Hitendra Kumar Patel

Diseases caused by the Xanthomonas oryzae pathovars are important constraints for global rice productivity. Despite being a well-studied pathosystem, the transcriptional mechanisms distinguishing resistance from susceptibility remain incompletely understood. Here, we present a systems-level meta-analysis of more than a hundred publicly available rice-Xanthomonas transcriptome datasets. Using appropriate analysis pipelines, stringent filtering criteria and metadata integration, we identified rice functions that distinguish disease resistance and susceptibility with temporal resolution. Compatible interactions were characterized by early activation of abscisic-acid biosynthetic and signaling genes, and extensive transcriptional plasticity associated with susceptibility gene activation. In contrast, incompatible interactions displayed a restrained transcriptome reprogramming, enrichment of phenylpropanoid and aromatic-amino-acid biosynthetic pathways, and enrichment of an AP2/ERF-GCC-box regulatory module. Transient over-expression of three conserved infection-responsive genes, OsJAZ11, OsSYP131b, and OsMYB45, modestly enhanced defense gene expression and reduced lesion length caused by X. oryzae pv. oryzae in rice leaves, thus providing a proof-of-concept relevance of the candidates to rice-Xoo interaction. We also developed RiceXtra, an openly available database hosting the analyzed data (http://tdb.ccmb.res.in/RiceXtra), for exploring gene expression patterns during rice-Xanthomonas interactions. Overall, our study proposes a mechanistic framework connecting hormonal signalling and transcriptional plasticity with disease outcome, offering a foundation for engineering durable disease resistance.

High-quality reference genomes enable detailed analysis of structural variation and its consequences for genome organization in crops. Here, we present a chromosome-scale genome assembly of Oryza sativa cv. Samba Mahsuri (SM), an elite Indian mega rice variety cultivated for its grain and cooking quality. Using PacBio HiFi sequencing in combination with Illumina reads and Bionano optical mapping, we generated a ∼395 Mb assembly (SMv1.0) with 97.7% BUSCO completeness. A robust annotation framework identified 31,138 evidence-guided protein-coding gene models alongside 59,152 ab initio predictions. Comparative genomic analyses revealed extensive macrosynteny with established rice reference genomes, while uncovering pronounced locus-specific sequence and structural polymorphisms. Notably, a complex inversion-match-inversion (IMI) configuration on chromosome 6 differentiates SM from the japonica reference Nipponbare, but not from the indica reference R498. Population-scale analyses of 533 cultivated and 4 wild rice accessions demonstrate that genetic variation within the IMI region produces a markedly sharper and more coherent population structure than is observed in flanking regions or genome-wide, including tight subpopulation-based clustering and segregation of alternative IMI configurations within indica rice. Together, these results establish SMv1.0 as a robust chromosome-scale reference genome sequence for rice and demonstrate how large structural polymorphisms can shape locus-specific patterns of relatedness that diverge from genome-wide ancestry. Significance Statement: We present a high-quality chromosome-scale genome sequence of the elite Indian rice variety Samba Mahsuri (SM), which, to the best of our knowledge, represents the first chromosome-scale reference genome from Indian rice germplasm assembled using a map-based method. Using this reference to analyze population-scale genotyping data from 533 cultivated and four wild rice accessions reveals markedly tighter population clustering within a megabase-scale inversion (IMI) region, than at the whole-genome scale, along with a pronounced split within indica rice that is independent of genome-wide ancestry.

Plants are constantly exposed to diverse pathogens and have evolved sophisticated defense mechanisms to detect and respond to microbial threats. Pathogen recognition is often mediated by pathogen-associated molecular patterns (PAMPs), such as cell wall components or secreted molecules. Quorum-sensing molecules, secreted by bacteria to regulate virulence factors, are an emerging class of PAMPs that plants can detect as signs of infection. One such molecule, diffusible signal factor (DSF), is secreted by Xanthomonas plant pathogens. Previous studies have shown that DSF induces immune responses in plants such as Arabidopsis and rice. However, the plant mechanisms involved in DSF perception and immune response remain poorly understood. In this study, we performed transcriptome analysis to investigate the molecular players involved in DSF-induced immunity in Arabidopsis. Our findings identified key molecules, including WRKY66, PEPR2, and WAK_PK, as players in DSF-mediated immune responses. However, none of these molecules appears to directly recognize DSF, as mutants still activate DSF-induced MAP kinase signaling. This suggests that additional unidentified receptors or signaling pathways may play a role in DSF perception. Our study elaborates the downstream events of DSF recognition as a PAMP and contributes to the growing body of knowledge on plant immune signaling. [ ] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Precise control of heading date is essential for optimizing regional adaptability, enhancing climate resilience, and maximizing grain yield in rice, making it a key breeding target. The SM93 rice line exhibits a 7-10-day earlier heading than the elite Indian variety, Samba Mahsuri (SM). F2 populations derived from a cross of SM with SM93 were phenotyped for heading date across three successive kharif (rainy) seasons (2019-2021), revealing consistent early heading and notable transgressive segregation. Initial QTL-seq analysis identified a high-confidence QTL on Chr3, qDTH3 , strongly associated with days to heading (DTH). KASP assays and association mapping were subsequently performed to refine the QTL, narrowing it down to a 2.53 Mb region, explaining ∼25% of the trait. SNP markers closely linked to heading were identified. Transcriptomic analysis revealed significant differential regulation of genes within qDTH3 and upregulation of the MADS- box network in SM93 during panicle initiation, suggesting their role in promoting early heading. Our integrative strategy led to the identification of candidate genes within qDTH3 , associated with heading date, phytohormone regulation, and protein turnover, include the transcription factors, OsMADS34/PAP2 ( Os03g0753100 ), OsZHD11 ( Os03g0718500 ), HSFA2A ( Os03g0745000 ), OsH3 ( Os03g0727200 ), OSH1/Oskn1 ( Os03g0727000 ), a histidine kinase, HK4 ( Os03g0717700 ), and a Serine carboxypeptidase, OsSCP19 ( Os03g0730400 ). Our findings provide SNP markers in and around these genes, as potentially valuable tools for breeding early-maturing rice varieties with improved adaptability. HIGHLIGHT: This study on the SM93 rice line identifies a major QTL for early heading and describes genes and SNP markers that are closely linked to this trait, which can be used in trait advancement. By fine-tuning heading date, we can help rice varieties better withstand temperature extremes, drought, and other climate-related stresses, making it a key target for genetic improvement and breeding strategies.

