Biology subjects

Sundaram, R. M.

Publications and source records attributed to Sundaram, R. M..

5 recordsLinked to original sources

bioRxiv2026

The emergence of bacterial blight pathogen followed the dispersal pattern of rice in Asia

Crop domestication has a significant effect on the evolutionary trajectory of plant pathogens by providing new ecological niches and abundant resources. The domestication of Asian rice (Oryza sativa) in Asia, approximately 9,000 years ago, might have shaped the genetic makeup of associated microbes into modern threats. In this study, we provide insight into the evolutionary history and dispersal pattern of the rice bacterial blight (BB) pathogen, Xanthomonas oryzae pv. oryzae (Xoo), one of the most destructive rice pathogens in the last century. The analysis of 433 Asian Xoo (AXoo) genomes identified twelve modern populations derived from three ancestral lineages (AXooL). Each population emerged with a unique genetic composition including the combination of pathogenicity factors. Bayesian reconstruction suggests that Xoo lineages emerged alongside O. sativa domestication hotspots and followed the dispersal pattern of rice across the continent. An ancient Xoo lineage (AXooL1) emerged in China and was likely dispersed with japonica rice. A second lineage (AXooL2) which could have turned up from China and spread across India, then evolved due to the domestication and spread of indica rice, and later on expanded eastward of Asia.. We also showed that recombination played a significant role in the emergence of AXooL3, which appeared more recently and might have spread with the rice trading routes. Our study aligns the evolution and dissemination of the phylogroup AXoo with the history of O. sativa, offering valuable insights for the formulation of precise disease management strategies. AUTHOR SUMMARYRice domestication was a crucial step in the development of Asian civilization. However, this process also affected the evolution of an associated pathogen, leading to its emergence as a global threat. Rice bacterial blight (BB), caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo), has been a scourge in many Asian countries. Using population genomics, we explored the diversity and evolutionary history of Xoo in Asia (AXoo). Here we show that two ancestral pathogen lineages emerged in rice domestication centers (China and India) and dispersed with rice across the continent. More recently, recombination played a crucial role in the appearance of a third lineage that spread through trading activity. This study provides the implications of the adaptation of AXoo in Oryza sativa, and might be valuable in forecasting BB outbreaks.

genomics↗

bioRxiv2026

KAMALA, a genome edited rice variety with improved yield by finetuning cytokinin oxidase activity released in India

Increasing yield is of major importance for Asian and African food security. Knock out mutants in the rice cytokinin oxidase gene CKX2 had shown potential for yield improvement. Here we explored whether subtle changes in CKX2 activity by editing FAD and cytokinin binding site sequences could improve the Indian mega-variety Samba Mahsuri. Knock out and single mutants in FAD and cytokinin binding sites induced by CRISPR/Cas12a caused moderate yield increases. Among 80 CKX2 alleles, five lines with in-frame mutations in both FAD and cytokinin binding domains produced even higher yield. One line, KAMALA, showed superior agronomic performance in 18 field locations (irrigated and rainfed ecologies) over three seasons in trials conducted by AICRPR (All India Coordinated Research Project on Rice), with an average 19% grain yield increase, early maturity, complete panicle emergence, and unaltered grain quality. KAMALA was registered as the first genome-edited variety ready for cultivation by Indian farmers.

plant biology↗

bioRxiv2025

A novel allele of Mitogen Activated Protein Kinase 6 is linked to disease resistance and constitutive immunity in rice.

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.

plant biology↗

bioRxiv2023

Genome-Wide Association Study for Yield and Yield related traits reveals MarkerTrait Associations in Germplasm lines of Rice

Rice germplasm has abundant genetic diversity, which provides a feasible solution for mapping loci of multiple traits simultaneously. In this study, a set of 72 rice germplasm lines were evaluated for yield and yield-related traits, and significant phenotypic variation was observed among the lines. Three accessions with high yield performance were identified. The germplasm set comprised five sub-populations and genome-wide association study (GWAS) identified a total of 6 marker-trait associations (MTAs) for the studied traits. These MTAs were located on rice chromosomes 1, 3, 7, 9, and 12 and explained the trait phenotypic variances ranging from 17.8 to 26.3%. Six novel MTAs were identified for yield and yield-related traits. A total of 28 putative annotated candidate genes were identified in a genomic region spanning [~]200 kb around the MTAs respectively. Among the important genes underlying the novel MTAs were OsFBK12, bHLH, WRKY, HVA22, and ZmEBE-1, which are known to be associated with the identified novel QTLs. These MTAs provide a pathway for improving high yield in rice genotypes through molecular breeding.

molecular biology↗

bioRxiv2022

Genome duplication and transposon mediated gene alteration shapes the pathogenicity of Rhizoctonia solani AG1-IA

Rhizoctonia solani AG1-IA is a polyphagous basidiomycete fungal pathogen that causes sheath blight disease in rice. In a high-quality genome assembly-based analysis, we report a recent whole genome duplication in R. solani AG1-IA. Duplicated syntenic gene blocks showed presence of district clusters of transposable elements (TEs), which introduced disruption in the continuity of synteny and caused alterations in gene structures. Genome duplication followed by TE-mediated gene structure alterations caused neofunctionalization of genes associated with pathogenicity, as experimentally shown by variation in expression patterns and their involvement during plant colonization. High throughput genome sequencing of forty-two rice field isolates of R. solani AG1-IA from different agro-climatic zones of India profiled the population genetic structure of the Indian isolates and classified those into three distinct groups and a subgroup of admixture, emphasizing exchange of genetic material under field conditions. Genetic diversity analysis of this population predicted the regions that are that are targets for diversifying and purifying selections. Experimental evidence showed that the genes undergoing diversifying and purifying selections were essential for pathogenicity. Together, our data and the analysis revealed profound impact of genome duplication and the transposable elements on genomic diversity and evolution that shaped the pathogenicity of R. solani AG1- IA.

evolutionary biology↗