Browsing by Author "Manivannan, Abinaya"

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Comparative transcriptomic and metabolite profiling reveals genotype-specific responses to Fe starvation in chickpea
(John Wiley & Sons, 2023) Singh, Gourav; Ambreen, Heena; Jain, Priyanka; Chakraborty, Anirban; Singh, Baljinder; Manivannan, Abinaya; Bhatia, Sabhyata
Iron deficiency is a major nutritional stress that severely impacts crop productivity worldwide. However, molecular intricacies and subsequent physiological and metabolic changes in response to Fe starvation, especially in leguminous crops like chickpea, remain elusive. In the present study, we investigated physiological, transcriptional, and metabolic reprogramming in two chickpea genotypes (H6013 and L4958) with contrasting seed iron concentrations upon Fe deficiency. Our findings revealed that iron starvation affected growth and physiological parameters of both chickpea genotypes. Comparative transcriptome analysis led to the identification of differentially expressed genes (DEGs) between the genotypes related to strategy I uptake, metal ions transporters, reactive oxygen species (ROS) associated genes, transcription factors, and protein kinases that could mitigate Fe deficiency. Our gene correlation network discovered several putative candidate genes like CIPK25, CKX3, WRKY50, NAC29, MYB4 and PAP18, which could facilitate the investigation of the molecular rationale underlying Fe tolerance in chickpea. Furthermore, the metabolite analysis also illustrated the differential accumulation of organic acids, amino acids and other metabolites associated with Fe mobilization in chickpea genotypes. Overall, our study demonstrated the comparative transcriptional dynamics upon Fe starvation. The outcomes of the current endeavour will enable the development of Fe deficiency tolerant chickpea cultivars.
Editorial: Silicon: A “Quasi-Essential” element’s role in plant physiology and development
(Frontiers Media S.A., 2023) Manivannan, Abinaya; Soundararajan, Prabhakaran; Jeong, Byoung Ryong
Silicon (Si) is the second most abundant element present in the Earth’s crust after oxygen, i.e., 28.8% in dry weight basis. Plants absorb Si in the form of orthosilicic acid [Si(OH)4]. Supplementation of Si has showed various beneficial effects on plants such as improved growth, yield, and tolerance against abiotic and biotic stress conditions. Owing to its benefits for plants, Si has been declared as a “Quasi-Essential” element. Accumulation of Si varies between plant species. Monocots such as rice accumulate approximately 10% of its dry weight, which is higher than essential elements such as nitrogen (N), phosphorus (P), and potassium (K). Application of Si has a remarkable impact against pathogens, pests, and insects invasion in several plant species (Song et al., 2021). Similarly, Si combats against various abiotic stresses such as drought, cold, salinity, UV-B, and heavy metals (Mir et al., 2022).
Global identification of metal ion transporters in chickpea and delineating the role of CaYSL4 in orchestrating iron content
(Elsevier B.V., 2025) Singh, Gourav; Manivannan, Abinaya; Pandey, Vimal; Bhatia, Sabhyata
Metal ion transporters (MITs) are vital to maintain proper metal homeostasis during growth and development of plants thereby necessitating their identification and characterization. Considering the economic importance of chickpea in human nutrition, the molecular behaviour and biological functions of the metal ion transporters (MIT) encoding gene families remains highly relevant in recent times. Global identification of MITs revealed a total of 12 CAXs, 6 CTRs, 11 MGTs, 15 MTPs, 9 NRAMPs, 16 OPTs, and 14 ZIPs responsible for metal ion transport. Assessment of phylogenetic relationships, chromosomal distribution, gene structure and motif analysis of MITs suggested their diverse functions. The yellow stripe-like (YSL) family of transporters is an important family whose members have been suggested to have a role in metal ion translocation and assimilation. Expression analysis of key YSLs including CaYSL1, CaYSL4, CaYSL6 and CaYSL16 indicated their significant involvement in conferring tolerance to Fe starvation. Notable was the expression of CaYSL4 that showed specific expression in flower, leaf, shoot, seed at 30 DAA and 40DAA after 7 and 10 day of Fe-deficiency treatment. It was found to be localized in the plasma membrane. RNAi-mediated silencing of CaYSL4 demonstrated its critical role in orchestrating Fe, Zn, Cu and Mn translocation in chickpea seeds. Collectively, the comprehensive analysis of MITs coupled with the functional role of CaYSL4 provides critical insight into the complex regulation of Fe ion transport and distribution that will enable breeding of nutritionally enhanced chickpea varieties.
