Understanding Rice Biology from Genome to Field
Our research is focused on understanding the genetic and molecular basis of important traits in rice and translating this knowledge into improved rice varieties.
The laboratory combines rice functional genomics, molecular plant–microbe interactions, genetic mapping, genome sequencing, bioinformatics, marker development and molecular breeding to study how rice responds to pathogens and pests, how agronomically important traits are controlled, and how naturally occurring and induced genetic variation can be exploited for crop improvement.
How does rice interact with its biotic environment?
How can genetic variation underlying useful traits be identified, validated and translated into improved rice?
Rice–Pathogen Interactions
Deciphering the molecular basis of bacterial blight
A major research theme of the laboratory is the interaction between rice and Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight of rice.
Our work has examined multiple components of the Xoo virulence machinery, including lipopolysaccharides (LPS), extracellular polysaccharides (EPS), cell-wall-degrading enzymes, the Type III secretion system (T3SS), and secreted Type III effectors.
Rather than treating bacterial virulence as a single process, our studies investigate how individual pathogen factors manipulate host biology and how these factors function together to suppress or alter rice immune responses. This work has included characterization of Xoo effectors such as XopQ, XopX, XopG and TAL9b, as well as bacterial factors required for virulence, motility and adaptation to environmental stress.
Recent work on TAL9b identified a broadly conserved rice disease-susceptibility locus involving OsS5H/FNS-03g, providing a mechanistic link between an Xoo effector, host gene activation and disease development.
Understanding how bacterial effectors manipulate plant immunity
The laboratory has investigated how Xoo effectors interact with host proteins and with one another to modulate plant defence.
Studies of XopQ and XopX demonstrated that interactions among pathogen effectors and rice 14-3-3 proteins can influence immune signalling, while subsequent work showed that XopG can suppress XopQ–XopX-induced immune responses. These studies contribute to a broader understanding of how pathogens manipulate interconnected host immune pathways rather than acting through isolated virulence factors.
The laboratory has also characterized host responses to pathogen-derived cell-wall-degrading enzymes, including the identification of rice defence-associated regulators such as OsPUB41, OsWRKY42 and OsAP2/ERF152.
Pathogen adaptation and bacterial physiology
The laboratory also investigates bacterial processes that contribute to pathogen fitness.
Studies of Exoribonuclease R (RNase R) in Xoo showed that this RNA-processing enzyme contributes to complete virulence, optimal motility and bacterial growth under stress. More recent work has revealed reversible phase variation in the LPS O-antigen biosynthetic cluster of Xoo during long-term stationary phase, highlighting the capacity of the pathogen to dynamically alter its surface properties.
Together, these studies connect bacterial physiology, genome variation and virulence with the outcome of the rice–pathogen interaction.
Sheath Blight (Rhizoctonia solani)
The second front, alongside bacterial blight
Sheath blight (ShB) is caused by Rhizoctonia solani, a necrotrophic, soil-borne fungus (principally anastomosis group AG1-IA). It ranks among the three most damaging rice diseases worldwide, and it is one of the biotic stresses we screen for directly in the Samba Mahsuri mutant population, alongside bacterial blight and yellow stem borer.
Why it resists conventional breeding
R. solani is an unusually stubborn target. It produces no spores: it persists as overwintering sclerotia that float onto flooded leaf sheaths, then climb the canopy through runner hyphae, spreading tiller to tiller.
No major single resistance gene has ever been found in cultivated rice. Every source of resistance identified so far is partial, polygenic and QTL-based, and many of those QTLs are entangled with plant-architecture traits such as height, tillering and canopy openness, each carrying its own yield trade-off.
Where this stands
This is an open line of work rather than a closed one: we do not yet have a published resistance gene of our own for sheath blight the way we do for bacterial blight. Candidate-gene leads from the wider field indicate the kind of mechanism we are looking for in our own mutant lines SB23 and TI87.
Genome Editing for Crop Improvement
Genome editing provides a powerful route for precisely modifying genes associated with desirable agricultural traits.
Our research employs CRISPR-based genome editing and rice transformation technologies to develop and characterize improved rice lines. Edited plants are evaluated for traits including yield, disease resistance and tolerance to biotic and abiotic stresses.
