Molecular and Physiological Alterations in Chickpea under Elevated CO2 Concentrations

Palit, P.; Ghosh, Raju; Tolani, Priya; Tarafdar, Avijit; Chitikineni, Annapurna; Bajaj, Prasad; Sharma, Mamta; Kudapa, Himabindu; Varshney, Rajeev K.

doi:10.1093/pcp/pcaa077

Cited by 18 publications

(10 citation statements)

References 61 publications

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“…The secondary metabolism category was considerably down-regulated in sorghum GPR under water-deficit and high [CO 2 ] conditions, with 148 DEGs repressed, approximately 8% of the total number of genes regulated (Table S3). It is already well known that E[CO 2 ] and drought also induce the production of secondary metabolites (Palit et al, 2020b; Palit et al, 2020a).…”

Section: Discussionmentioning

confidence: 99%

Integrative Analysis ofSorghum BicolorGreen Prop Roots Under Elevated CO₂and Water Deficit Conditions

T¹,

Lwp²,

Guedes³

et al. 2021

Preprint

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Elevated CO2 (E[CO2]) improves the biomass and yield when combined with water-stress in C4 plants. Although several studies described the molecular response of the C4 plant Sorghum bicolor during drought exposure, none reported its combinatorial effect with E[CO2] in the roots. We decided to perform a molecular analysis using green prop roots, the portion of the radicular system photosynthetically active and more sensible to drought. Whole-transcriptome analysis identified 394 up- and 1,471 down-regulated genes. Among the E[CO2] induced pathways, photosynthesis stood out. Carbon fixation, phenylpropanoid, phenolic compounds, and fatty acid biosynthesis-related pathways were repressed. Protein family analysis showed induction of chlorophyll a-b binding protein family, and repression of glutathione-related enzymes. Protein-protein interaction networks exhibited well-defined clusters, including genes related to cell organization and biogenesis, oxi-reduction process, and photosynthesis being induced. The findings suggest that the E[CO2] mitigates the water deficit by antioxidant and osmoregulation activity, as well as by accumulation of sugar-alcohols in the green prop roots, which may be responsible by the increase in biomass together with the cell proliferation. The higher carbon uptake explains the increase in photosynthetic and primary metabolism activities. Our data revealed that green prop roots present an intriguing metabolism under water deficit and E[CO2], showing its crucial role in the drought tolerance acquisition in a predicted future global atmosphere.

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Section: Discussionmentioning

confidence: 99%

Integrative Analysis ofSorghum BicolorGreen Prop Roots Under Elevated CO₂and Water Deficit Conditions

T¹,

Lwp²,

Guedes³

et al. 2021

Preprint

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“…In legumes, for example, hybrid comprehensive assemblies were generated in the case of pigeonpea (Kudapa et al., 2012) and chickpea (Kudapa et al., 2014) by analyzing sequencing data from three different platforms (Sanger, FLX/454, and Illumina). In a different study, transcriptome analysis under elevated CO 2 concentrations identified stress responsive candidate genes and pathways mainly involved in sugar and starch metabolism, chlorophyll, and secondary metabolites biosynthesis (Palit et al., 2020a). Gene expression profiling data from developed transcriptome assemblies enabled identification of candidate genes associated with different traits of interest and stress response.…”

Section: Rapidly Evolving Omics Approachesmentioning

confidence: 99%

Systems biology for crop improvement

et al. 2021

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In recent years, generation of large-scale data from genome, transcriptome, proteome, metabolome, epigenome, and others, has become routine in several plant species.Most of these datasets in different crop species, however, were studied independently and as a result, full insight could not be gained on the molecular basis of complex traits and biological networks. A systems biology approach involving integration of multiple omics data, modeling, and prediction of the cellular functions is required to understand the flow of biological information that underlies complex traits. In this context, systems biology with multiomics data integration is crucial and allows a holistic understanding of the dynamic system with the different levels of biological organization interacting with external environment for a phenotypic expression. Here, we present recent progress made in the area of various omics studies-integrative and systems biology approaches with a special focus on application to crop improvement. We have also discussed the challenges and opportunities in multiomics data integration, modeling, and understanding of the biology of complex traits underpinning yield and stress tolerance in major cereals and legumes.

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“…Measuring transcriptome dynamics is a comprehensive method for assessing environmental responses and their alteration due to genetic, developmental and physiological factors ( Han et al. 2020 , Palit et al. 2020 , Ye et al.…”

Section: Introductionmentioning

confidence: 99%

Genomic Basis of Transcriptome Dynamics in Rice under Field Conditions

Kashima

Sakamoto

Saito

et al. 2021

Plant and Cell Physiology

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How genetic variations affect gene expression dynamics of field-grown plants remains unclear. Expression quantitative trait loci (eQTL) analysis is frequently used to find genomic regions underlying gene expression polymorphisms. This approach requires transcriptome data for the complete set of the QTL mapping population under the given conditions. Therefore, only a limited range of environmental conditions is covered by a conventional eQTL analysis. We sampled sparse time-series of field-grown rice from chromosome segment substitution lines (CSSLs) and conducted RNA-sequencing (RNA-Seq). Then, by using statistical analysis integrating meteorological data and the RNA-Seq data, we identified 1675 expression quantitative trait loci (eQTLs) leading to polymorphisms in expression dynamics under field conditions. A genomic region on chromosome 11 influences the expression of several defense-related genes in a time-of-day- and scaled-age-dependent manner. This includes the eQTLs that possibly influence the time-of-day- and scaled-age-dependent differences in the innate immunity between Koshihikari and Takanari. Based on the eQTL and meteorological data, we successfully predicted gene expression under environments different from training environments, and in rice cultivars with more complex genotypes than the CSSLs. Our novel approach of eQTL identification facilitated the understanding of the genetic architecture of expression dynamics under field conditions, which is difficult to assess by conventional eQTL studies. The prediction of expression based on eQTLs and environmental information would contribute to the understanding of plant traits under diverse field conditions. (224/250 words)

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Molecular and Physiological Alterations in Chickpea under Elevated CO2 Concentrations

Cited by 18 publications

References 61 publications

Integrative Analysis ofSorghum BicolorGreen Prop Roots Under Elevated CO₂and Water Deficit Conditions

Integrative Analysis ofSorghum BicolorGreen Prop Roots Under Elevated CO₂and Water Deficit Conditions

Systems biology for crop improvement

Genomic Basis of Transcriptome Dynamics in Rice under Field Conditions

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Molecular and Physiological Alterations in Chickpea under Elevated CO2 Concentrations

Cited by 18 publications

References 61 publications

Integrative Analysis ofSorghum BicolorGreen Prop Roots Under Elevated CO2and Water Deficit Conditions

Integrative Analysis ofSorghum BicolorGreen Prop Roots Under Elevated CO2and Water Deficit Conditions

Systems biology for crop improvement

Genomic Basis of Transcriptome Dynamics in Rice under Field Conditions

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Product

Resources

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Integrative Analysis ofSorghum BicolorGreen Prop Roots Under Elevated CO₂and Water Deficit Conditions

Integrative Analysis ofSorghum BicolorGreen Prop Roots Under Elevated CO₂and Water Deficit Conditions