Heat stress mitigation by silicon nutrition in plants: A comprehensive overview
(Springer Nature Publishing AG, 2023) Shilpha, Jayabalan; Manivannan, Abinaya; Soundararajan, Prabhakaran; Jeong, Byoung Ryong
Rapid climatic changes have exacerbated the severity of extreme weather events in agricultural regions, such as rainfall, elevated temperatures, and drought stress. As a result, heat stress (HS) has emerged as one of the most serious abiotic risks to crop development, productivity, and nutritional security due to the continued rise in global mean temperature. According to the IPCC, average global temperatures will rise by 3–6 °C by 2100. Importantly, excessive temperature stress during the reproductive stage results in a significant reduction of crop output. Consequently, there is an urgent need to comprehend food crops’ response and tolerance mechanisms to heat stress. Plants respond to high-temperature stress by initiating a series of physiological, biochemical, and molecular events and adapt by activating many stress-responsive genes. Silicon (Si) is a subtle element that improves plant growth and development and protects it against numerous abiotic and biotic challenges. Several studies have proved that the exogenous application of Si has significantly mitigated the negative impacts of abiotic stresses. However, there have only been a few investigations on the Si’s role in reducing the deleterious consequences of heat stress. Therefore, this chapter summarizes the heat-induced responses and damages in plants. In a few examples, we discuss the versatile functions of Si in mitigating abiotic stresses, including heat stress and Si-mediated molecular mechanisms of heat stress tolerance.
Innovations in industrial and functional food applications of lentil in the era of biofortification
(Springer Nature Publishing AG, 2025) Padhy, Asish Kumar; Chaurasia, Shiksha; Manivannan, Abinaya; Tripathi, Kuldeep; Sapna, Sapna; Bhatia, Sabhyata
Lentil can serve as a prebiotic and therapeutic healthy food due to the presence of essential micronutrients, functional proteins, minerals, and carbohydrates, as well as phytochemicals that have shown to be promising in the prevention of several chronic diseases. Nutraceutical properties derived from the phytochemicals present in lentil has expanded its scope of usage to a broader perspective. In this regard, a lot of innovations have been carried out to use lentil in the form of crisps, chips, bakery products, yogurt, pasta, including in the brewing industries. Eforts are being carried out to develop meat analogs out of lentil four. However, niche area specifc consumer preferences have limited its explorations in other innovative areas. This will also necessitate developing genetic resources and varieties aligning to the needs of producers and consumers with acceptable sensory properties. Hence, demand driven development of breeding materials for biofortifcation and crop improvement programs needs considerable amount of investment in research and development of the crop. This review is a campedium of innovations in development of industrial, functional food products from lentil along with their nutritional properties and sensory acceptability serve a foundation for the researchers to invent more to popularize lentil among the consumers to ensure nutritional security.
Mentha arvensis and Mentha × piperita-vital herbs with myriads of pharmaceutical benefits
(MDPI AG, 2023) Wei, Hao; Kong, Shuai; Jayaraman, Vanitha; Selvaraj, Dhivya; Soundararajan, Prabhakaran; Manivannan, Abinaya
Mentha arvensis L. and Mentha × piperita L. are herbal plants belonging to the Lamiaceae family and are widely cultivated for their essential oils and culinary uses. These herbs are commercially valuable mints used in the preparation of herbal formulations, cosmetics, pharmaceuticals, and in food industries. Due to the presence of potential secondary metabolites, mints were employed to treat various disorders since ancient times in traditional medicines. The extracts of M. arvensis and M. × piperita can improve the function of digestive system, central nervous system and respiratory system of the human body. Majority of the health benefits of these herbs are attributed by the essential oil components. In addition, the administration of M. arvensis and M. × piperita under various pathological conditions studied in vitro and in vivo facilitated the recovery of detrimental ailments. Due to the increasing demand for natural product-based medicines, research is focused on the utilization of phytochemicals to treat various ailments. In order to provide a comprehensive overview of health benefits of M. arvensis and M. × piperita, the present endeavor deals with the antioxidant property, anti-inflammatory property, anti-microbial, and anti-cancer activities of both species. However, a deeper knowledge on the specific metabolites of M. arvensis and M. × piperita and their mode of action against different disease targets will accelerate the discovery of novel natural drugs with less side effects and higher efficiency.
