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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.


(A) Number of total and differentially expressed genes (DEGs) showing either upregulation or downregulation at different Q-values in roots (GF677 rootstock) and leaves (graft, var. Catherina). Up: upregulated genes (red); down: downregulated genes (blue). (B,C) Relative expression of DEGs selected at Q-value < 0.01 in roots and leaves. The color intensity indicates the level of the change in expression: a darker color represents a larger change in expression. The x-axis indicates the range of Log2FC. The fold change (FC) was calculated as the ratio between the drought-stressed and control plants, while the y-axis indicates the number of detected DEGs.
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Figure 2: (A) Number of total and differentially expressed genes (DEGs) showing either upregulation or downregulation at different Q-values in roots (GF677 rootstock) and leaves (graft, var. Catherina). Up: upregulated genes (red); down: downregulated genes (blue). (B,C) Relative expression of DEGs selected at Q-value < 0.01 in roots and leaves. The color intensity indicates the level of the change in expression: a darker color represents a larger change in expression. The x-axis indicates the range of Log2FC. The fold change (FC) was calculated as the ratio between the drought-stressed and control plants, while the y-axis indicates the number of detected DEGs.

Mentions: In order to explore the transcriptional response to drought stress, genes in both roots and leaves were tested for differential expression between the control and drought conditions. Expression levels for each gene were calculated and normalized to RPKM values. Initially, the multiple testing correction involved a Q-value < 0.05 and a total of 1,171 genes were found to exhibit differential expression (813 in the roots and 358 in the leaves). Subsequently, a more stringent Q-value was applied (< 0.01) in order to identify the most reliable DEGs. In this analysis, 500 DEGs were identified in the roots and 236 in the leaves. The distribution of these genes is provided in Figure 2. As illustrated, in drought stress conditions, the number of downregulated genes was slightly higher than the number of upregulated genes. Furthermore, the analysis revealed that there were approximately twice the number of DEGs in the roots than in the leaves, confirming the expectations that (i) the root is the first organ that senses and is affected by drought stress and (ii) roots respond faster to stress than leaves, undergoing more complex gene regulation during water deprivation. These results further highlight the key role of rootstocks as stress buffers.


Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing
(A) Number of total and differentially expressed genes (DEGs) showing either upregulation or downregulation at different Q-values in roots (GF677 rootstock) and leaves (graft, var. Catherina). Up: upregulated genes (red); down: downregulated genes (blue). (B,C) Relative expression of DEGs selected at Q-value < 0.01 in roots and leaves. The color intensity indicates the level of the change in expression: a darker color represents a larger change in expression. The x-axis indicates the range of Log2FC. The fold change (FC) was calculated as the ratio between the drought-stressed and control plants, while the y-axis indicates the number of detected DEGs.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: (A) Number of total and differentially expressed genes (DEGs) showing either upregulation or downregulation at different Q-values in roots (GF677 rootstock) and leaves (graft, var. Catherina). Up: upregulated genes (red); down: downregulated genes (blue). (B,C) Relative expression of DEGs selected at Q-value < 0.01 in roots and leaves. The color intensity indicates the level of the change in expression: a darker color represents a larger change in expression. The x-axis indicates the range of Log2FC. The fold change (FC) was calculated as the ratio between the drought-stressed and control plants, while the y-axis indicates the number of detected DEGs.
Mentions: In order to explore the transcriptional response to drought stress, genes in both roots and leaves were tested for differential expression between the control and drought conditions. Expression levels for each gene were calculated and normalized to RPKM values. Initially, the multiple testing correction involved a Q-value < 0.05 and a total of 1,171 genes were found to exhibit differential expression (813 in the roots and 358 in the leaves). Subsequently, a more stringent Q-value was applied (< 0.01) in order to identify the most reliable DEGs. In this analysis, 500 DEGs were identified in the roots and 236 in the leaves. The distribution of these genes is provided in Figure 2. As illustrated, in drought stress conditions, the number of downregulated genes was slightly higher than the number of upregulated genes. Furthermore, the analysis revealed that there were approximately twice the number of DEGs in the roots than in the leaves, confirming the expectations that (i) the root is the first organ that senses and is affected by drought stress and (ii) roots respond faster to stress than leaves, undergoing more complex gene regulation during water deprivation. These results further highlight the key role of rootstocks as stress buffers.

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 &ldquo;locomotion,&rdquo; &ldquo;hormone metabolic process,&rdquo; and &ldquo;detection of stimulus,&rdquo; 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.