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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.
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    Genomic and transcriptomic approaches to developing abiotic stress-resilient crops
    (MDPI AG, 2023) Kamali, Saravanappriyan; Singh, Amarjeet
    In the realm of agriculture, a pressing concern remains the abiotic stresses, such as temperature fluctuation, drought, soil salinity, and heavy metal contamination. These adverse growth conditions hamper crop yields and global food security. In this review, we present a comprehensive examination of the recent advancements in utilizing genomics and transcriptomics, tools to enhance crop resilience against these stress factors. Genomics aids in the identification of genes responsive to stress, unravels regulatory networks, and pinpoints genetic variations linked to stress tolerance. Concurrently, transcriptomics sheds light on the intricate dynamics of gene expression during stress conditions, unearthing novel stress-responsive genes and signaling pathways. This wealth of knowledge shapes the development of stress-tolerant crop varieties, achieved through conventional breeding programs and state-of-the-art genetic engineering and gene editing techniques like CRISPR-Cas9. Moreover, the integration of diverse omics data and functional genomics tools empowers precise manipulation of crop genomes to fortify their stress resilience. In summary, the integration of genomics and transcriptomics holds substantial promise in elucidating the molecular mechanisms behind crop stress tolerance, offering a path towards sustainable agriculture and safeguarding food security amidst shifting environmental challenges.
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    Progress of genomics-driven approaches for sustaining underutilized legume crops in the post-genomic era
    (Frontiers Media S.A., 2022) Jha, Uday Chand; Nayyar, Harsh; Parida, Swarup K.; Bakır, Melike; von Wettberg, Eric J. B.; Siddique, Kadambot H. M.
    Legume crops, belonging to the Fabaceae family, are of immense importance for sustaining global food security. Many legumes are profitable crops for smallholder farmers due to their unique ability to fix atmospheric nitrogen and their intrinsic ability to thrive on marginal land with minimum inputs and low cultivation costs. Recent progress in genomics shows promise for future genetic gains in major grain legumes. Still it remains limited in minor legumes/underutilized legumes, including adzuki bean, cluster bean, horse gram, lathyrus, red clover, urd bean, and winged bean. In the last decade, unprecedented progress in completing genome assemblies of various legume crops and resequencing efforts of large germplasm collections has helped to identify the underlying gene(s) for various traits of breeding importance for enhancing genetic gain and contributing to developing climate-resilient cultivars. This review discusses the progress of genomic resource development, including genome-wide molecular markers, key breakthroughs in genome sequencing, genetic linkage maps, and trait mapping for facilitating yield improvement in underutilized legumes. We focus on 1) the progress in genomic-assisted breeding, 2) the role of whole-genome resequencing, pangenomes for underpinning the novel genomic variants underlying trait gene(s), 3) how adaptive traits of wild underutilized legumes could be harnessed to develop climate-resilient cultivars, 4) the progress and status of functional genomics resources, deciphering the underlying trait candidate genes with putative function in underutilized legumes 5) and prospects of novel breeding technologies, such as speed breeding, genomic selection, and genome editing. We conclude the review by discussing the scope for genomic resources developed in underutilized legumes to enhance their production and play a critical role in achieving the “zero hunger” sustainable development goal by 2030 set by the United Nations.
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    Dissecting the nutrient partitioning mechanism in rice grain using spatially resolved gene expression profiling
    (Oxford University Press, 2021) Ram, Hasthi; Singh, Anmol; Katoch, Megha; Kaur, Ravneet; Sardar, Shaswati; Palia, Shubham; Satyam, Rohit; Sonah, Humira; Deshmukh, Rupesh; Pandey, Ajay Kumar; Gupta, Ishaan; Sharma, Tilak Raj
    Rice, a staple food worldwide, contains varying amounts of nutrients in different grain tissues. The underlying molecular mechanism of such distinct nutrient partitioning remains poorly investigated. Here, an optimized rapid laser capture microdissection (LCM) approach was used to individually collect pericarp, aleurone, embryo and endosperm from grains 10 days after fertilization. Subsequent RNA-Seq analysis in these tissues identified 7760 differentially expressed genes. Analysis of promoter sequences of tissue-specific genes identified many known and novel cis-elements important for grain filling and seed development. Using the identified differentially expressed genes, comprehensive spatial gene expression pathways were built for accumulation of starch, proteins, lipids, and iron. The extensive transcriptomic analysis provided novel insights about nutrient partitioning mechanisms; for example, it revealed a gradient in seed storage protein accumulation across the four tissue types analysed. The analysis also revealed that the partitioning of various minerals, such as iron, is most likely regulated through transcriptional control of their transporters. We present the extensive analysis from this study as an interactive online tool that provides a much-needed resource for future functional genomics studies aimed to improve grain quality and seed development.
