Institutional Publications

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    Genome sequencing efforts in minor millets: Current knowledge and emerging insights
    (Springer Nature Publishing AG, 2025) Singh, Roshan Kumar; Panchal, Anurag; Muthamilarasan, Mehanathan; Prasad, Manoj
    Small millets (or minor millets) include finger millet (Eleusine coracana), foxtail millet (Setaria italica), proso millet (Panicum miliaceum), barnyard millet (Echinochloa crus-galli), kodo millet (Paspalum scrobiculatum), little millet (Panicum sumatrense), teff (Eragrostis tef), fonio (Digitaria exilis), job’s tears (Coix lacryma-jobi), guinea millet (Brachiaria deflexa), and browntop millet (Urochloa ramosa). These millets are highly nutritious and climate-resilient but marginally cultivated for the production and consumption of particular communities. Though called “poor men’s crops,” minor millets possess the potential to ensure food and nutritional security amid the threat of global climate change. Thus, scope exists to improve the agronomic traits of these minor millets for commercial cultivation; however, lack of genomic resources remains a bottleneck to this advancement. Genome sequencing not only provides an opportunity to decode the genes encoded by the genome, but also provides avenue for the development of genomic resources. The success of genome sequencing for resource development and further implementation of these resources have been proven in other crop plants. Among minor millets, genomes of a few species have been sequenced, including finger millet, foxtail millet, proso millet, barnyard millet, teff, fonio, and job’s tears. However, the genomes of kodo millet, little millet, guinea millet, and browntop millet remains to be sequenced. In this context, the chapter summarizes the outcomes of sequencing efforts and the application of genome sequence information in accelerating genomics studies in minor millets. The chapter also enumerates the status of transcriptome sequencing and its application in dissecting the genes underlying important traits.
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    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.
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    Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size
    (BioMed Central Ltd, 2023) Mahto, Arunima; Yadav, Antima; Aswathi, P. V.; Parida, Swarup K.; Tyagi, Akhilesh K.; Agarwal, Pinky
    Background Rice grain size (GS) is an essential agronomic trait. Though several genes and miRNA modules influencing GS are known and seed development transcriptomes analyzed, a comprehensive compendium connecting all possible players is lacking. This study utilizes two contrasting GS indica rice genotypes (small-grained SN and large-grained LGR). Rice seed development involves five stages (S1–S5). Comparative transcriptome and miRNome atlases, substantiated with morphological and cytological studies, from S1–S5 stages and flag leaf have been analyzed to identify GS proponents. Results Histology shows prolonged endosperm development and cell enlargement in LGR. Stand-alone and comparative RNAseq analyses manifest S3 (5–10 days after pollination) stage as crucial for GS enhancement, coherently with cell cycle, endoreduplication, and programmed cell death participating genes. Seed storage protein and carbohydrate accumulation, cytologically and by RNAseq, is shown to be delayed in LGR. Fourteen transcription factor families influence GS. Pathway genes for four phytohormones display opposite patterns of higher expression. A total of 186 genes generated from the transcriptome analyses are located within GS trait-related QTLs deciphered by a cross between SN and LGR. Fourteen miRNA families express specifically in SN or LGR seeds. Eight miRNA-target modules display contrasting expressions amongst SN and LGR, while 26 (SN) and 43 (LGR) modules are differentially expressed in all stages. Conclusions Integration of all analyses concludes in a “Domino effect” model for GS regulation highlighting chronology and fruition of each event. This study delineates the essence of GS regulation, providing scope for future exploits. The rice grain development database (RGDD) ( www.nipgr.ac.in/RGDD/index.php; https://doi.org/10.5281/zenodo.7762870) has been developed for easy access of data generated in this paper.
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    Transcriptome landscape of early inflorescence developmental stages identifies key flowering time regulators in chickpea
    (Springer Nature Publishing AG, 2022) Basu, Udita; Hegde, Venkatraman S.; Daware, Anurag; Jha, Uday Chand; Parida, Swarup K.
