Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea

Garg, Rohini; Shankar, Rama; Thakkar, Bijal; Kudapa, Himabindu; Krishnamurthy, L.; Mantri, Nitin; Varshney, Rajeev K.; Bhatia, Sabhyata; Jain, Mukesh

doi:10.1038/srep19228

Cited by 175 publications

(162 citation statements)

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“…Surprisingly, after quality control, the total number of clean reads generated from the RNA libraries of the drought-stressed plants was lower than the number for the control plants ( Table 2 ). This is in contrast with previous studies, which have reported an activated plant transcriptome in response to drought (Tang et al, 2013; Garg et al, 2016). We thus hypothesize that a drought period of 16 days may be too short to drive the full upregulation of the P. persica genome, especially as the rootstock used was selected for its tolerance to drought (Jiménez et al, 2013).…”

Section: Discussioncontrasting

confidence: 99%

“…Moreover, non-enzymatic scavenging genes were upregulated, highlighting the need to protect against oxidative stress. Although, studies have reported high levels of GST activity during drought (Liu et al, 2015; Garg et al, 2016), six of the genes associated with GST were exclusively expressed in the leaves of the control plants and they were not detected in the drought-stressed plants. These may be due to the effect of the drought-tolerant GF677 rootstock masking the effects of the drought.…”

Section: Discussionmentioning

confidence: 93%

“…These tissues were chosen as the roots are the first plant tissue to perceive drought stress, while leaves are central to the control of water loss (Garg et al, 2016). Our data contribute to the understanding of drought responses in plants and serve as a publicly available resource for future gene expression, genomic, and functional studies of Prunus spp.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

et al. 2016

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Prunus persica L. Batsch, or peach, is one of the most important crops and it is widely established in irrigated arid and semi-arid regions. However, due to variations in the climate and the increased aridity, drought has become a major constraint, causing crop losses worldwide. The use of drought-tolerant rootstocks in modern fruit production appears to be a useful method of alleviating water deficit problems. However, the transcriptomic variation and the major molecular mechanisms that underlie the adaptation of drought-tolerant rootstocks to water shortage remain unclear. Hence, in this study, high-throughput sequencing (RNA-seq) was performed to assess the transcriptomic changes and the key genes involved in the response to drought in root tissues (GF677 rootstock) and leaf tissues (graft, var. Catherina) subjected to 16 days of drought stress. In total, 12 RNA libraries were constructed and sequenced. This generated a total of 315 M raw reads from both tissues, which allowed the assembly of 22,079 and 17,854 genes associated with the root and leaf tissues, respectively. Subsets of 500 differentially expressed genes (DEGs) in roots and 236 in leaves were identified and functionally annotated with 56 gene ontology (GO) terms and 99 metabolic pathways, which were mostly associated with aminobenzoate degradation and phenylpropanoid biosynthesis. The GO analysis highlighted the biological functions that were exclusive to the root tissue, such as “locomotion,” “hormone metabolic process,” and “detection of stimulus,” indicating the stress-buffering role of the GF677 rootstock. Furthermore, the complex regulatory network involved in the drought response was revealed, involving proteins that are associated with signaling transduction, transcription and hormone regulation, redox homeostasis, and frontline barriers. We identified two poorly characterized genes in P. persica: growth-regulating factor 5 (GRF5), which may be involved in cellular expansion, and AtHB12, which may be involved in root elongation. The reliability of the RNA-seq experiment was validated by analyzing the expression patterns of 34 DEGs potentially involved in drought tolerance using quantitative reverse transcription polymerase chain reaction. The transcriptomic resources generated in this study provide a broad characterization of the acclimation of P. persica to drought, shedding light on the major molecular responses to the most important environmental stressor.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

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Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

et al. 2016

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“…By contrast, although drought during early reproductive stages (before booting) also impacted wheat development and yield potential (Oosterhuis and Cartwright, 1983; Qu, 1989; Ji et al, 2010), there have been no reported transcript study on the genes responsive to drought during these periods. Since many drought-related genes are genotype and growth stage specific (Garg et al, 2016), investigating wheat transcriptome changes under drought stress during early reproductive stages will help us to understand how drought affects gene expression during wheat development.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomics Analyses Reveal Wheat Responses to Drought Stress during Reproductive Stages under Field Conditions

Wang

et al. 2017

Front. Plant Sci.

