Institutional Publications
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Item Next-generation translational genomics for developing future crops(Springer Nature Publishing AG, 2025) Basu, Udita; Parida, Swarup K.Advancements in translational genomics have revolutionized crop breeding, driving us from traditional breeding methods towards next-generation strategies that integrate genomic, transcriptomic, and phenotypic data to expedite crop improvement. There has been a shift from single genomes to pan-genomes, which better capture intraspecific diversity, and from bulk transcriptome analyses to single-cell transcriptomics, enabling cell-specific insights into gene regulation and functional genomics. Both high throughput genopyting and phenotyping approaches are now possible due to rapid technological advancement in the field of translational genomics. Large-scale phenotyping data from multi-environment field trials is now possible due to AI-enabled digital and drone-based scanning. In the era of artificial intelligence and machine learning we have developed flexible models to handle complex genetic architecture of trait regulation using various tools and approaches. These genetic and genomic resources are the foundation for generating novel, adaptable, and high-yielding varieties, accelerating trait discovery and mapping. This review explores the comprehensive landscape of modern translational genomics, highlighting key shifts and innovations that enhance our capacity to address agricultural challenges. Integrative pipelines that unify these next-generation approaches could facilitate faster, more precise, and sustainable crop improvement, ultimately meeting the growing demands for future-ready crops.Item Molecular approaches for improving nutritional quality in crops(John Wiley & Sons, 2024) Gandhi, Nidhi; Singh, Amar PalThe increasing rate of occurrence of chronic diseases in the human population is creating a global awareness of consuming a healthy diet. It has been shown that regular consumption of a nutritious diet plays a vital role in the prevention of malnutrition as well as a variety of deadly diseases. Food is defined as functional if it provides additional benefits along with basic nutrition, either by reducing the risk of diseases or by improving the health state. There are different strategies and techniques for the identification and quantification of the desired phytochemicals, metabolites, and minerals in the crops and for introducing the superior alleles responsible for the desired traits in the germplasm. By using genome-level genetic studies like GWAS, the genomic regions can be identified that are responsible for the superior metabolic trait. Recently, precise genome editing using CRISPR/ Cas9 technology and overexpression of a few genes in crop plants offer to enhance the production of desired metabolites and micronutrients. Many crops have been produced in the last few years by altering the expression of genes via gene silencing, genome-level editing, mutagenesis, or other strategies of advanced genetic engineering. In this chapter, we summarize the different approaches for enhancing the yield and nutritional quality of crops. The successful attempts to increase the essential vitamins and micronutrients or other beneficial phytochemicals in the crops will be discussed. Altogether, we describe the application of different techniques and strategies to manipulate the genome or precise gene in the crop plants to enhance the food's nutritional quality.Item CRISPR/Cas9 directed editing of lycopene epsilon-cyclase modulates metabolic flux for β-carotene biosynthesis in banana fruit(Elsevier B.V., 2020) Kaur, Navneet; Alok, Anshu; Shivani; Kumar, Pankaj; Kaur, Navjot; Awasthi, Praveen; Chaturvedi, Siddhant; Pandey, Pankaj; Pandey, Ashutosh; Pandey, Ajay K.; Tiwari, SiddharthBanana is one of the most economically important fruit crops worldwide. Genetic improvement in banana is a challenging task due to its parthenocarpic nature and triploid genome. Genetic modification of crops via the CRISPR/Cas9 module has emerged as a promising tool to develop important traits. In the present work, a CRISPR/Cas9-based approach was used to develop the β-carotene-enriched Cavendish banana cultivar (cv.) Grand Naine (AAA genome). The fifth exon of the lycopene epsilon-cyclase (LCYε) gene was targeted. The targeting specificity of the designed guide-RNA was also tested by its ability to create indels in the LCYε gene at the A genome of cv. Rasthali (AAB genome). Sequence analysis revealed multiple types of indels in the genomic region of Grand Naine LCYε (GN-LCYε). Metabolic profiling of the fruit pulp of selected edited lines showed enhanced accumulation of β-carotene content up to 6-fold (~24 μg/g) compared with the unedited plants. These lines also showed either an absence or a drastic reduction in the levels of lutein and α-carotene, suggesting metabolic reprogramming, without any significant effect on the agro-morphological parameters. In addition, differential expression of carotenoid pathway genes was observed in the edited lines in comparison to unedited plants. Overall, this is the first report in banana to improve nutritional trait by using a precise genome editing approach.Item CRISPR-Cas9 system: A new-fangled dawn in gene editing(Elsevier B.V., 2019) Gupta, Darshana; Bhattacharjee, Oindrila; Mandal, Drishti; Sen, Madhab Kumar; Dey, Dhritiman; Dasgupta, Adhiraj; Kazi, Tawsif Ahmed; Gupta, Rahul; Sinharoy, Senjuti; Acharya, Krishnendu; Chattopadhyay, Dhrubajyoti; Ravichandiran, V.; Roy, Syamal; Ghosh, DipanjanTill date, only three techniques namely Zinc Finger Nuclease (ZFN), Transcription-Activator Like Effector Nucleases (TALEN) and Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-Associated 9 (CRISPR-Cas9) are available for targeted genome editing. CRISPR-Cas system is very efficient, fast, easy and cheap technique for achieving knock-out gene in the cell. CRISPR-Cas9 system refurbishes the targeted genome editing approach into a more expedient and competent way, thus facilitating proficient genome editing through embattled double-strand breaks in approximately any organism and cell type. The off-target effects of CRISPR Cas system has been circumnavigated by using paired nickases. Moreover, CRISPR-Cas9 has been used effectively for numerous purposes, like knock-out of a gene, regulation of endogenous gene expression, live-cell labelling of chromosomal loci, edition of single-stranded RNA and high-throughput gene screening. The execution of the CRISPR-Cas9 system has amplified the number of accessible scientific substitutes for studying gene function, thus enabling generation of CRISPR-based disease models. Even though many mechanistic questions are left behind to be answered and the system is not yet fool-proof i.e., a number of challenges are yet to be addressed, the employment of CRISPR-Cas9–based genome engineering technologies will increase our understanding to disease processes and their treatment in the near future. In this review we have discussed the history of CRISPR-Cas9, its mechanism for genome editing and its application in animal, plant and protozoan parasites. Additionally, the pros and cons of CRISPR-Cas9 and its potential in therapeutic application have also been detailed here.