    The early stages of inflorescence development in plants are as crucial as the later floral developmental stages. Several traits, such as inflorescence architecture and flower developmental timings, are determined during those early stages. In chickpea, diverse forms of inflorescence architectures regarding meristem determinacy and the number of flowers per node are observed within the germplasm. Transcriptome analysis in four desi chickpea accessions with such unique inflorescence characteristics identifies the underlying shared regulatory events leading to inflorescence development. The vegetative to reproductive stage transition brings about major changes in the transcriptome landscape. The inflorescence development progression associated genes identified through co-expression network analysis includes both protein-coding genes and long non-coding RNAs (lncRNAs). Few lncRNAs identified in our study positively regulate flowering-related mRNA stability by acting competitively with miRNAs. Bulk segregrant analysis and association mapping narrowed down an InDel marker regulating flowering time in chickpea. Deletion of 11 bp in first exon of a negative flowering time regulator, Early Flowering 3a gene, leads to early flowering phenotype in chickpea. Understanding the key players involved in vegetative to reproductive stage transition and floral meristem development will be useful in manipulating flowering time and inflorescence architecture in chickpea and other legumes.
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    Variety-specific transcript accumulation during reproductive stage in drought- stressed rice
    (John Wiley & Sons, 2022) Gour, Pratibha; Kansal, Shivani; Agarwal, Priyanka; Mishra, Bhuwaneshwar Sharan; Sharma, Deepika; Mathur, Saloni; Raghuvanshi, Saurabh
    The divergence of natural stress tolerance mechanisms between species is an intriguing phenomenon. To study it in rice, a comparative transcriptome analysis was carried out in ‘heading’ stage tissue (flag leaf, panicles and roots) of Nagina 22 (N22; drought-tolerant) and IR64 (drought-sensitive) plants subjected to field drought. Interestingly, N22 showed almost double the number of differentially expressed genes (DEGs) than IR64. Many DEGs colocalized within drought-related QTLs responsible for grain yield and drought tolerance and also associated with drought tolerance and critical drought-related plant traits such as leaf rolling, trehalose content, sucrose and cellulose content. Besides, co-expression analysis of the DEGs revealed several ‘hub’ genes known to actively regulate drought stress response. Strikingly, 1366 DEGs, including 21 ‘hub’ genes, showed a distinct opposite regulation in the two rice varieties under similar drought conditions. Annotation of these variety-specific DEGs (VS-DEGs) revealed that they are distributed in various biological pathways. Furthermore, 103 VS-DEGs were found to physically interact with over 1300 genes, including 32 that physically interact with other VS-DEGs as well. The promoter region of these genes have sequence variations among the two rice varieties, which might be in part responsible for their unique expression pattern.
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    Transcript profiling reveals potential regulators for oxidative stress response of a necrotrophic chickpea pathogen Ascochyta rabiei
    (Springer Nature Publishing AG, 2020) Maurya, Ranjeet; Singh, Yeshveer; Sinha, Manisha; Singh, Kunal; Mishra, Pallavi; Singh, Shreenivas Kumar; Verma, Sandhya; Prabha, Kanchan; Kumar, Kamal; Verma, Praveen K.
    Necrotrophic pathogens experience host-generated oxidative stress during pathogenesis. They overcome such hostile environment by intricate mechanisms which are largely understudied. In this article, reference-based transcriptome analysis of a devastating Ascochyta Blight (AB) disease causing chickpea pathogen Ascochyta rabiei was explored to get insights into survival mechanisms under oxidative stress. Here, expression profling of mock-treated and menadione-treated fungus was carried out by RNA-Seq approach. A signifcant number of genes in response to oxidative stress were overrepresented, suggestive of a robust and coordinated defense system of A. rabiei. A total 73 diferentially expressed genes were fltered out from both the transcriptomes, among them 64 were up-regulated and 9 were found down-regulated. The gene ontology and KEGG mapping were conducted to comprehend the possible regulatory roles of diferentially expressed genes in metabolic networks and biosynthetic pathways. Transcript profling, KEGG pathway and gene ontology-based enrichment analysis revealed 12 (16.43%) stress responsive factors, 25 (34.24%) virulence associated genes, 10 (13.69%) putative efectors and 28 (38.35%) important interacting proteins associated with various metabolic pathways. In addition, genes with diferential expression were further explored for underlying putative pathogenicity factors. We identifed fve genes ST47_g10291, ST47_g9396, ST47_g10294, ST47_g4395, and ST47_g7191 that were common to stress and fungal pathogenicity. The factors recognized in this work can be used to establish molecular tools to explain the regulatory gene networks engaged in stress response of fungal pathogens and disease management.