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Drought is a major abiotic stress that limits wheat production worldwide. To ensure food security for the rapidly increasing world population, improving wheat yield under drought stress is urgent and relevant. In this study, an RNA-seq analysis was conducted to study the effect of drought on wheat transcriptome changes during reproductive stages under field conditions. Our results indicated that drought stress during early reproductive periods had a more severe impact on wheat development, gene expression and yield than drought stress during flowering. In total, 115,656 wheat genes were detected, including 309 differentially expressed genes (DEGs) which responded to drought at various developmental stages. These DEGs were involved in many critical processes including floral development, photosynthetic activity and stomatal movement. At early developmental stages, the proteins of drought-responsive DEGs were mainly located in the nucleus, peroxisome, mitochondria, plasma membrane and chloroplast, indicating that these organelles play critical roles in drought tolerance in wheat. Furthermore, the validation of five DEGs confirmed their responsiveness to drought under different genetic backgrounds. Functional verification of DEGs of interest will occur in our subsequent research. Collectively, the results of this study not only advanced our understanding of wheat transcriptome changes under drought stress during early reproductive stages but also provided useful targets to manipulate drought tolerance in wheat at different development stages.

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“…Seed drying management not only improves the quality and quantity of oil in camellia species but also other oilseed plants (Tibaldi et al 2010;Dušková et al 2016;Evaristo et al 2016;Tibaldi et al 2013). Several transcriptome analyses showed that drying management affects transcript abundances and the genetic regulatory networks in seeds, resulting in the selective change of specific transcripts (Rohini et al 2016;Fu et al 2016;Pan et al 2016). However, very little is known about the relationship with expression of genes involved in the fatty acid pathway and oil accumulation during drying management.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome comparative analysis of two Camellia species reveals lipid metabolism during mature seed natural drying

Feng

Yang

Weiwei

et al. 2017

Trees

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Key message The molecular mechanisms of fatty acid biosynthesis and accumulation during Camellia meiocarpa and Camellia oleifera seed natural drying are characterized through transcriptome analyses. Abstract Camellia seed oil has been used as high quality and healthy food for over two thousand years. Seed drying affects oil quality and quantity; however, the molecular mechanisms of fatty acid biosynthesis and accumulation during the drying process remain unknown. In this study, the transcriptomes of Camellia meiocarpa and C. oleifera seed were characterized at five moisture content levels (10-50%) to identify the major processes and reveal genes affecting lipid metabolism in response to natural drying. We found a total of 111,156 unigenes by de novo assembled from RNA-Seq libraries of five moisture content levels during after-ripening of C. meiocarpa (74,016) and C. oleifera (76,374). Ten pathways were closely linked to changes in oil content and composition with 244 genes involved in fatty acid synthesis and accumulation. Gene ontology enrichment of differentially expressed genes (DEGs) indicated that fatty acid synthesis and accumulation are essential in C. meiocarpa while fatty acid accumulation in C. oleifera during natural drying process. Comparative analyses of DEGs between any two consecutive moisture contents identified six and three key unigenes in C. meiocarpa and C. oleifera seeds, respectively, and one additional unigene responsible for the difference between the two species' fatty acid synthesis and accumulation. Natural drying has improved the quality and quantity of the camellia seed oil. The study provided: (a) global transcriptional profiles at five moisture content levels during seed natural drying, (b) highlighting transcripts putatively involved in the regulation of gene expression program and in specific processes likely essential for lipid metabolism, and (c) discovery of genes associated with oil seed quantity and quality improvement for the studied two camellia species.Communicated by M. Buckeridge. Electronic supplementary materialThe online version of this article

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Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea

Cited by 175 publications

References 69 publications

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

Transcriptomics Analyses Reveal Wheat Responses to Drought Stress during Reproductive Stages under Field Conditions

Transcriptome comparative analysis of two Camellia species reveals lipid metabolism during mature seed natural drying

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