CSIR – Centre for Cellular & Molecular Biology

Decoding how pathogens attack rice, and how rice fights back.

We work at the molecular interface of bacterial and fungal virulence and plant immunity, using Xanthomonas oryzae pv. oryzae and Rhizoctonia solani against rice as model systems, to find the genes that make the difference between a susceptible field and a resistant one.

Explore Research See the Mutant Resource

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Signature Resource

A forward-genetics engine: the Samba Mahsuri mutant population

We developed and maintain a large-scale ethyl methanesulphonate (EMS)-induced mutant population in the background of Samba Mahsuri (BPT5204), one of India's most widely grown mega rice varieties. The population captures novel variation across morphological, physiological, and biotic-stress-tolerance traits, and is screened at scale for agronomic value.

One line from this population, BB42, was found to carry broad-spectrum resistance to hypervirulent Xoo isolates. Genetic mapping traced the resistance to a single recessive locus on chromosome 6: a missense SNP in OsMAPK6 (S84P), a novel allele not previously seen across more than 4,000 sequenced rice genomes, associated with constitutively active basal immunity.

See the full gene discovery story →

MutagenEMS

Genetic backgroundSamba Mahsuri (BPT5204)

Traits screenedMorphology · Physiology · Biotic stress

Biotic stresses targetedBacterial blight · Sheath blight · Yellow stem borer

Pest/disease hitsYSB & BB tolerant lines identified

Flagship lineBB42: broad-spectrum BB resistance

Causal geneOsMAPK6 (novel allele, S84P)

Research Program

Seven connected lines of work

Rice–Pathogen Interactions

How the virulence machinery of Xanthomonas oryzae pv. oryzae, from LPS and EPS to the T3SS and effectors such as XopQ, XopX, XopG and TAL9b, manipulates rice immunity.

Sheath Blight (Rhizoctonia solani)

A necrotrophic, soil-borne fungus with no known single resistance gene in cultivated rice. We screen it across the Samba Mahsuri mutant population to separate ShB tolerance from plant architecture.

Genome Editing

CRISPR-based editing and rice transformation to develop and characterize improved lines, evaluated for yield, disease resistance and stress tolerance.

Functional Genomics & Trait Discovery

The Samba Mahsuri EMS mutant collection, MutMap and QTL-seq, carrying a phenotype through to a candidate gene and a validated marker.

Multi-Omics for Stress & Resistance

Bulk-segregant analysis, QTL-seq, RNA sequencing and metabolite profiling combined to map yellow stem borer tolerance in the rice line SM92.

Reference Genomes & Structural Variation

A chromosome-scale PacBio HiFi assembly of Samba Mahsuri, and the locus-specific structural variation that separates it from Nipponbare.

Translating Genomics into Rice Improvement

Germplasm, molecular markers and disease-resistant, agronomically improved lines: the step that turns a mapped gene into something a farmer can plant, building on the development and deployment of Improved Samba Mahsuri.

Varieties Released

From gene discovery to the field

Ten lines released to farmers so far. Click any card to read its pamphlet in full.

News & Updates

From the lab

6–10 Jul 2026 Workshop

RICE Re-Imagined: a five-day hands-on genome editing masterclass

CSIR-CCMB, Hyderabad

The lab ran Rice Re-Imagined: Hands on Genome Editing Masterclass (RICE-1), a five-day hands-on training workshop at CSIR-Centre for Cellular and Molecular Biology, for faculty, researchers from universities, institutes and industry, and others working in life sciences and allied areas. It covered the basic techniques of genome editing and tissue culture as used in real experiments, combining lectures with bench work, instrument set-up and data analysis.

See all photos in the gallery →

23 Apr 2026 Preprint

Our Samba Mahsuri genome assembly is now on bioRxiv

bioRxiv: preprint, not yet peer reviewed

SMv1.0: a ~395 Mb chromosome-scale assembly at 97.7% BUSCO completeness, built from PacBio HiFi reads with Illumina and Bionano optical mapping. An inversion–match–inversion block on chromosome 6 separates Samba Mahsuri from the japonica reference Nipponbare but not from indica R498, and across 533 cultivated and 4 wild accessions, variation inside that block resolves population structure far more sharply than the genome-wide picture does.

Read the Preprint →

17 Apr 2026 Award

Anjana Sharma wins the best oral presentation award

International Conference on Global Sustainability through Life Science

Congratulations to Anjana Sharma, Senior Research Fellow in the lab, for the best oral presentation award at the International Conference on Global Sustainability through Life Science: Green Energy, Climate Resilience & SDG Integration, held at St Pious Degree College in collaboration with Dallas Baptist University, Texas, USA.

Meet the Team →

7 Feb 2026 Award

Dr. Jamaloddin wins the best poster presentation award at ICCRA 2026

ICCRA 2026 · Banaras Hindu University, Varanasi

Congratulations to Dr. Jamaloddin, Project Research Scientist in the lab, for the best poster presentation award at the International Conference on Climate-Resilient Agriculture for Sustainable Development: Innovations and Solutions (ICCRA 2026), held at Banaras Hindu University, Varanasi. The poster was titled TILLING-based identification of OsTFIIAγ1 and Os11N3 mutants and their classification for BLB resistance in rice.

Meet the Team →

2026 Publication

Strong-culm mapping paper published in Planta, with ICAR-IIRR

Planta · CSIR-CCMB & ICAR-IIRR collaboration

A collaborative study between our lab at CSIR-CCMB and ICAR-IIRR. QTL mapping and MutMap run side by side converged on the same genomic regions for culm strength (the trait underneath lodging resistance) in the Samba Mahsuri background.

Read the Paper →

25 Mar 2025 Preprint

Our Samba Mahsuri OsMAPK6 preprint is now on bioRxiv

bioRxiv: preprint, not yet peer reviewed

The BB42 story in full: broad-spectrum bacterial blight resistance traced to a single recessive locus on chromosome 6, and a missense change in OsMAPK6 not found across more than 4,000 sequenced rice genomes.

Read the Preprint →

See the full publication record →

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