Biology subjects

Ramireddy, E.

Publications and source records attributed to Ramireddy, E..

8 recordsLinked to original sources

bioRxiv2026

Cytokinin-mediated repression of jacalin lectins reinforces root immunity

The root cap is essential for perceiving environmental cues surrounding the root. However, the molecular mechanisms underlying root cap-mediated immunity and how it defends against invading pathogens remain largely unresolved. Our results indicate that cytokinin plays a major role in regulating soil-borne pathogen such as Ralstonia pseudosolanacearum load around the root and root cap. As Ralstonia populations increase, cytokinin signalling is activated and represses the expression of its downstream signalling targets such as root cap-specific proteins JAL10 and JAL20, to impart the tolerance against the Ralstonia. The functional analysis jacalin-associated lectin family proteins JAL10 and JAL20, revealed that loss-of-function leads to enhance tolerance to Ralstonia whereas gain-of-function leads to susceptibility compared to Col-0. Our Glycoproteomic and metabolomic analyses indicate that JAL10 and JAL20 act as negative regulators of cell wall remodelling and likely to promotes cell wall thickening, thereby enhancing resistance to soil-borne infections. The knockdown of ortholog of JAL protein in Tomato also revealed its conserved function in imparting tolerance to Ralstonia pseudosolanacearum. Further we also show downregulation of JALs by other soil-borne pathogen infection, suggesting that cytokinin might protecting the vulnerable areas of root tip regions by regulating the expression of root cap-specific JALs and thereby fortifying the cell wall.

plant biology↗

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

Systematic analysis of lectin gene family reveals dynamic modes of paralogue evolution and immune regulatory functions in tomato

Lectins are a structurally diverse class of carbohydrate-binding proteins implicated in plant development and stress responses. In this study, we present a comprehensive structural, evolutionary, and functional analysis of the lectin gene family in tomato (Solanum lycopersicum cv. Heinz). We identified 247 lectin genes across eight major families, exhibiting diverse domain architectures, including merolectins, hololectins, and chimerolectins. Gene ontology enrichment, tissue-specific expression profiling, and stress-responsive transcriptomics highlighted key roles of lectin genes in development and pathogen defense. Comparative genomic analyses across five Solanum species and ancestral outgroups (Vitis vinifera and Amborella trichopoda) revealed both conserved and lineage-specific expansions driven by whole-genome and small-scale duplications. Evolutionary modeling indicated that most lectin gene duplications are under purifying selection, with some genes exhibit signatures of adaptive evolution. Expression and co-expression variance among duplicated paralogues revealed three distinct evolutionary fates -balance, dominance, and divergence. Notably, small-scale duplications frequently led to functional divergence, whereas whole-genome duplicates largely retained ancestral expression patterns. Functional validation through virus-induced gene silencing (VIGS) of two GNA chimerolectins, Solyc04g077390 and Solyc07g063700, revealed their role as negative regulators of immunity. Silencing these genes enhanced resistance to Ralstonia solanacearum, reduced bacterial colonization, and triggered stronger induction of defense-related genes. Together, these findings highlight the structural innovation, evolutionary dynamics, and immune regulatory roles of lectin genes in tomato, and identifies promising targets for breeding disease-resistant cultivars in Solanum lycopersicum and related crops.

plant biology↗

bioRxiv2025

Integrative spatial transcriptomic analysis pinpoints the role of TaMCO3 encoding ferroxidase in wheat root tip iron mobilization

Roots play an critical role in the sensing and absorption of essential minerals from the rhizosphere. Iron (Fe) deficiency, for example, triggers a well-known series of physiological and molecular responses within roots that facilitate uptake, which differs between monocots and dicots. In monocots, little is known about molecular responses that occur within specific root development zones in response to iron deprivation, and how these differences results in overall nutrient uptake. Here, we conducted a transcriptome analysis of wheat root tips under Fe deficiency (-Fe) and performed a comparative transcriptome analysis with the previous datasets generated from the whole root. Gene ontology analysis of differentially expressed genes highlighted the significance of oxidoreductase activity and metal/ion transport in the root tip, which are critical for Fe mobilisation. Interestingly, wheat, an allohexaploid species consisting of three different genomes (A, B, and D) displayed varying gene expression levels arising from the three genomes that contributed to similar molecular functions. Detailed analysis of oxidoreductase function at the root tip revealed multiple multi-copper oxidase (MCO) proteins, such as Fe-responsive TaMCO3, that likely contribute to the overall ferroxidase activity. Detailed characterisation of TaMCO3 shows that it complements the yeast FET3 mutant and rescues the -Fe sensitivity phenotype of Arabidopsis atmco3 mutants by enhancing vascular Fe loading. Transgenic wheat lines overexpressing TaMCO3 exhibited increased root Fe accumulation and improved tolerance to -Fe by augmenting the expression of Fe-mobilizing genes. Our findings highlight the role of spatially resolved gene expression in -Fe responses, suggesting strategies to reprogram cells for improved nutrient stress tolerance.