SUMMARY: Bacterial Blight (BB) is the most serious bacterial disease of rice. Usage of resistant cultivars has been a successful strategy in controlling BB. However, constant selection pressure causes the evolution of hypervirulent pathogenic strains that break down resistance, thus necessitating additional sources of resistance. An induced-mutant line derived from the elite rice cultivar Samba Mahsuri was identified to exhibit broad-spectrum resistance to BB. Using next-generation gene mapping approaches, we identified a genomic interval in chromosome 6 to be linked to BB resistance. Analysis of the SNPs in the locus and subsequent linkage analysis indicated that a missense SNP located in the second exon of the Mitogen-Activated Protein Kinase 6 ( OsMAPK6 ) could be the causal mutation. A detailed examination of OsMAPK6 gene sequences in over 4000 rice genomes revealed that the mutant allele identified in this study is novel to rice germplasm. The candidate SNP causes the substitution of an invariant Serine residue with a Proline residue (S84P), thus likely affecting the protein function. Global transcriptome, metabolome, biochemical, and molecular analyses suggested that BB42 exhibit constitutive immunity. On the mechanistic front, the mutation seems to result in diminished brassinosteroid signaling in BB42. Taken together, we report a novel allele of a highly conserved MAPK gene and provide evidence for its possible association with constitutive immunity and disease resistance in rice.

Xanthomonas oryzae pv. oryzae ( Xoo), the causal agent of bacterial blight of rice, translocates multiple transcription activator-like effectors (TALEs) into rice cells. The TALEs localize to the host cell nucleus, where they bind to the DNA in a sequence-specific manner and enhance gene expression to promote disease susceptibility. Xoo strain PXO99^A encodes 19 TALEs, but the host targets of all these TALEs have not been defined. A meta-analysis of rice transcriptome profiles revealed a gene annotated as flavonol synthase/flavanone-3 hydroxylase (henceforth OsS5H/FNS-03g) to be highly induced upon Xoo infection. Further analyses revealed that this gene is induced by PXO99^A using Tal9b, a broadly conserved TALE of Xoo. Disruption of tal9b rendered PXO99^A less virulent. OsS5H/FNS-03g functionally complemented its Arabidopsis homologue AtDMR6, a well-studied disease susceptibility locus. Biochemical analyses suggested that OsS5H/FNS-03g is a bifunctional protein with salicylic acid 5′ hydroxylase (S5H) and flavone synthase-I (FNS-I) activities. Further, an exogenous application of apigenin, the flavone that is enzymatically produced by OsS5H/FNS-03g, on rice leaves promoted virulence of PXO99^A tal9b^–. Overall, our study suggests that OsS5H/FNS-03g is a bifunctional enzyme, and its product, apigenin, is potentially involved in promoting Xoo virulence. [ ] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Key message By deploying a multi-omics approach, we unraveled the mechanisms that might help rice to combat Yellow Stem Borer infestation, thus providing insights and scope for developing YSB resistant rice varieties. Abstract Yellow Stem Borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), is a major pest of rice, that can lead to 20–60% loss in rice production. Effective management of YSB infestation is challenged by the non-availability of adequate sources of resistance and poor understanding of resistance mechanisms, thus necessitating studies for generating resources to breed YSB resistant rice and to understand rice-YSB interaction. In this study, by using bulk-segregant analysis in combination with next-generation sequencing, Quantitative Trait Loci (QTL) intervals in five rice chromosomes were mapped that could be associated with YSB resistance at the vegetative phase in a resistant rice line named SM92. Further, multiple SNP markers that showed significant association with YSB resistance in rice chromosomes 1, 5, 10, and 12 were developed. RNA-sequencing of the susceptible and resistant lines revealed several genes present in the candidate QTL intervals to be differentially regulated upon YSB infestation. Comparative transcriptome analysis revealed a putative candidate gene that was predicted to encode an alpha-amylase inhibitor. Analysis of the transcriptome and metabolite profiles further revealed a possible link between phenylpropanoid metabolism and YSB resistance. Taken together, our study provides deeper insights into rice-YSB interaction and enhances the understanding of YSB resistance mechanism. Importantly, a promising breeding line and markers for YSB resistance have been developed that can potentially aid in marker-assisted breeding of YSB resistance among elite rice cultivars.

