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Transcriptional profiling of the leaves of near-isogenic rice lines with contrasting drought tolerance at the reproductive stage in response to water deficit.

Moumeni A, Satoh K, Venuprasad R, Serraj R, Kumar A, Leung H, Kikuchi S - BMC Genomics (2015)

Bottom Line: In IR77298-14-1-2-B-10, the induced genes were characterized by the presence of regulatory motifs in their promoters, including TGGTTAGTACC and ([CT]AAC[GT]G){2}, which are specific to the TFIIIA and Myb transcription factors, respectively.In IR77298-5-6-B-18, promoters containing a GCAC[AG][ACGT][AT]TCCC[AG]A[ACGT]G[CT] motif, common to MADS(AP1), HD-ZIP, AP2 and YABBY, were induced, suggesting that these factors may play key roles in the regulation of drought tolerance in these two DTNs under severe WD.The present study serves as a resource for marker discovery and provides detailed insight into the gene-expression profiles of rice leaves, including the main functional categories of drought-responsive genes and the genes that are involved in drought-tolerance mechanisms, to help breeders identify candidate genes (both up- and down-regulated) associated with drought tolerance and suitable targets for manipulating the drought-tolerance trait in rice.

View Article: PubMed Central - PubMed

Affiliation: Rice Research Institute of Iran, Mazandaran Branch, Agricultural Research, Education and Extension Organization (AREEO), PO Box 145, Postal Code 46191-91951, Km8 Babol Rd., Amol, Mazandaran, Iran. amoumeni@areo.ir.

ABSTRACT

Background: Drought tolerance is a complex quantitative trait that involves the coordination of a vast array of genes belonging to different pathways. To identify genes related to the drought-tolerance pathway in rice, we carried out gene-expression profiling of the leaves of near-isogenic lines (NILs) with similar genetic backgrounds and different set of QTLs but contrasting drought tolerance levels in response to long-term drought-stress treatments. This work will help differentiate mechanisms of tolerance in contrasting NILs and accelerate molecular breeding programs to improve drought tolerance in this crop.

Results: The two pairs of rice NILs, developed at the International Rice Research Institute, along with the drought-susceptible parent, IR64, showed distinct gene-expression profiles in leaves under different water-deficit (WD) treatments. Drought tolerance in the highly drought-tolerant NIL (DTN), IR77298-14-1-2-B-10, could be attributed to the up-regulation of genes with calcium ion binding, transferase, hydrolase and transcription factor activities, whereas in the moderate DTN, IR77298-5-6-B-18, genes with transporter, catalytic and structural molecule activities were up-regulated under WD. In IR77298-14-1-2-B-10, the induced genes were characterized by the presence of regulatory motifs in their promoters, including TGGTTAGTACC and ([CT]AAC[GT]G){2}, which are specific to the TFIIIA and Myb transcription factors, respectively. In IR77298-5-6-B-18, promoters containing a GCAC[AG][ACGT][AT]TCCC[AG]A[ACGT]G[CT] motif, common to MADS(AP1), HD-ZIP, AP2 and YABBY, were induced, suggesting that these factors may play key roles in the regulation of drought tolerance in these two DTNs under severe WD.

Conclusions: We report here that the two pairs of NILs with different levels of drought tolerance may elucidate potential mechanisms and pathways through transcriptome data from leaf tissue. The present study serves as a resource for marker discovery and provides detailed insight into the gene-expression profiles of rice leaves, including the main functional categories of drought-responsive genes and the genes that are involved in drought-tolerance mechanisms, to help breeders identify candidate genes (both up- and down-regulated) associated with drought tolerance and suitable targets for manipulating the drought-tolerance trait in rice.

