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

View Article: PubMed Central - PubMed

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

Levels of expression of DEGs identified in roots (GF677 rootstock) and leaves (graft, var. Catherina). (A) DEGs involved in signaling and regulatory processes. (B) DEGs involved in functional processes. Details are provided in Supplementary Table S3. The scale bar on the left represents the observed changes in expression in terms of Log2FC from upregulation (red squares) to downregulation (blue squares). The dark blue pattern with stars indicates genes uniquely expressed in leaves in the control group. The fold change was calculated as the ratio between the drought-stressed and control plants. ERT, ethylene-responsive transcription factor; GRF5, growth-regulating factor 5; ABA, abscisic acid; ETH, ethylene; AUX, auxin; GA, gibberellin; BR, brassinosteroid; APX, ascorbate peroxidase; nLTPs, non-specific-lipid transfer proteins; LTPs, lipid transfer proteins; ABC, ATP-binding cassette.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5120087&req=5

Figure 5: Levels of expression of DEGs identified in roots (GF677 rootstock) and leaves (graft, var. Catherina). (A) DEGs involved in signaling and regulatory processes. (B) DEGs involved in functional processes. Details are provided in Supplementary Table S3. The scale bar on the left represents the observed changes in expression in terms of Log2FC from upregulation (red squares) to downregulation (blue squares). The dark blue pattern with stars indicates genes uniquely expressed in leaves in the control group. The fold change was calculated as the ratio between the drought-stressed and control plants. ERT, ethylene-responsive transcription factor; GRF5, growth-regulating factor 5; ABA, abscisic acid; ETH, ethylene; AUX, auxin; GA, gibberellin; BR, brassinosteroid; APX, ascorbate peroxidase; nLTPs, non-specific-lipid transfer proteins; LTPs, lipid transfer proteins; ABC, ATP-binding cassette.

Mentions: Regulatory genes play an important role in eliciting responses to abiotic stress. In this study, we detected 103 DEGs involved in signaling and regulation, of which only 15 were leaf DEGs (Figure 5A; Supplementary Table S3A). These DEGs included protein kinases and receptors (32), calcium sensors (7), phospholipases (2), phosphatases (4), TFs (30), and hormone-related genes (28). The identification of such a large number of genes indicates that plants use a large array of signaling mediators and complex pathways to combat drought stress.


Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing
Levels of expression of DEGs identified in roots (GF677 rootstock) and leaves (graft, var. Catherina). (A) DEGs involved in signaling and regulatory processes. (B) DEGs involved in functional processes. Details are provided in Supplementary Table S3. The scale bar on the left represents the observed changes in expression in terms of Log2FC from upregulation (red squares) to downregulation (blue squares). The dark blue pattern with stars indicates genes uniquely expressed in leaves in the control group. The fold change was calculated as the ratio between the drought-stressed and control plants. ERT, ethylene-responsive transcription factor; GRF5, growth-regulating factor 5; ABA, abscisic acid; ETH, ethylene; AUX, auxin; GA, gibberellin; BR, brassinosteroid; APX, ascorbate peroxidase; nLTPs, non-specific-lipid transfer proteins; LTPs, lipid transfer proteins; ABC, ATP-binding cassette.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5120087&req=5

Figure 5: Levels of expression of DEGs identified in roots (GF677 rootstock) and leaves (graft, var. Catherina). (A) DEGs involved in signaling and regulatory processes. (B) DEGs involved in functional processes. Details are provided in Supplementary Table S3. The scale bar on the left represents the observed changes in expression in terms of Log2FC from upregulation (red squares) to downregulation (blue squares). The dark blue pattern with stars indicates genes uniquely expressed in leaves in the control group. The fold change was calculated as the ratio between the drought-stressed and control plants. ERT, ethylene-responsive transcription factor; GRF5, growth-regulating factor 5; ABA, abscisic acid; ETH, ethylene; AUX, auxin; GA, gibberellin; BR, brassinosteroid; APX, ascorbate peroxidase; nLTPs, non-specific-lipid transfer proteins; LTPs, lipid transfer proteins; ABC, ATP-binding cassette.
Mentions: Regulatory genes play an important role in eliciting responses to abiotic stress. In this study, we detected 103 DEGs involved in signaling and regulation, of which only 15 were leaf DEGs (Figure 5A; Supplementary Table S3A). These DEGs included protein kinases and receptors (32), calcium sensors (7), phospholipases (2), phosphatases (4), TFs (30), and hormone-related genes (28). The identification of such a large number of genes indicates that plants use a large array of signaling mediators and complex pathways to combat drought stress.

View Article: PubMed Central - PubMed

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus