ICAR-Indian Agricultural Research Institute (IARI), New Delhi
Microbial plant pathogens are major threat to agricultural production worldwide. Agriculturally adapted and rapidly evolving pathogens belong to all major taxa especially fungi, virus and bacteria has the potential to reduce the genetic capability of crop plant. In order to sustain agricultural production, a sound and effective disease mitigation strategy must be in place. With the increasing global connectivity, threat of invasive pathogen and exotic diseases affecting our crop production is quite a reality. Rapid advancement in genomics technology in the recent years has altered the landscape of plant pathology research once for all. Therefore, it is hoped that the modern genomics technologies have the potential to assist the development of new strategies for crop protection.
Objective
- To develop pathogenome browsers for nationally important plant pathogens, Tilletia, Bipolaris, Ralstonia and Magnaporthe spp. affecting agricultural and horticultural crops.
- To develop high-throughput array based genomic chips for rapid monitoring of plant pathogens of national relevance.
- To identify novel sporulation inhibitors /detoxifying agents based on transcriptomics data generated.
- To identify host specific transcripts involved in pathogenesis from the transcriptomics data.
- To develop human resources in pathogen genomics through workshop and training.
Research targets/activities
- To generate whole genome of five Nationally Important plant pathogens viz. Tilletia indica, Magnaporthe oryzae isolate and highly virulent race 4/biovar 3 of Ralstonia solanacearum isolate CaRs_Mep, Magnaporthe grisea isolate, Bipolaris sorokiniana, identify pathogenicity-related genes and comparative genome genomic wide analysis of their genomes.
- Development of a quick and reliable qPCR and LAMP-based diagnostic assay to detect Tilletia indica in soil.
- Development of genotyping tool for population genetic analysis of different and specific molecular markers for pathogens infecting the host.
- Genome-assisted molecular phylogenetics and pathotyping of pathogens.
Genomics assisted structural and functional chara
Cterization of nationally important plant pathogens are being carried out in the sub project under CRP Genomics which will enable us to develop novel and durable disease management strategies for these economically important plant diseases.
1. Pathogenomicsof Tilletia indica infecting wheat
Karnal bunt of wheat caused by Tilletiaindica is a re-emerging disease of wheat in North western plain zone of India. It Infects wheat at the flowering stage prior to seed formation, hence the symptoms are visible only when the grains have fully developed in ear heads.
- Genome sequenced TilletiaindicaRAKB_UP_1causing Karnal bunt of wheat. The genome sequence of TilletiaindicaRAKB_UP_1is available in the GenBank database under the accession number MBSW00000000. Genome size is 33.7 Mbwith GC content of 55%, providing coverage of 99.91%.
2. Pathogenomics of Bipolaris sorokiniana infecting wheat
B. sorokinianais an aggressive fungal pathogen that causes small, dark brown colored lesions on leaves with the length of 1- 2 mm without chlorotic margin. These lesions become dark brown in 4 to 5 days and extend to several centimeters in susceptible genotypes inducing leaf abscission.
- Genome sequenced of highly virulent isolate of Bipolarissorokiniana(BS112) infecting wheat using hybrid assembly approach. The assembly size of the genome was 35.64Mb with GC content of 50.2%, providing coverage of 97.6% on reference ND90Pr genome. This whole-genome sequencing project has been deposited in DDBJ/ENA/GenBank under the accession number RCTM00000000, BioProject number PRJNA489551, and BioSample identification (ID) SAMN09901300.
- Reference based transcriptomeanalysis of wheat and fungal (B. sorokiniana) mycelium was doneusing the Illumina Hi-seq paired end sequencing. The raw data and transcriptome assembly in the Sequence Read Archive, NCBI was generated with BioProject ID PRJNA747867; with Biosample identification SAMN20297821, SAMN20297823, SAMN20297824 and SAMN20297825.
3. Pathogenomics of Ralstoniasolanacearum
Genome sequencing of Ralstoniasolanacearumrace 4 causing bacterial wilt in crop plants belong to Zingiberaceae.
India is one of the endemic places for race 4 isolates of Ralstoniasolanacearum causing bacterial wilt disease in Zingiberaceae crops like ginger, turmeric, and cardamom. The race 4 isolates also incited wilt in tomato – economically important vegetable crops. The symptoms of the disease are typical wilting of plants wherein all the leaves rolled upward toward the center of midrib, turned yellow, and the whole plant finally died.
- Genome sequenced an isolate CaRs_Mep causing bacterial wilt of cardamom. The genome sequence of R. solanacearum strain CaRs_Mep is available in the GenBank database under the accession number MCBM00000000. Genome size is 5.7 Mb coding for a total of 5,127 genes with sizes ranging from 60 bp to 14,142 bp.This is first report of genome sequencing of race 4 strain of Ralstoniasolanacearum
4. Pathogenomics of Magnaportheoryzae infecting rice
Genome sequencing of Magnaporthespecies causing blast disease in crop plants belong to Poaceae.
India is one of the endemic places for blast disease on rice, finger millet, pearl millet and grasses. The fungus also incited blast disease on other economically important crops like wheat under experimental conditions. The symptoms of the blast disease on rice are typical dark brown lesions on leaf wherein characteristic shades of color depicting necrotic tissues along with grey sporulating center can be seen. The grey center is responsible for horizontal transmission of conidia triggering blast epidemics in fields.
- Genome sequenced MagnaportheoryzaeRMg_Dl causing blast disease of rice. The genome sequence of MagnaportheoryzaeRMg_Dl is available in the GenBank database under the accession number MBSD02000000. Genome size is 34.82 Mb coding for a total of 12747 genes with sizes ranging from 201 bp to 14,916 bp.
5. Pathogenomics of Magnaporthegrisea infecting pearl millet
The symptoms of the blast disease on pearl millet are typical dark brown lesions on leaf wherein characteristic shades of color depicting necrotic tissues along with yellow halo can be seen. The lesion is responsible for horizontal transmission of conidia triggering blast epidemics in fields.
- Genome sequenced MagnaporthegriseaPMg_Dl causing blast disease of pearl millet. The genome sequence of MagnaporthegriseaPMg_Dl is available in the GenBank database under the accession number RHLM01000000. Genome size is 47.90 Mb coding for a total of 10,451 with sizes. This is first report of genome sequencing of pearl millet infecting Magnaporthegrisea