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Related in: MedlinePlus

Hierarchical cluster analysis of the differentially expressed specific genes in the leaves of the two DTNs compared to their susceptible counterparts under different WD treatments. In this figure, the heat map displays the expression level of the differentially expressed specific genes in rice NILs and the parent IR64. The numbers are 10 = IR77298-14-1-2-B-10, 13 = IR77298-14-1-2-B-13, 11 = IR77298-5-6-B-11 and 18 = IR77298-5-6-B-18, respectively. 0.2 FTSW and 0.5 FTSW are for leaves under severe and mild WD treatments, respectively. In the color panels, each horizontal line represents a single gene, and the color of the line indicates the expression level (in a log scale) of the gene relative to the median in a specific sample: high expression in red, low expression in green
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Fig4: Hierarchical cluster analysis of the differentially expressed specific genes in the leaves of the two DTNs compared to their susceptible counterparts under different WD treatments. In this figure, the heat map displays the expression level of the differentially expressed specific genes in rice NILs and the parent IR64. The numbers are 10 = IR77298-14-1-2-B-10, 13 = IR77298-14-1-2-B-13, 11 = IR77298-5-6-B-11 and 18 = IR77298-5-6-B-18, respectively. 0.2 FTSW and 0.5 FTSW are for leaves under severe and mild WD treatments, respectively. In the color panels, each horizontal line represents a single gene, and the color of the line indicates the expression level (in a log scale) of the gene relative to the median in a specific sample: high expression in red, low expression in green

Mentions: To identify the putative genes responsible for intrinsic drought tolerance in the two rice DTNs, IR77298-14-1-2-B-10 and IR77298-5-6-B-18, we focused on the genes found to be exclusively differentially expressed in the two DTNs compared to their corresponding DSNs and the parent IR64 in response to the WD treatments. We defined a gene as specifically differentially expressed in the DTNs if it was inversely differentially expressed or if there was no change in expression in its DSN counterpart and IR64. We conducted a cluster analysis on non-redundant DEGs that were specifically expressed in the two DTNs (Fig. 4). The results indicated that the two WD treatments applied in this study were classified into two distinctive clusters. The rice genotypes including DTNs, DSNs and IR64 were also located in separate sub-clusters. We then conducted a GO analysis to convert the specific differentially expressed gene identifiers to standard and interoperable identifiers and to find the main functional categories in terms of biological processes, molecular functions, and cellular components. We then compared the enriched categories between the two DTNs. Table 2 provides an overview of the annotated gene IDs, GO terms and significant GO terms for the differentially expressed specific genes in the two DTNs in response to WD treatments.Fig. 4


Transcriptional profiling of the leaves of near-isogenic rice lines with contrasting drought tolerance at the reproductive stage in response to water deficit.

Moumeni A, Satoh K, Venuprasad R, Serraj R, Kumar A, Leung H, Kikuchi S - BMC Genomics (2015)

Hierarchical cluster analysis of the differentially expressed specific genes in the leaves of the two DTNs compared to their susceptible counterparts under different WD treatments. In this figure, the heat map displays the expression level of the differentially expressed specific genes in rice NILs and the parent IR64. The numbers are 10 = IR77298-14-1-2-B-10, 13 = IR77298-14-1-2-B-13, 11 = IR77298-5-6-B-11 and 18 = IR77298-5-6-B-18, respectively. 0.2 FTSW and 0.5 FTSW are for leaves under severe and mild WD treatments, respectively. In the color panels, each horizontal line represents a single gene, and the color of the line indicates the expression level (in a log scale) of the gene relative to the median in a specific sample: high expression in red, low expression in green
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4696290&req=5

Fig4: Hierarchical cluster analysis of the differentially expressed specific genes in the leaves of the two DTNs compared to their susceptible counterparts under different WD treatments. In this figure, the heat map displays the expression level of the differentially expressed specific genes in rice NILs and the parent IR64. The numbers are 10 = IR77298-14-1-2-B-10, 13 = IR77298-14-1-2-B-13, 11 = IR77298-5-6-B-11 and 18 = IR77298-5-6-B-18, respectively. 0.2 FTSW and 0.5 FTSW are for leaves under severe and mild WD treatments, respectively. In the color panels, each horizontal line represents a single gene, and the color of the line indicates the expression level (in a log scale) of the gene relative to the median in a specific sample: high expression in red, low expression in green
Mentions: To identify the putative genes responsible for intrinsic drought tolerance in the two rice DTNs, IR77298-14-1-2-B-10 and IR77298-5-6-B-18, we focused on the genes found to be exclusively differentially expressed in the two DTNs compared to their corresponding DSNs and the parent IR64 in response to the WD treatments. We defined a gene as specifically differentially expressed in the DTNs if it was inversely differentially expressed or if there was no change in expression in its DSN counterpart and IR64. We conducted a cluster analysis on non-redundant DEGs that were specifically expressed in the two DTNs (Fig. 4). The results indicated that the two WD treatments applied in this study were classified into two distinctive clusters. The rice genotypes including DTNs, DSNs and IR64 were also located in separate sub-clusters. We then conducted a GO analysis to convert the specific differentially expressed gene identifiers to standard and interoperable identifiers and to find the main functional categories in terms of biological processes, molecular functions, and cellular components. We then compared the enriched categories between the two DTNs. Table 2 provides an overview of the annotated gene IDs, GO terms and significant GO terms for the differentially expressed specific genes in the two DTNs in response to WD treatments.Fig. 4

