Emerging Advances in Computational Omics Tools for Systems Analysis of Gramineae Family Grass Species and Their Abiotic Stress Responsive Functions

Muthuramalingam, Pandiyan; Jeyasri, Rajendran; Dhamodharan, Kalaiyarasi; Subramanian, A.; Krishnan, Subramanian Radhesh; Pandian, Shunmugiah Karutha

doi:10.1002/9781119509967.ch10

Cited by 6 publications

(9 citation statements)

References 99 publications

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“…Interestingly, genome and transcriptome sequencing, annotation projects and recent literatures paved the way to identify the candidate genes through omics databases, which are predicted to be involved in individual and combined abiotic stress (CAbS) responses. This claim supports to understanding the stress tolerance mechanism and environmental adaptation, as well as promoting the green revolution of all other food crops [47,48].…”

Section: Sorghum (Sorghum Bicolor L)supporting

confidence: 63%

An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics

Jeyasri

Muthuramalingam

Satish

et al. 2021

Plants

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Abiotic stresses (AbS), such as drought, salinity, and thermal stresses, could highly affect the growth and development of plants. For decades, researchers have attempted to unravel the mechanisms of AbS for enhancing the corresponding tolerance of plants, especially for crop production in agriculture. In the present communication, we summarized the significant factors (atmosphere, soil and water) of AbS, their regulations, and integrated omics in the most important cereal crops in the world, especially rice, wheat, sorghum, and maize. It has been suggested that using systems biology and advanced sequencing approaches in genomics could help solve the AbS response in cereals. An emphasis was given to holistic approaches such as, bioinformatics and functional omics, gene mining and agronomic traits, genome-wide association studies (GWAS), and transcription factors (TFs) family with respect to AbS. In addition, the development of omics studies has improved to address the identification of AbS responsive genes and it enables the interaction between signaling pathways, molecular insights, novel traits and their significance in cereal crops. This review compares AbS mechanisms to omics and bioinformatics resources to provide a comprehensive view of the mechanisms. Moreover, further studies are needed to obtain the information from the integrated omics databases to understand the AbS mechanisms for the development of large spectrum AbS-tolerant crop production.

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Section: Sorghum (Sorghum Bicolor L)supporting

confidence: 63%

An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics

Jeyasri

Muthuramalingam

Satish

et al. 2021

Plants

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“…Recent advancements in biological sciences, particularly emerging sequencing and throughput omics approaches, have enabled the way to generate a huge spectrum of omics data, including transcriptome, epigenome, proteome, metabolome, hormonome, signalome, ionome, and phenome at the genome level from O. sativa grown under diverse climatic conditions [ 18 , 188 , 189 , 190 ]. Nevertheless, the public availability of a wide range of cell and molecular data researchers is still far away through categorizing and characterizing the molecular physiological responses of O. sativa datasets are extremely underutilized.…”

Section: Modern Multi-omics Era To Improve the Salinity Tolerancementioning

confidence: 99%

“…In addition, several other new technologies have also emerged, in association with molecular signalome/interactome analyses used for unraveling the interactions formed by protein-nucleic acids (DNA and RNA) and protein-protein interactions (PPI) [ 193 ]. Plant hormonal profiling was used to understand cellular signaling [ 18 , 194 ], metabolic pathway analysis by metabolomics [ 195 , 196 , 197 ], and plant morpho-physiological changes were analyzed by phenomic approach [ 198 ]. These omics approaches and genomic datasets treat all the molecular mechanisms as interconnected elements of plant cellular and molecular physiological systems.…”

