Functional Genomics: Applications in Plant Science

Jha, Uday Chand; Bhat, Jayant S.; Patil, B. S.; Hossain, Firoz; Barh, Debmalya

doi:10.1007/978-81-322-2172-2_4

Cited by 7 publications

(9 citation statements)

References 508 publications

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“…Yellow or orange coloured QPM maize can have greater impact on nutritional health of target countries particularly in Sub Saharan Africa and South Asia. Development of high yielding and stable QPM varieties for different maturity groups and different ecologies may provide effective opportunity to widen the adoption spectrum of these varieties (Hossain et al., 2016). Integration of modern tools like omics and genome editing can further accelerate the development of multinutrient–stress resilient and high yielding QPM varieties (Jha et al., 2015). Intensive and coordinated efforts by authorities and public sector institutes through policies and campaigns for efficient input–output linkages for QPM production may lead to significant increase in the adoption of QPM varieties. Strengthening the maize seed system to ensure the availability, affordability and accessibility to quality seed of QPM varieties is also one of the important steps to fast track the deployment of these varieties among small landholding farmers. Provision of subsidized seed or other inputs like fertilizers, etc.…”

Section: Adoption Of Qpm Varieties: Challenges and Opportunitiesmentioning

confidence: 99%

Quality protein maize (QPM): Importance, genetics, timeline of different events, breeding strategies and varietal adoption

Maqbool¹,

Issa²,

Khokhar³

2021

Plant Breeding

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Lysine and tryptophan are two essential amino acids and these are deficit in maize grain thus posing the problem of nutritional deficiencies in the consumers. A wide range of deficiency symptoms like cognitive disorder, kwashiorkor disease, reduced appetite, impaired skeleton development, delayed growth and aberrant behaviour are associated with lysine and tryptophan deficiency. These amino acids are also important to cure the Pellagra disease. Researchers identified several mutants in maize especially opaque‐2 which are responsible for higher lysine and tryptophan contents. Few years later, it was observed that opaque‐2 mutant has several pleiotropic effects on maize grain and plant. Efforts of researchers are spanning over the period of four decades to develop quality protein maize (QPM). QPM is described as nutritionally superior maize with high lysine and tryptophan contents and desired kernel characteristics as compared to its normal maize counterparts. Biological value of QPM was almost equivalent to egg protein. Breeding of maize for quality protein is based on three genetic systems like opaque‐2 genetic system, endosperm modifier genetic system and associated gene systems. Keeping in view the importance of QPM, current review article is compiled to discuss the genetic basis, genetic systems and breeding strategies. Timeline for various events is also drafted like discovery of various mutants, several conventional and modern approaches for development and deployment of QPM varieties across the world. Despite its nutritional benefits, the rate of adoption of QPM is generally at low pace in the developing world and this review article discuss the challenges and potential opportunities for QPM adoption.

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Section: Adoption Of Qpm Varieties: Challenges and Opportunitiesmentioning

confidence: 99%

Quality protein maize (QPM): Importance, genetics, timeline of different events, breeding strategies and varietal adoption

Maqbool¹,

Issa²,

Khokhar³

2021

Plant Breeding

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“…In contrast, functional genomics aims to understand the complex relationship between the genome and phenotypic manifestations, focusing on the dynamic aspects of genes and the biochemical and physiological functions of all gene products [61]. Consequently, functional genomics comprises a wide range of omics disciplines that measure molecular activities, and is the focus of this thesis.…”

Section: The Omics Technologies and Bioinformaticsmentioning

confidence: 99%

Development of bioinformatics resources for the integrative analysis of Next Generation omics data

Diego¹

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Advances in high-throughput sequencing techniques and the technological development accompanying them have favoured the development and popularisation of a new range of genomic research disciplines, collectively known as the omics. These technologies are capable of simultaneously measuring thousands of molecules which are essential for life, including DNA, RNA, proteins, and metabolites. Historically, classical genomic research has followed a reductionist approach by studying the structure, regulation, and function of these biological units independently. However, despite being a powerful analytical tool, the reductionist method cannot explain many of the biological phenomena that take place in living systems. This is because these biological events are not represented by the sum of their components, rather, only the interacting dynamics of the different omics elements can explain their complexity.In recent years Systems Biology has established itself as a multidisciplinary area of research which tries to model the dynamic behaviour of biological systems by holistically studying the interactions between the different omics disciplines; it combines simultaneous measurements of different types of molecules and integrates multiple sources of information in order to identify changing components in a coordinated way and under controlled study conditions. Thus, Systems Biology is an interdisciplinary area that requires biologists, mathematicians, biochemists, and other researchers to work closely together, and in which computer sciences plays a fundamental role because of the volume and complexity of the data handled.iii This thesis addresses the problem of data management, integration, and analysis in multi-omics studies. More specifically, this research focused on two of the most characteristic computational challenges in Systems Biology: the development of integrated databases and the problem of integrative visualisation.Therefore, the first part of this work was devoted to designing and creating a bioinformatics resource for managing multi-omics experiments. The resulting platform, known as STATegra Experiment Management System (EMS), offers a complete set of tools that facilitate the storage and organisation of the large datasets generated during omics experiments, and also provides tools for data annotation in the later stages of processing and analysis of the information.The development of this platform required overcoming problems created by the heterogeneity, volume, and high variability of the data. Thus, as part of the solution to these problems, detailed metadata can be recorded within STATegra EMS, allowing dataset discrimination and successful data integration. To aid this process, the platform also offers a collaborative and easy-to-use web interface that combines modern web technologies and well-known community standards to represent the different components of the integrated experiments.The second part of this thesis examines the current situation and challenges in integrative data visualisati...