Bottom Line: In IR77298-14-1-2-B-10, the induced genes were characterized by the presence of regulatory motifs in their promoters, including TGGTTAGTACC and ([CT]AAC[GT]G){2}, which are specific to the TFIIIA and Myb transcription factors, respectively.In IR77298-5-6-B-18, promoters containing a GCAC[AG][ACGT][AT]TCCC[AG]A[ACGT]G[CT] motif, common to MADS(AP1), HD-ZIP, AP2 and YABBY, were induced, suggesting that these factors may play key roles in the regulation of drought tolerance in these two DTNs under severe WD.The present study serves as a resource for marker discovery and provides detailed insight into the gene-expression profiles of rice leaves, including the main functional categories of drought-responsive genes and the genes that are involved in drought-tolerance mechanisms, to help breeders identify candidate genes (both up- and down-regulated) associated with drought tolerance and suitable targets for manipulating the drought-tolerance trait in rice.

View Article: PubMed Central - PubMed

Affiliation: Rice Research Institute of Iran, Mazandaran Branch, Agricultural Research, Education and Extension Organization (AREEO), PO Box 145, Postal Code 46191-91951, Km8 Babol Rd., Amol, Mazandaran, Iran. amoumeni@areo.ir.

ABSTRACT

Background: Drought tolerance is a complex quantitative trait that involves the coordination of a vast array of genes belonging to different pathways. To identify genes related to the drought-tolerance pathway in rice, we carried out gene-expression profiling of the leaves of near-isogenic lines (NILs) with similar genetic backgrounds and different set of QTLs but contrasting drought tolerance levels in response to long-term drought-stress treatments. This work will help differentiate mechanisms of tolerance in contrasting NILs and accelerate molecular breeding programs to improve drought tolerance in this crop.

Results: The two pairs of rice NILs, developed at the International Rice Research Institute, along with the drought-susceptible parent, IR64, showed distinct gene-expression profiles in leaves under different water-deficit (WD) treatments. Drought tolerance in the highly drought-tolerant NIL (DTN), IR77298-14-1-2-B-10, could be attributed to the up-regulation of genes with calcium ion binding, transferase, hydrolase and transcription factor activities, whereas in the moderate DTN, IR77298-5-6-B-18, genes with transporter, catalytic and structural molecule activities were up-regulated under WD. In IR77298-14-1-2-B-10, the induced genes were characterized by the presence of regulatory motifs in their promoters, including TGGTTAGTACC and ([CT]AAC[GT]G){2}, which are specific to the TFIIIA and Myb transcription factors, respectively. In IR77298-5-6-B-18, promoters containing a GCAC[AG][ACGT][AT]TCCC[AG]A[ACGT]G[CT] motif, common to MADS(AP1), HD-ZIP, AP2 and YABBY, were induced, suggesting that these factors may play key roles in the regulation of drought tolerance in these two DTNs under severe WD.

Conclusions: We report here that the two pairs of NILs with different levels of drought tolerance may elucidate potential mechanisms and pathways through transcriptome data from leaf tissue. The present study serves as a resource for marker discovery and provides detailed insight into the gene-expression profiles of rice leaves, including the main functional categories of drought-responsive genes and the genes that are involved in drought-tolerance mechanisms, to help breeders identify candidate genes (both up- and down-regulated) associated with drought tolerance and suitable targets for manipulating the drought-tolerance trait in rice.

No MeSH data available.


Related in: MedlinePlus