Pangenome-wide identification, evolutionary analysis, and characterization of WOX gene family among Brassica Triangle of U's genomes
(Elsevier B.V., 2025) Soundararajan, Prabhakaran; Vivek, AT; Suresh, Gokul Babu; Shukla, Bhavya; Singh, Kanchan B.M.; Kumar, Shailesh; Manivannan, Abinaya
WUSCHEL-related homeobox (WOX) is an evolutionarily important gene family involved in key developmental processes such as embryo patterning, stem cell regulation, apical meristem maintenance, etc. Brassica contains several widely diversified and economically important vegetables grown worldwide. In this study, a pangenome-wide identification and characterization of the WOX gene family among all the species of Brassica Triangle of U's have been performed. WOX gene family was identified from the genomes of 31 Brassica species/morphotypes. About 26–28, 28, and 26–31 copies of WOX genes are present in diploid progenitors such as B. rapa (AA), B. nigra(BB), and B. oleracea (CC), respectively. In allotetraploid species, the number of WOX genes exceeds more than 50 copies. However, their number varies between morphotypes at the pangenome level. Motif and gene structure analysis showed distinct and conserved patterns between homoeologous genes. Non-synonymous (Ka)/Synonymous (Ks) ratio indicated that more number of modern/WUS clade orthologs underwent positive selection followed by those of the intermediate clade. Interacting networks between the WOX and miRNA showed that the CC genome has more complex network pattern compared to the AA genome. Although the WOX-miRNA interactions observed in both AABB and AACC genomes were distinct, they exhibited similarity in overlapping connections. Transcriptome data, analyzed from unfertilized ovule to seven developmental stages of embryos and their seed coat, sourced from public databases across six genomes, illustrated that WOX genes are expressed in a spatio-temporal manner throughout these developmental stages. Furthermore, qPCR analysis of WOX genes at two stages, such as 2–3 days old (leaf and root primordia) and 3 weeks old seedlings (leaf and root) in B. juncea and B. oleracea provides details of stage- and tissues-specific expression patterns between AB and C genomes. Overall, the present study sheds light on evolution and characterization of the WOX gene family in Brassica at the pangenome level for further functional validation.
Paradigm and framework of WUS-CLV feedback loop in stem cell niche for SAM maintenance and cell identity transition
(MDPI AG, 2022) Agarwal, Yamini; Shukla, Bhavya; Manivannan, Abinaya; Soundararajan, Prabhakaran
Shoot apical meristem (SAM) consists of stem cells that act as a reservoir for the aerial growth. It plays an important role in the differential architectural development in plants. SAM actively performs parallel functions by maintaining the pluripotent of stem cells and continuous organogenesis throughout the plant’s life cycle. Molecular mechanisms regulating the signaling networks of this dual function of the SAM have been progressively understood. In the SAM, the feedback loop of WUSCHEL (WUS)-CLAVATA (CLV) has been found to be the key regulator in stabilizing stem cell proliferation and differentiation. In general, WUS migrates into central zone (CZ) from organizing center (OC) and activates the expression of CLV3 by binding to the promoter elements. CLV3 acts as a ligand to interact with the CLV1, leucine rich repeats (LRR) receptor-like kinase (RLK) and LRR receptor-like protein CLV2, and protein kinase coryne (CRN) (CLV2/CRN) to restrict WUS transcription to the OC. Evolution of CLV3 is one of the main factors contributing to the transformation of two dimensional (2D) to 3D plants. WUS-CLV loop is involved in several pathways and networks that integrate on meristem maintenance and cell identity transition. WUSCLV maintains stem cells with simultaneous differentiation signals by the spatial-temporal signaling of the phytohormones. WUS-CLV loop has an interaction with reactive oxygen species (ROS), an important signaling molecules regulating cell proliferation and developmental transition. WUS also forms feedback loop with AGAMOUS (AG) for differentiation, proliferation, and termination of floral meristem. These loops might also involve in interaction with vernalization and its regulatory factors that oversees the precise timing of flowering after exposure to cold temperatures. In this review, we highlight the evolutionary and developmental importance of the WUS-CLV feedback loop on SAM maintenance and cell identity transition for inflorescence and floral meristem development.
Transcriptome-wide identification and expression analysis of expansin genes in big and small leaf-morphotypes of Adhatoda vasica
(Springer Nature Publishing AG, 2025) Soundararajan, Prabhakaran; Singh, Pooja; Letro, Awele; Singh, Gourav; Manivannan, Abinaya
In the present study the expansin genes were identified from Adhatoda vasica, a potential medicinal plant. It consists of two morphotypes S (small leaf bearing plants with low alkaloid content) and B (large leaf bearing plants with high alkaloid content). The difference in the leaf size influence the alkaloid content and it act as the economically important trait for this medicinal plant. Therefore, exploring the expression of expansins will facilitate the molecular regulation of leaf expansion in A. vasica. For the identification of expansins, Hidden Markov model (HMM) profiles of double-psi beta-barrel (DPBB) and pollen allergen domains were utilized and searched against the genomes of Arabidopsis thaliana, Catharanthus roseus and Camellia sinensis and confirmed with BLAST search against published expansins of A. thaliana. The resulted expansins were used for homology-based identification of expansin transcripts in A. vasica transcriptome assembly. A total of 22 expansin transcripts were identified in A. vasica leaf transcriptome. The phylogenetic tree illustrated that the expansins were clustered into four subfamily EXPA, EXPB, EXPLA, and EXPLB. Interactome analysis revealed that the expansins interacted with genes involved in cell wall modification. In addition, leaf transcriptome analysis of S and B morphotypes revealed that majority of the expansins were upregulated in B morphotype than S morphotype. Further, qPCR analysis of selected expansin genes from transcriptome were validated in the young and mature leaf tissues of both morphotypes. Overall, the outcomes of the present study will facilitate the understanding the expansins based molecular regulation of leaf size in A. vasica which will aid in the higher production of pharmaceutically important alkaloids.