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    Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis
    (Springer Nature Publishing AG, 2020) Smita, Shuchi; Katiyar, Amit; Lenka, Sangram Keshari; Dalal, Monika; Kumar, Amish; Mahtha, Sanjeet Kumar; Yadav, Gitanjali; Chinnusamy, Viswanathan; Pandey, Dev Mani; Bansal, Kailash Chander
    Abiotic stress tolerance is a complex trait regulated by multiple genes and gene networks in plants. A range of abiotic stresses are known to limit rice productivity. Meta-transcriptomics has emerged as a powerful approach to decipher stress-associated molecular network in model crops. However, retaining specificity of gene expression in tolerant and susceptible genotypes during meta-transcriptome analysis is important for understanding genotype-dependent stress tolerance mechanisms. Addressing this aspect, we describe here “abiotic stress tolerant” (ASTR) genes and networks specifically and differentially expressing in tolerant rice genotypes in response to different abiotic stress conditions. We identified 6,956 ASTR genes, key hub regulatory genes, transcription factors, and functional modules having significant association with abiotic stress–related ontologies and cis-motifs. Out of the 6956 ASTR genes, 73 were co-located within the boundary of previously identified abiotic stress trait–related quantitative trait loci. Functional annotation of 14 uncharacterized ASTR genes is proposed using multiple computational methods. Around 65% of the top ASTR genes were found to be differentially expressed in at least one of the tolerant genotypes under different stress conditions (cold, salt, drought, or heat) from publicly available RNAseq data comparison. The candidate ASTR genes specifically associated with tolerance could be utilized for engineering rice and possibly other crops for broad-spectrum tolerance to abiotic stresses.
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    Morpho-physiological and transcriptome profiling reveal novel zinc deficiency-responsive genes in rice
    (Springer, 2017) Bandyopadhyay, Tirthankar; Mehra, Poonam; Hairat, Suboot; Giri, Jitender
    Intensive farming has depleted the soil zinc (Zn) availability resulting in decreased crop productivity. Here, we attempt to understand the Zn deficiency response in rice through temporal transcriptome analysis. For this, rice seedlings were raised under Zn-deficient conditions up to 4 weeks followed by Zn re-supply for 3 days. Zn-deficient plants developed characteristic deficiency symptoms such as leaf bronzing, decrease in biomass, total chlorophyll, PSII efficiency, decreased carbonic anhydrase activity and increased ROS production. Interestingly, severe alterations in root system architecture were also observed. Comprehensive transcriptome analyses of rice seedlings were carried out after 2 (DEF2W) and 4 weeks (DEF4W) of Zn deficiency with respect to transcriptome profiles of corresponding Zn sufficient conditions (SUF2W, SUF4W). Additionally, to detect the potential Zn-responsive genes, transcriptome profile of Zn-recovered seedlings was compared with DEF4W. All differentially expressed Zn-responsive genes were categorized into early and late Zn deficiency response, and a set of 77 genes, induced and repressed on Zn deficiency and re-supply, respectively, was identified. These genes could be used as low Zn-responsive marker genes. Further, genes involved in membrane transport, phytosiderophore activity and organic acid biosynthesis showed high differential expression. Additionally, the present study unravelled several genes putatively associated with alterations in root system architecture under Zn deficiency and provides novel insights into the interpretation of morpho-physiological, biochemical and molecular regulation of zinc deficiency responses in rice.
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    Dissecting the root nodule transcriptome of chickpea (Cicer arietinum L.)
    (PLOS, 2016) Kant, Chandra; Pradhan, Seema; Bhatia, Sabhyata
    A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea.
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    Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds
    (Frontiers Media S.A., 2014) Pradhan, Seema; Bandhiwal, Nitesh; Shah, Niraj; Kant, Chandra; Gaur, Rashmi; Bhatia, Sabhyata
    Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L.) seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilized to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analyzed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs), about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.