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Final Report Summary - RXOMICS (Identification of novel genes conditioning bacterial blight resistance in rice using genomic resources and functional analysis tools.)

One of the challenges of the RXOMICS project is to understand how rice interacts with bacterial pathogens to result in resistance or disease. The main goal is to accelerate the gene discovery for resistance to rice bacterial diseases. We have tackled this challenge from both the plant (rice) and pathogen (X.oryzae) sides by integrating molecular, genomic and genetic approaches performed in our laboratories (Leach and Verdier) and field (with our partners in Mali, Burkina-Faso, Colombia and the Philippines). Our goals are to identify sources of broad-spectrum disease resistance effective against at least two bacterial diseases.

Rice and its bacterial pathogens, Xanthomonas oryzae pvs, provide an excellent model system to assess the potential of biotechnology tools for delivery into practical products in the field. Xanthomonas oryzae is a group of plant pathogenic bacteria composed of both weak and highly virulent members that are genetically and geographically distinct from one another. Pathogenic Xanthomonas oryzae cause important bacterial diseases of rice known as bacterial blight (BB) and bacterial leaf streak (BLS). These diseases which occur as vascular wilt and leaf streak at different stages of the crop severely affect rice production worldwide, particularly in irrigated rice growing areas. Within the Xanthomonas oryzae group, both X.oryzae pv. oryzae (Xoo) and oryzicola (Xoc) that are considered quarantine organisms in all rice-growing countries, represent significant threats for riziculture and global food security. Given the severity of these bacterial diseases, achieving stable resistance against will provide yield stability, and increase profitability of rice farming.The main goal in the RXOMICS project is to accelerate the gene discovery for important agronomic traits, focusing on resistance to BB and BLS. The main achievement was the discovery and characterization of resistance genes to bacterial diseases by revealing novel resistance loci in rice varieties. To facilitate the strategic deployment of rice cultivars with resistance to bacterial diseases, new approaches for rapid diagnostic of the diseases were developed. Altogether the major achievements of the RXOMICS project should allow the development of ecologically sustainable forms of rice bacterial disease control.
The work accomplished during RXOMICS was conducted at Colorado State University and IRD France. New skills and knowledge in plant genetics, genomics, and diagnostics of pathogens were developed. Collaborations established among partners at Colorado State University, IRD Montpellier and other institutions in the USA and France will allow long-lasting partnership among diverse institutions.

Major results:
• An indica rice Multi-parent Advanced Generation Inter-Cross (MAGIC) population, a novel mapping resource that allows high resolution for detecting quantitative trait loci (QTL), was obtained and used. A random subset of lines (eighth selfed generation S8) was selected and genotyped by sequencing, along with the eight founders. To identify QTL conferring broad spectrum resistance, the S8 subset and founders were phenotyped with Xoc and Xoo strains in the greenhouse. In 2014 this subset was phenotyped in Mali with several Xoc and Xoo strains representing different lineages or races known so far. Genome-wide association and interval mapping analysis were performed to map disease resistance QTL. This approach allowed the identification of novel disease resistant QTL effective against Xoc and Xoo, suggesting potential new sources of broad-spectrum resistance.
• We demonstrated the ability of X11-5A to express and deliver TAL effectors. We demonstrated that heterologous expression of selected TAL effectors in US X. oryzae strain X11-5A caused a substantial increase in virulence on diverse rice varieties. Using X11-5A containing a new TAL (TAL7b) on a subset of MAGIC lines allowed us to identify new loci involved in resistance to this new virulence factor.
• We identify, in the heirloom variety Carolina Gold Select, a new mechanism of rice resistance involving TAL effectors. This resistance manifests in a strong suppression of disease development in response to diverse TAL effectors from both X. oryzae pathovars. The resistance is conferred by a single dominant locus, designated Xo1(t), that maps on chromosome 4 of the rice genome and confers complete resistance to African strains of X. oryzae pv. oryzicola. This is the first dominant resistance locus against bacterial leaf streak in rice
• New draft genomic sequence of African X. oryzae strains were acquired and used to develop specific diagnostic primers. Primers were designed based on predicted ORFs specific to 3 African Xoo strains, and others specific to African X. oryzae pv. oryzicola (Xoc) strains. The same strategy was conversely used to design primers specific to Asian strains of Xoo and Xoc.
• A recent advance in molecular diagnostics is the novel loop mediated isothermal amplification (LAMP) method. We adapted existing genomics-based molecular diagnostic tools for these pathogens into a reliable, sensitive LAMP assay.
• We studied the genetic relatedness of X. c. pv. leersiae with X. oryzae. X. campestris pv. leersiae causes bacterial streak on the perennial, weedy grass, Leersia hexandra that is a reservoir of pathogenic X.oryzae. We propose to rename X. campestris pv. leersiae.

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