Section: Modern Multi-omics Era To Improve the Salinity Tolerancementioning

confidence: 99%

“…These issues alarm to throw more light on plant stress biologists to evaluate the biochemical and molecular stress machinery and their signaling network in rice. Significantly, the available whole rice genome and transcriptome projects [ 15 ], multi-omics approaches [ 16 , 17 ], bioinformatic platforms [ 18 ], agricultural practicing elements [ 19 , 20 , 21 , 22 ], breeding [ 23 ], and recent literature pave the way to identify and annotate the stress-responsive key players with their regulatory functions and also provide the deeper molecular insights. These integrated approaches and holistic strategies used for the dissection of dynamic networks and altering the repercussions in plants support them in controlling abiotic stresses, particularly salinity stress.…”

Section: Introductionmentioning

confidence: 99%

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Multi-Omics and Integrative Approach towards Understanding Salinity Tolerance in Rice: A Review

Muthuramalingam

Jeyasri

Rakkammal

et al. 2022

Biology

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Rice (Oryza sativa L.) plants are simultaneously encountered by environmental stressors, most importantly salinity stress. Salinity is the major hurdle that can negatively impact growth and crop yield. Understanding the salt stress and its associated complex trait mechanisms for enhancing salt tolerance in rice plants would ensure future food security. The main aim of this review is to provide insights and impacts of molecular-physiological responses, biochemical alterations, and plant hormonal signal transduction pathways in rice under saline stress. Furthermore, the review highlights the emerging breakthrough in multi-omics and computational biology in identifying the saline stress-responsive candidate genes and transcription factors (TFs). In addition, the review also summarizes the biotechnological tools, genetic engineering, breeding, and agricultural practicing factors that can be implemented to realize the bottlenecks and opportunities to enhance salt tolerance and develop salinity tolerant rice varieties. Future studies pinpointed the augmentation of powerful tools to dissect the salinity stress-related novel players, reveal in-depth mechanisms and ways to incorporate the available literature, and recent advancements to throw more light on salinity responsive transduction pathways in plants. Particularly, this review unravels the whole picture of salinity stress tolerance in rice by expanding knowledge that focuses on molecular aspects.

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“…Significant improvements in next-generation sequencing (NGS) have paved the way for a promising generation of diverse omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, hormonomics, and phenomics, which have also been well implemented in crops, especially rice [ 19 , 20 ]. These omics-based approaches, particularly transcriptomics with high-throughput techniques, will enable molecular analysis of the precise systems regulating seed dormancy in rice and other crops.…”

Section: Introductionmentioning

confidence: 99%

Seed Dormancy and Pre-Harvest Sprouting in Rice—An Updated Overview

Sohn

Subramanian

Thamilarasan

et al. 2021

IJMS

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Pre-harvest sprouting is a critical phenomenon involving the germination of seeds in the mother plant before harvest under relative humid conditions and reduced dormancy. As it results in reduced grain yield and quality, it is a common problem for the farmers who have cultivated the rice and wheat across the globe. Crop yields need to be steadily increased to improve the people’s ability to adapt to risks as the world’s population grows and natural disasters become more frequent. To improve the quality of grain and to avoid pre-harvest sprouting, a clear understanding of the crops should be known with the use of molecular omics approaches. Meanwhile, pre-harvest sprouting is a complicated phenomenon, especially in rice, and physiological, hormonal, and genetic changes should be monitored, which can be modified by high-throughput metabolic engineering techniques. The integration of these data allows the creation of tailored breeding lines suitable for various demands and regions, and it is crucial for increasing the crop yields and economic benefits. In this review, we have provided an overview of seed dormancy and its regulation, the major causes of pre-harvest sprouting, and also unraveled the novel avenues to battle pre-harvest sprouting in cereals with special reference to rice using genomics and transcriptomic approaches.

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Emerging Advances in Computational Omics Tools for Systems Analysis of Gramineae Family Grass Species and Their Abiotic Stress Responsive Functions

Cited by 6 publications

References 99 publications

An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics

An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics

Multi-Omics and Integrative Approach towards Understanding Salinity Tolerance in Rice: A Review

Seed Dormancy and Pre-Harvest Sprouting in Rice—An Updated Overview

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