The long-term objective is to translate knowledge of gene function into precise and sustainable crop improvement strategies. Current CCMB research programmes led by Dr. Patel specifically include genome editing in rice, rice tissue culture and transformation, plant phenotyping and bioinformatics.
Rice Functional Genomics & Trait Discovery
Exploiting genetic variation for crop improvement
Alongside plant–pathogen biology, the laboratory has developed a strong programme in rice functional genomics and molecular breeding.
A major resource for this work has been the extensive collection of EMS-induced mutants of the elite rice cultivar Samba Mahsuri (BPT 5204). Genome-scale characterization of these mutants revealed substantial variation affecting agronomic, yield, stress and other traits, creating a resource for both gene discovery and rice improvement.
The laboratory uses these genetic resources to move from an observable phenotype to the underlying genomic variation and candidate genes.
MutMap, QTL-seq and genetic mapping
We integrate bulk-segregant analysis, MutMap, QTL mapping, QTL-seq, whole-genome sequencing and transcriptome analysis to identify genomic regions and candidate genes controlling complex rice traits.
One example is the study of complete panicle exsertion (CPE), an agronomically important trait associated with grain yield. Using mutant populations derived from Samba Mahsuri, the work combined genetic mapping and QTL-seq to identify consistent genomic regions associated with CPE and subsequently developed KASP markers for candidate variants.
This illustrates the laboratory's broader strategy:
Multi-Omics for Rice Stress & Resistance
Integrating genomes, transcriptomes and metabolites
Complex traits rarely arise from a single gene acting in isolation. Our research therefore integrates multiple molecular layers to understand rice responses to environmental and biological stresses.
A prominent example is the study of rice–yellow stem borer interaction.
Using the tolerant rice line SM92, the laboratory and collaborators combined bulk-segregant analysis, QTL-seq, SNP-marker development, RNA sequencing and metabolite profiling to investigate tolerance to Scirpophaga incertulas.
Five chromosomal regions associated with yellow stem borer tolerance were identified, while transcriptomic and metabolomic analyses highlighted candidate genes and a possible role for phenylpropanoid metabolism in the tolerance response. Markers associated with tolerance were developed as potential tools for marker-assisted breeding.
This work represents an important expansion of the laboratory's research from pathogen resistance to insect resistance and multi-omics-assisted crop improvement.
Reference Genomes & Structural Variation
Building genomic resources for Indian rice
The laboratory is increasingly applying long-read sequencing and genome-scale comparative analysis to develop improved genomic resources for elite Indian rice varieties.
The most recent example is the chromosome-scale genome assembly of Samba Mahsuri, generated using PacBio HiFi sequencing, Illumina sequencing and Bionano optical mapping. The resulting SMv1.0 assembly is approximately 395 Mb, with 97.7% BUSCO completeness, and provides a high-quality reference for an elite Indian rice cultivar.
The analysis goes beyond assembly and annotation. Comparative genomics identified substantial locus-specific sequence and structural variation, including a complex inversion–match–inversion configuration on chromosome 6 that distinguishes Samba Mahsuri from Nipponbare.
Population-scale analysis of more than 500 rice accessions further showed that genetic variation within this region produces a much stronger local population structure than is apparent from genome-wide ancestry alone.
This work establishes genome assembly and structural variation as an important emerging component of the laboratory's rice functional genomics programme.
Translating Genomics into Rice Improvement
From candidate genes to breeding resources
A defining feature of our research is the effort to move beyond gene discovery towards practical crop improvement.
The laboratory contributes to the development and characterization of rice germplasm, molecular markers and disease-resistant and agronomically improved lines. This work builds on longstanding involvement in the development and deployment of Improved Samba Mahsuri, a bacterial-blight-resistant, low-glycaemic-index rice variety.
Our research therefore connects:
- Genetic resources
- Genomic discovery
- Candidate genes and variants
- Functional validation
- Molecular markers / genome engineering
- Improved rice germplasm
A continuum, not a handover
We believe that meaningful crop improvement requires a continuum from mechanistic biology to genomic discovery and finally to field-relevant validation.
Our laboratory therefore brings together:
to understand rice as both a genetic system and an agricultural crop.
The ultimate goal is to convert knowledge of rice genes, genomes and plant–microbe interactions into robust genetic resources, molecular markers and improved rice varieties that can contribute to sustainable agriculture and food security.