SUMMARY: Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight of rice, translocates multiple Transcription Activator-Like Effectors (TALEs) into rice cells. The TALEs localize to the host cell nucleus, where they bind to the DNA in a sequence-specific manner and enhance gene expression to promote disease susceptibility. Xoo strain PXO99 ^A encodes nineteen TALEs, but the host targets of all these TALEs have not been defined. A meta-analysis of rice transcriptome profiles revealed a gene annotated as flavonol synthase/flavanone-3 hydroxylase (henceforth OsS5H/FNS-03g ) to be highly induced upon Xoo infection. Further analyses revealed that this gene is induced by PXO99 ^A using TAL9b, a broadly conserved TALE of Xoo. Disruption of tal9b rendered PXO99 ^A less virulent. OsS5H/FNS-03g functionally complemented its Arabidopsis homologue AtDMR6, a well-studied disease susceptibility locus. Biochemical analyses suggested that OsS5H/FNS-03g is a bifunctional protein with Salicylic Acid 5’ Hydroxylase (S5H) and Flavone Synthase-I (FNS-I) activities. Further, an exogenous application of apigenin on rice leaves, the flavone that is enzymatically produced by OsS5H/FNS-03g, promoted virulence of PXO99 ^A tal9b -. Overall, our study suggests that OsS5H/FNS-03g is a bifunctional enzyme and its product apigenin is potentially involved in promoting Xoo virulence.

Lodging, a phenomenon characterized by the bending or breaking of rice plants, poses substantial constraints on productivity, particularly during the harvesting phase in regions susceptible to strong winds. The rice strong culm trait is influenced by the intricate interplay of genetic, physiological, epigenetic, and environmental factors. Stem architecture, encompassing morphological and anatomical attributes, alongside the composition of both structural and non-structural carbohydrates, emerges as a critical determinant of lodging resistance. The adaptive response of the rice culm to various biotic and abiotic environmental factors further modulates the propensity for lodging. Advancements in next-generation sequencing technologies have expedited the genetic dissection of lodging resistance, enabling the identification of pertinent genes, quantitative trait loci, and novel alleles. Concurrently, contemporary breeding strategies, ranging from biparental approaches to more sophisticated methods such as multi-parent-based breeding, gene pyramiding, genomic selection, genome-wide association studies, and haplotype-based breeding, offer perspectives on the genetic underpinnings of culm strength. This review comprehensively delves into physiological attributes, culm histology, epigenetic determinants, and gene expression profiles associated with lodging resistance, with a specialized focus on leveraging next-generation sequencing for candidate gene discovery.

SUMMARY: Yellow stem borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), is a major pest of rice in India, that can lead to 20-60% loss in rice production. Effective management of YSB infestation is challenged by the non-availability of adequate source of resistance and poor understanding of resistance mechanisms, thus necessitating studies for generating resources to breed YSB resistant rice and to understand rice-YSB interaction. In this study, by using bulk-segregant analysis in combination with next-generation sequencing, Quantitative Trait Loci (QTL) intervals in five rice chromosomes were mapped that could be associated with YSB tolerance at vegetative phase in a highly tolerant rice line named SM92. Further, multiple SNP markers that showed significant association with YSB tolerance in rice chromosomes 1, 5, 10, and 12 were developed. RNA-sequencing of the susceptible and tolerant lines revealed multiple genes present in the candidate QTL intervals to be differentially regulated upon YSB infestation. Comparative transcriptome analysis revealed a putative candidate gene that was predicted to encode an alpha-amylase inhibitor. Analysis of the transcriptome and metabolite profiles further revealed a possible link between phenylpropanoid metabolism and YSB tolerance. Taken together, our study provides insights on rice-YSB interaction at genomic, transcriptomic and metabolomic level, thereby facilitating the understanding of tolerance mechanism. Importantly, a promising breeding line and markers for YSB tolerance have been developed that can potentially aid in marker-assisted breeding of YSB resistance among elite rice cultivars. SIGNIFICANCE STATEMENT: Global rice production is threatened by various pests, among which stem borers pose serious challenges. Hence, understanding the molecular intricacies of rice-stem borer interaction is necessary for effective pest management. Here, we used a multi-omics approach to unravel the mechanisms that might help rice combat yellow stem borer infestation, thus providing insights and scope for developing YSB tolerant rice varieties. To facilitate the latter, we developed markers that co-segregate with tolerance.