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Understanding salinity responses and adopting 'omics-based' approaches to generate salinity tolerant cultivars of rice.

Das P, Nutan KK, Singla-Pareek SL, Pareek A - Front Plant Sci (2015)

Bottom Line: Soil salinity is one of the main constraints affecting production of rice worldwide, by reducing growth, pollen viability as well as yield of the plant.Therefore, detailed understanding of the response of rice towards soil salinity at the physiological and molecular level is a prerequisite for its effective management.In addition, we have highlighted the importance of integration of various 'omics' approaches to develop an understanding of the machinery involved in salinity response in rice and to move forward to develop salt tolerant cultivars of rice.

View Article: PubMed Central - PubMed

Affiliation: Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University New Delhi, India.

ABSTRACT
Soil salinity is one of the main constraints affecting production of rice worldwide, by reducing growth, pollen viability as well as yield of the plant. Therefore, detailed understanding of the response of rice towards soil salinity at the physiological and molecular level is a prerequisite for its effective management. Various approaches have been adopted by molecular biologists or breeders to understand the mechanism for salinity tolerance in plants and to develop salt tolerant rice cultivars. Genome wide analysis using 'omics-based' tools followed by identification and functional validation of individual genes is becoming one of the popular approaches to tackle this task. On the other hand, mutation breeding and insertional mutagenesis has also been exploited to obtain salinity tolerant crop plants. This review looks into various responses at cellular and whole plant level generated in rice plants toward salinity stress thus, evaluating the suitability of intervention of functional genomics to raise stress tolerant plants. We have tried to highlight the usefulness of the contemporary 'omics-based' approaches such as genomics, proteomics, transcriptomics and phenomics towards dissecting out the salinity tolerance trait in rice. In addition, we have highlighted the importance of integration of various 'omics' approaches to develop an understanding of the machinery involved in salinity response in rice and to move forward to develop salt tolerant cultivars of rice.

No MeSH data available.


Related in: MedlinePlus

‘Omics-based’ approaches and their integration to develop salinity tolerant rice cultivars. Flow of information from various ‘omics-based’ platforms such as phenomics, genomics, transcriptomics, proteomics, and metabolomics needs to be integrated to understand complex traits such as salinity tolerance. Ultimately, the key genes/regulators responsible for salt tolerance need identification and validation using the tools of functional genomics.
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Figure 3: ‘Omics-based’ approaches and their integration to develop salinity tolerant rice cultivars. Flow of information from various ‘omics-based’ platforms such as phenomics, genomics, transcriptomics, proteomics, and metabolomics needs to be integrated to understand complex traits such as salinity tolerance. Ultimately, the key genes/regulators responsible for salt tolerance need identification and validation using the tools of functional genomics.

Mentions: ‘Omics’ approaches seems to be overlapping and dependent on each other, and integration of all the ‘omics’ approaches is necessary to reach at an ultimate step i.e., raising of stress tolerant cultivars (Figure 3). Proteomic studies show vast overlapping in vital metabolism (e.g., Calvin cycle and carbohydrate metabolism) under salt stress. However, different metabolic pathways have been found to control and regulate under metabolomic level, mostly the biosynthesis of amino acid, photorespiration and citric acid pathway (Ma et al., 2013). This is probably due to the participation of downstream enzymatic reaction instead of cellular injury reactions, which encourage the pathways of complex metabolites. The proteomic approach presumes that the raise in quantity of protein amount is always escorted by biologically active compound, but in fact it may include the factors by posttranslational alterations, that may alter characteristics of the proteins. So, the function of the metabolite changing occured at the metabolomic point is not very much clear. Hence, it can be said that the growth of bioinformatics, in linking to the response at transcription level to either metabolomic or proteomic alterations, is yet to be done. The quick evolution in ‘omics’ research has led to more and more generation of data sets throughout all branches in life science studies. Different investigative applications, that are vital for the efficient incorporation of data resources, have been published in various databases. These huge datasets are found via four main stages: (a) data generation (b) data processing (c) data integration and the final step is (d) data analysis (Mochida and Shinozaki, 2011). The dispute in the incorporation of omics data investigation has been argued (Edwards and Batley, 2004). It was shown that the main trouble occurred from the partial and dissimilar form of information accessible on bioinformatics data sources. Hence, algorithmic methods have been planned as the solution for this kind of trouble (Ge et al., 2003). Currently, many servers have been established which allows the integration of high-throughput data and these servers also able to display the outcomes in a meaningful pathway of biology (Tuncbag et al., 2012).