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“…Functional genomics, as a multidisciplinary field, encompasses a wide range of applications that have significantly contributed to our understanding of cellular and organismal functions (1,6,19). These applications have revolutionized biological research by providing powerful tools and methodologies to investigate complex biological systems.…”

Section: Applications Of Function Genomicsmentioning

confidence: 99%

“…Some of the key applications of functional genomics include identifying novel gene functions and interactions, elucidating disease mechanisms, studying gene regulation and expression, discovering novel biomarkers for disease diagnosis, understanding the impact of environmental factors on gene expression, personalized medicine, and enhancing drug discovery and development (17,(19)(20)(21). By integrating multiple data sets, such as gene expression profiles, protein-protein interaction maps, genetic interaction, and phenotypic data, functional association networks can be generated to reveal the roles of individual genes and their interactions in various biological processes and pathways (Figure 1.2).…”

Section: Applications Of Function Genomicsmentioning

confidence: 99%

Investigation of Novel Gene Functions in Yeast Using Functional Genomics

Jagadeesan

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Systems biology, a diverse and complex field, relies heavily on functional genomics and highthroughput methods to understand the intricacy of cellular and molecular interactions. Through large-scale, comprehensive genome screening experiments, we generate considerable amounts of data, referred to as "big data," that unravel the complex biochemical interactions within living cells. In this context, Saccharomyces cerevisiae, commonly referred to as baker's yeast serves as a pivotal model organism in scientific research. Its widespread utilization is attributed to the readily available high-throughput techniques, substantial genetic similarity to humans, ease of manipulation, and the wealth of genetic and biochemical resources at its disposal. Our research primarily targets the dissection of the intricate molecular machinery involved in the translation initiation pathway, specifically structured messenger RNAs(mRNAs) in Saccharomyces cerevisiae.Recognizing the centrality of translation to cellular functionality and its perturbation in disease conditions, we employ functional genomic strategies and high-throughput techniques to unearth previously unrecognized gene functions within this process. We examine around 5000 nonessential yeast genes for their effect on the translation of reporter genes, unmasking four previously unidentified gene functions: PEX11, RIM20, YRF1-6, and DBP7. These genes significantly modulate the translation of mRNAs that feature structured 5'UTRs.Further, we leverage a functional genomics computational platform to uncover novel genes implicated in the DNA damage pathway. Integrating protein-protein interactions (PPI), genetic interactions, and gene expression data, we identified three unknown gene functions, GAL7, YMR130W, and YHI9, which are associated with double-strand break repair via both homologous and non-homologous end-joining pathways. These genetic associations are further validated through experimental methodologies. Additionally, we aim to elucidate the inhibitory mechanisms of the SARS-CoV-2 NSP1 gene on translation pathway, proposing the involvement of several other proteins and translation initiation factors critical to viral translation.This research provides profound insights into the complexity of the translation initiation iii pathway, integral to cellular functionality and survival. The revelation of new gene functionalities expands our present understanding and paves the way for further exploration of translational perturbations in disease conditions, thus potentially aiding the development of innovative therapeutic strategies. The integration of large-scale functional genomics and computational strategies enhances our ability to simultaneously evaluate thousands of genes, enriching the depth of our investigations. Also, the investigation of SARS-CoV-2 NSP1 translation inhibitory mechanism using functional genomics approach may expose new targets for antiviral interventions. Given the genetic parallels between baker's yeast and humans, our discoveries could significantly i...

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Functional Genomics: Applications in Plant Science

Cited by 7 publications

References 508 publications

Quality protein maize (QPM): Importance, genetics, timeline of different events, breeding strategies and varietal adoption

Quality protein maize (QPM): Importance, genetics, timeline of different events, breeding strategies and varietal adoption

Development of bioinformatics resources for the integrative analysis of Next Generation omics data

Investigation of Novel Gene Functions in Yeast Using Functional Genomics

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