Browsing by Author "Ghatak, Arindam"

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Deciphering cold stress resilience: multiomics insights in contrasting wheat genotypes from the western himalayas
(John Wiley & Sons, 2026) Jan, Sofora; Jan, Farkhandah; Rathore, Mukesh; Singh, Yogita; Kapoor, Prexha; Chaturvedi, Palak; Ghatak, Arindam; Ramesh, Palakurthi; Kumar, Upendra; Prasad, Manoj; Kumar, Sundeep; Rustgi, Sachin; Weckwerth, Wolfram; Kalia, Sanjay; Varshney, Rajeev Kumar; Mir, Reyazul Rouf
Cold stress threatens wheat productivity, particularly in regions with extreme climatic conditions. To elucidate the molecular mechanisms underlying wheat's response to cold stress, we performed a multiomics analysis integrating lipidomics, transcriptomics, proteomics and metabolomics. Our study focused on two wheat genotypes with contrasting cold tolerance levels, SKAU_52 (tolerant) and SKAU_4301 (susceptible) to capture genotype-specific responses under cold stress. Lipidomic analysis revealed significant changes in lipid composition, with unsaturated lipids such as digalactosyldiacyl glycerols (DGDGs) and monogalactosyldiacylglycerols (MGDGs) upregulated in response to cold stress. These lipids are associated with maintaining membrane fluidity, whereas saturated lipids were downregulated in the cold-tolerant genotype. Transcriptomics analysis provides a strong evidence that cold tolerance in wheat is governed by coordinated activation of the ICE-CBF-COR regulatory cascade, with the cold-tolerant genotype ‘SKAU_52’ showing stronger and more sustained induction across pathway tiers than the cold susceptible wheat genotype ‘SKAU_4301’. Similarly, proteomic data highlighted differential abundance of proteins involved in antioxidative defence, osmotic adjustment and signal transduction, including late embryogenesis abundant (LEA) proteins. Metabolome assessment revealed substantial alterations in carbohydrate and amino acid metabolism, with sucrose and amino acids such as hydroxyproline identified as key contributors to cold tolerance. Additionally, defence hormones such as salicylic acid (SA), jasmonic acid (JA) and abscisic acid (ABA) exhibited genotype-specific regulation with higher accumulation in cold-tolerant genotype. Overall, this integrated multi-omics approach provides novel insights into the complex molecular mechanisms underlying cold stress adaptation in wheat, supporting the development of resilient wheat varieties capable of thriving in challenging cold environments.
Millets for a sustainable future
(Oxford University Press, 2025) Ghatak, Arindam; Pierides, Iro; Singh, Roshan Kumar; Srivastava, Rakesh K; Varshney, Rajeev K; Prasad, Manoj; Chaturvedi, Palak; Weckwerth, Wolfram
Our current agricultural system faces a perfect storm-climate change, burgeoning population, and unpredictable outbreaks like COVID-19 disrupt food production, particularly for vulnerable populations in developing countries. A paradigm shift in agriculture practices is needed to tackle these issues. One solution is the diversification of crop production. While ~56% of the protein consumed from plants stems from three major cereal crops (rice, wheat and maize), underutilized crops such as millets, legumes and other cereals are highly neglected by farmers and the research community. Millets are one of the most ancient and versatile orphan crops with attributes like fast-growing, high-yielding, withstanding harsh environments, and rich in micronutrients such as iron and zinc, making them appealing to achieve agronomic sustainability. Here, we highlight the contribution of millet to agriculture and pay attention to the latest research on the genetic diversity of millet, genomic resources, and next-generation omics and their applications under various stress conditions. Additionally, integrative omics technologies could identify and develop millets with desirable phenotypes having high agronomic value and mitigating climate change. Here, we emphasize that biotechnological interventions, such as genome-wide association, genomic selection, genome editing, and artificial intelligence/machine learning, can improve and breed millets more effectively.
Network-based multiomics and transgenic validation reveal that OsPHR3 modulates phosphate-carbon metabolic trade-offs during rice seed development
(Elsevier B.V., 2026) Pazhamala, Lekha; Pandey, Mandavi; Deveshwar, Priyanka; Ghatak, Arindam; Weckwerth, Wolfram; Chaturvedi, Palak; Giri, Jitender
Phosphate (Pi) allocation during the grain-filling stage is a major determinant of crop yield, supporting macromolecule synthesis, energy metabolism, and nutrient storage. However, its storage as phytic acid (PA) reduces nutritional quality by chelating essential minerals. Despite its importance, a comprehensive understanding of the molecular mechanisms integrating Pi transport, carbohydrate metabolism, and PA biosynthesis during seed development remains incomplete. To address this gap, we investigated stage-specific phosphate regulatory networks in rice by integrating transcriptomic, proteomic, and metabolomic approaches. Temporal expression profiling and gene coexpression network analyses of phosphate regulators and transporter genes revealed their distinct roles during early and mid-grain filling stages. PHOSPHATE STARVATION RESPONSE 3 (OsPHR3) emerged as a central regulatory hub, coordinating the balance of Pi, sugar, starch and phytate, along with other metabolites. Network-based multiomics integration further identified 126 genes involved in nutrient storage and stress tolerance, with myo-inositol-1-phosphate synthase (OsMIPS1) and starch synthase 3 (OsSSIII) as key genes. CRISPR/Cas9-generated osphr3 knockout lines confirmed the critical role of OsPHR3 in regulating these target genes. Mutants exhibited significantly reduced seed starch, PA, and total phosphorus contents, while scanning electron microscopy revealed aberrant starch granule morphology. Loss-of-function of OsPHR3 lowered PA levels by 19.46–22.50 %, with moderate trade-offs in yield-related traits. Although, OsPHR3 is known to contribute to nitrogen and phosphorus homeostasis, our findings establish it as a key regulator orchestrating a stage-specific phosphate-carbon allocation during seed development. These insights provide key targets for refining nutrient partitioning to achieve increased yields, reduced phytic acid, and enhanced phosphorus use efficiency for agricultural sustainability.