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    Induced mutagenesis enhances lodging resistance and photosynthetic efficiency of kodomillet (Paspalum scrobiculatum)
    (MDPI AG, 2020) Jency, James Poornima; Rajasekaran, Ravikesavan; Singh, Roshan Kumar; Muthurajan, Raveendran; Prabhakaran, Jeyakumar; Mehanathan, Muthamilarasan; Prasad, Manoj; Ganesan, Jeeva
    The present research was focused in the development of photosynthetically efficient (PhE) and non-lodging mutants by utilizing ethyl methane sulphonate (EMS) and gamma radiation in the kodomillet variety CO 3, prone to lodging. Striking variations in a number of anatomical characteristics of leaf anatomy for PhE and culm thickness for lodging resistance was recorded in M2 (second mutant) generation. The identified mutants were subjected to transcriptomic studies to understand their molecular basis. Expression profiling was undertaken for pyruvate phosphate dikinase (PPDK), Nicotinamide Adenine Dinucleotide Phosphate Hydrogen—(NADPH) and NADP-dependent malate dehydrogenase (NADP-MDH) in the mutants CO 3-100-7-12 (photosynthetically efficient) and in CO 3-200-13-4 (less efficient). For lodging trait, two mutants CO 3-100-18-22 (lodged) and CO 3-300-7-4 (non-lodged) were selected for expression profiling using genes GA2ox6 and Rht-B. The studies confirmed the expression of PPDK increased 30-fold, NADP-ME2 ~1-fold and NADP-MDH10 was also highly expressed in the mutant CO 3-100-7-12. These expression profiles suggest that kodomillet uses an NADP-malic enzyme subtype C4 photosynthetic system. The expression of Rht-B was significantly up regulated in CO 3-300-7-4. The study highlights the differential expression patterns of the same gene in different lines at different time points of stress as well as non-stress conditions. This infers that the mutation has some effect on their expression; otherwise the expression levels will be unaltered. Enhancement in grain yield could be best achieved by developing a phenotype with high PhE and culm with thick sclerenchyma cells.
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    Rice A20/AN1 zinc-finger containing stress-associated proteins (SAP1/11) and a receptor-like cytoplasmic kinase (OsRLCK253) interact via A20 zinc-finger and confer abiotic stress tolerance in transgenic Arabidopsis plants
    (Wiley-Blackwell, 2011) Giri, Jitender; Vij, Shubha; Dansana, Prasant K.; Tyagi, Akhilesh K.
    The inbuilt mechanisms of plant survival have been exploited for improving tolerance to abiotic stresses. Stress-associated proteins (SAPs), containing A20/AN1 zinc-finger domains, confer abiotic stress tolerance in different plants, however, their interacting partners and downstream targets remain to be identified. •In this study, we have investigated the subcellular interactions of rice SAPs and their interacting partner using yeast two-hybrid and fluorescence resonance energy transfer (FRET) approaches. Their efficacy in improving abiotic stress tolerance was analysed in transgenic Arabidopsis plants. Regulation of gene expression by genome-wide microarray in transgenics was used to identify downstream targets. •It was found that the A20 domain mediates the interaction of OsSAP1 with self, its close homolog OsSAP11 and a rice receptor-like cytoplasmic kinase, OsRLCK253. Such interactions between OsSAP1/11 and with OsRLCK253 occur at nuclear membrane, plasma membrane and in nucleus. Functionally, both OsSAP11 and OsRLCK253 could improve the water-deficit and salt stress tolerance in transgenic Arabidopsis plants via a signaling pathway affecting the expression of several common endogenous genes. •Components of a novel stress-responsive pathway have been identified. Their stress-inducible expression provided the protection against yield loss in transgenic plants, indicating the agronomic relevance of OsSAP11 and OsRLCK253 in conferring abiotic stress tolerance.
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    Glycinebetaine and abiotic stress tolerance in plants
    (Landes Bioscience, 2011) Giri, Jitender
    The accumulation of osmolytes like glycinebetaine (GB) in cell is known to protect organisms against abiotic stresses via osmoregulation or osmoprotection. Transgenic plants engineered to produce GB accumulate very low concentration of GB, which might not be sufficient for osmoregulation. Therefore, other roles of GB like cellular macromolecule protection and ROS detoxification have been suggested as mechanisms responsible for abiotic stress tolerance in transgenic plants. In addition, GB influences expression of several endogenous genes in transgenic plants. The new insights gained about the mechanism of stress tolerance in GB accumulating transgenic plants are discussed.