop-Mediated Isothermal Amplification) Assay for Detection of Pseudomonas fuscovaginae from Rice

The vast amount of data available through next-generation sequencing technology is facilitating the design of diagnostic marker systems. This study reports the use of draft genome sequences from the bacterial plant pathogen Pseudomonas fuscovaginae, the cause of sheath brown rot of rice, to describe the genetic diversity within a worldwide collection of strains representing the species. Based on a comparative analysis with the draft sequences, primers for a loop-mediated isothermal amplification (LAMP) assay were developed to identify P. fuscovaginae. The assay reported here reliably differentiated strains of P. fuscovaginae isolated from rice from a range of other bacteria that are commonly isolated from rice and other plants using a primer combination designated Pf8. The LAMP assay identified P. fuscovaginae purified DNA, live or heat-killed cells from pure cultures, and detected the bacterium in extracts or exudates from infected host plant material. The P. fuscovaginae LAMP assay is a suitable diagnostic tool for the glasshouse and laboratory and could be further developed for in-field surveys.