Understanding salinity responses and adopting 'omics-based' approaches to generate salinity tolerant cultivars of rice.

Das P, Nutan KK, Singla-Pareek SL, Pareek A - Front Plant Sci (2015)

‘Omics-based’ approaches and their integration to develop salinity tolerant rice cultivars. Flow of information from various ‘omics-based’ platforms such as phenomics, genomics, transcriptomics, proteomics, and metabolomics needs to be integrated to understand complex traits such as salinity tolerance. Ultimately, the key genes/regulators responsible for salt tolerance need identification and validation using the tools of functional genomics.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4563168&req=5

Figure 3: ‘Omics-based’ approaches and their integration to develop salinity tolerant rice cultivars. Flow of information from various ‘omics-based’ platforms such as phenomics, genomics, transcriptomics, proteomics, and metabolomics needs to be integrated to understand complex traits such as salinity tolerance. Ultimately, the key genes/regulators responsible for salt tolerance need identification and validation using the tools of functional genomics.
Mentions: ‘Omics’ approaches seems to be overlapping and dependent on each other, and integration of all the ‘omics’ approaches is necessary to reach at an ultimate step i.e., raising of stress tolerant cultivars (Figure 3). Proteomic studies show vast overlapping in vital metabolism (e.g., Calvin cycle and carbohydrate metabolism) under salt stress. However, different metabolic pathways have been found to control and regulate under metabolomic level, mostly the biosynthesis of amino acid, photorespiration and citric acid pathway (Ma et al., 2013). This is probably due to the participation of downstream enzymatic reaction instead of cellular injury reactions, which encourage the pathways of complex metabolites. The proteomic approach presumes that the raise in quantity of protein amount is always escorted by biologically active compound, but in fact it may include the factors by posttranslational alterations, that may alter characteristics of the proteins. So, the function of the metabolite changing occured at the metabolomic point is not very much clear. Hence, it can be said that the growth of bioinformatics, in linking to the response at transcription level to either metabolomic or proteomic alterations, is yet to be done. The quick evolution in ‘omics’ research has led to more and more generation of data sets throughout all branches in life science studies. Different investigative applications, that are vital for the efficient incorporation of data resources, have been published in various databases. These huge datasets are found via four main stages: (a) data generation (b) data processing (c) data integration and the final step is (d) data analysis (Mochida and Shinozaki, 2011). The dispute in the incorporation of omics data investigation has been argued (Edwards and Batley, 2004). It was shown that the main trouble occurred from the partial and dissimilar form of information accessible on bioinformatics data sources. Hence, algorithmic methods have been planned as the solution for this kind of trouble (Ge et al., 2003). Currently, many servers have been established which allows the integration of high-throughput data and these servers also able to display the outcomes in a meaningful pathway of biology (Tuncbag et al., 2012).

Bottom Line: Soil salinity is one of the main constraints affecting production of rice worldwide, by reducing growth, pollen viability as well as yield of the plant.Therefore, detailed understanding of the response of rice towards soil salinity at the physiological and molecular level is a prerequisite for its effective management.In addition, we have highlighted the importance of integration of various 'omics' approaches to develop an understanding of the machinery involved in salinity response in rice and to move forward to develop salt tolerant cultivars of rice.

View Article: PubMed Central - PubMed

Affiliation: Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University New Delhi, India.

ABSTRACT
Soil salinity is one of the main constraints affecting production of rice worldwide, by reducing growth, pollen viability as well as yield of the plant. Therefore, detailed understanding of the response of rice towards soil salinity at the physiological and molecular level is a prerequisite for its effective management. Various approaches have been adopted by molecular biologists or breeders to understand the mechanism for salinity tolerance in plants and to develop salt tolerant rice cultivars. Genome wide analysis using 'omics-based' tools followed by identification and functional validation of individual genes is becoming one of the popular approaches to tackle this task. On the other hand, mutation breeding and insertional mutagenesis has also been exploited to obtain salinity tolerant crop plants. This review looks into various responses at cellular and whole plant level generated in rice plants toward salinity stress thus, evaluating the suitability of intervention of functional genomics to raise stress tolerant plants. We have tried to highlight the usefulness of the contemporary 'omics-based' approaches such as genomics, proteomics, transcriptomics and phenomics towards dissecting out the salinity tolerance trait in rice. In addition, we have highlighted the importance of integration of various 'omics' approaches to develop an understanding of the machinery involved in salinity response in rice and to move forward to develop salt tolerant cultivars of rice.

No MeSH data available.


Related in: MedlinePlus