plant biology↗

bioRxiv2024

Crops under continuous cultivation exhibit less plasticity than those under interrupted cultivation

Evolutionary studies indicate that species in stable environments often evolve with reduced plasticity, whereas those in variable environments tend to maintain higher plasticity to adapt to changing conditions. Our study explores whether this evolutionary principle extends to cultivated crops. In crop science, phenotypic plasticity is generally understood as a short-term response to environmental factors. Yet, the long-term evolutionary changes in both plastic and non-plastic traits under different cultivation regimes remain largely unexamined. Herein, we developed a novel mechanistic crop growth model, collectively termed the Trait-Environment Fitness Interaction (TEFI) Model, to study if and how trait plasticity varies among crops under different cultivation regimes. Our results, based on the TEFI Model, show higher trade-offs between fitness and plasticity. Specifically, we observed the evolution of higher plasticity in crops subjected to intermittent cultivation, which experienced more variable environments. However, this higher plasticity does not compensate for fitness losses due to the high rate of environmental unpredictability. Conversely, species under relatively stable conditions tend to evolve with reduced plasticity. Using real-world crop datasets, we validated the theoretical predictions of the TEFI Model, which suggest that the longer the interruption, the higher the plasticity. Our results highlight the evolutionary impact of cultivation patterns on trait plasticity and its importance in crop fitness. Ultimately, our findings illustrate how evolutionary principles of plasticity, as captured by the TEFI Model, can inform sustainable crop improvement strategies.

plant biology↗

bioRxiv2024

Distinct genetic architecture for trait mean and plasticity in chickpea

Crop plants often face rapid environmental changes, and their ability to adapt to novel conditions depends on whether specific traits can adjust to match these changes. This capacity for adjustment, known as phenotypic plasticity, is frequently regarded as a mere "response" rather than a distinct trait with its own genetic basis, particularly in agricultural science. As a result, plasticity is often oversimplified and viewed as an undesirable phenomenon when the goal is to achieve trait stability. In this study, we present a quantitative metric to measure phenotypic plasticity and provide evidence, through genome-wide association studies (GWAS) in chickpea, that plasticity is indeed a genetically based trait, comparable to any other agronomic trait. This foundational study paves the way for future GWAS efforts to harness phenotypic plasticity, offering new insights for crop improvement strategies.

plant biology↗

bioRxiv2024

High plasticity increases phenotype-environment mismatch leading to sub-optimal performance in underutilized crop species

As climate change threatens agricultural yields, crop diversification, including the reintroduction of underutilized species, has emerged as a proposed solution for resilience. But what determines the extent of environmental change that underutilized crop species can cope with upon their reintroduction? One critical factor is maladaptive plasticity, a theoretical concept suggesting that populations may respond negatively to rapid environmental shifts, at least in the short term. To test this empirically, we conducted a repeated-measures study using historically underutilized Amaranthus species as a model. Upon reintroduction, we observed higher plasticity in vegetative and reproductive traits than in life-history traits. This suggests that while these species adapt to immediate environmental changes through adjustments in growth and reproduction, limited plasticity in life-history traits may constrain long-term adaptation. Our study aimed to (1) identify the environmental factors driving these plastic responses, (2) determine whether these responses are maladaptive, and (3) assess if maladaptive plasticity also occurs within native environments. Using machine learning models, we found that temperature was a primary driver of plastic responses. Generalized Additive Model (GAM) reaction norm analysis further revealed these temperature-induced responses to be maladaptive, suggesting a mismatch between Amaranthus traits and the new environment. Applying transfer learning to predict responses in native settings, we found similar maladaptive responses to temperature, indicating that maladaptive plasticity may not be limited to non-native environments, thereby complicating climate adaptation efforts. This study underscore the need for detailed trait plasticity assessments before crop reintroduction for agricultural resilience.

plant biology↗

bioRxiv2020

Classification of grain amaranths using chromosome-level genome assembly of ramdana, A. hypochondriacus

In the age of genomics-based crop improvement, a high-quality genome of a local landrace adapted to the local environmental conditions is critically important. Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. Towards this end, our lab had initiated sequencing the genome of Amaranthus (A.) hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. We selected this landrace because it is well adapted for cultivation in India during the last century and is currently a candidate for TILLING-based crop improvement. More recently, a high-quality chromosome-level assembly of A. hypochondriacus (PI558499, Plainsman) was reported. Here, we report a chromosome-level assembly of A.hyp_K_white (AhKP) using low-coverage PacBio reads, contigs from the reported draft genome of A.hyp_K_white, raw HiC data and reference genome of Plainsman. The placement of A.hyp_K_white on the phylogenetic tree of grain amaranths of known accessions clearly suggests that A.hyp_K_white is genetically distal from Plainsman and is most closely related to the accession PI619259 from Nepal (Ramdana). Furthermore, the classification of another accession, Suvarna, adapted to the local environment and selected for yield and other desirable traits, is clearly A. cruentus. A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few.

genomics↗