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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.

No MeSH data available.


Hierarchical cluster analysis of gene-expression pattern in leaves of five rice genotypes under two water-deficit treatments. The differentially expressed genes under water-deficit treatments with adjusted P < 0.05 and −1 ≤ log2ratio ≤ +1 (fold change ≥ 2). K-means clustering was performed to identify 8 clusters (I to VIII), each containing various numbers of genes with a similar gene-expression profile under two WD treatments. 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 and 0.5 FTSW are severe and mild WD treatment, respectively. Gene identifiers corresponding to each transcript are from MSU version 6.1 of Rice Oligoarray from Rice Genome Annotation Project (RGAP) 6.1 (http://rice.plantbiology.msu.edu/). A fold change > 2.0 is shown in red (up-regulated), a fold change < −2.0 is shown in green (down-regulated), and no change is shown in black (FDR < 0.05)
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Fig2: Hierarchical cluster analysis of gene-expression pattern in leaves of five rice genotypes under two water-deficit treatments. The differentially expressed genes under water-deficit treatments with adjusted P < 0.05 and −1 ≤ log2ratio ≤ +1 (fold change ≥ 2). K-means clustering was performed to identify 8 clusters (I to VIII), each containing various numbers of genes with a similar gene-expression profile under two WD treatments. 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 and 0.5 FTSW are severe and mild WD treatment, respectively. Gene identifiers corresponding to each transcript are from MSU version 6.1 of Rice Oligoarray from Rice Genome Annotation Project (RGAP) 6.1 (http://rice.plantbiology.msu.edu/). A fold change > 2.0 is shown in red (up-regulated), a fold change < −2.0 is shown in green (down-regulated), and no change is shown in black (FDR < 0.05)

Mentions: Gene ontology (GO) enrichment analysis was conducted to identify the main functional classifications of drought-responsive genes (genes that differentially express commonly in all rice genotypes) through the parametric analysis of gene set enrichment (PAGE) method and genes involved in the drought-tolerance mechanism using the singular enrichment analysis (SEA) method [30]. A relatively large number of drought-responsive genes, including 6003 (36.2 %), 1058 (11.7 %) and 854 (5 %), were differentially expressed common genes in the rice NILs at 0.2 FTSW, 0.5 FTSW and both WDs, respectively (Table 1). We also conducted K-means clustering on the DEGs to analyze the co-expression setting, and eight clusters with coordinated gene-expression profiles were identified (Fig. 2). These clusters reflected the general distribution of gene-expression profiles in leaves in response to WD treatments in different rice genotypes in this study. The complete list of genes in each cluster, including log2ratio, can be found in Additional files 2a-h. Cluster I contains 5644 genes with fewer changes in different lines at two WDs with drastically down-regulated genes in IR77298-14-1-2-B-13, whereas clusters II and III contained 3346 and 2877 genes that were highly up- and down-regulated in different lines at severe WDTs, respectively. Clusters IV, V, VI, VII and VIII contained a distribution of 1966, 1658, 1503, 1064 and 975 genes, respectively, with various up-egulated genes in IR77298-14-1-2-B-10 and IR77298-5-6-B-11 and down-regulated genes in IR64, IR77298-14-1-2-B-13 and IR77298-5-6-B-18. These sets of DEGs were subjected to further analysis to investigate the biological functions of the two major groups of DEGs, i.e., differentially expressed common- and specific genes in response to water-deficit treatments. The biological functions of the over-represented drought-responsive genes were obtained by performing a GO analysis (FDR; adjusted P < 0.05) of the differentially expressed common genes in the different NILs under the two WDs.Table 1


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 gene-expression pattern in leaves of five rice genotypes under two water-deficit treatments. The differentially expressed genes under water-deficit treatments with adjusted P < 0.05 and −1 ≤ log2ratio ≤ +1 (fold change ≥ 2). K-means clustering was performed to identify 8 clusters (I to VIII), each containing various numbers of genes with a similar gene-expression profile under two WD treatments. 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 and 0.5 FTSW are severe and mild WD treatment, respectively. Gene identifiers corresponding to each transcript are from MSU version 6.1 of Rice Oligoarray from Rice Genome Annotation Project (RGAP) 6.1 (http://rice.plantbiology.msu.edu/). A fold change > 2.0 is shown in red (up-regulated), a fold change < −2.0 is shown in green (down-regulated), and no change is shown in black (FDR < 0.05)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Hierarchical cluster analysis of gene-expression pattern in leaves of five rice genotypes under two water-deficit treatments. The differentially expressed genes under water-deficit treatments with adjusted P < 0.05 and −1 ≤ log2ratio ≤ +1 (fold change ≥ 2). K-means clustering was performed to identify 8 clusters (I to VIII), each containing various numbers of genes with a similar gene-expression profile under two WD treatments. 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 and 0.5 FTSW are severe and mild WD treatment, respectively. Gene identifiers corresponding to each transcript are from MSU version 6.1 of Rice Oligoarray from Rice Genome Annotation Project (RGAP) 6.1 (http://rice.plantbiology.msu.edu/). A fold change > 2.0 is shown in red (up-regulated), a fold change < −2.0 is shown in green (down-regulated), and no change is shown in black (FDR < 0.05)
Mentions: Gene ontology (GO) enrichment analysis was conducted to identify the main functional classifications of drought-responsive genes (genes that differentially express commonly in all rice genotypes) through the parametric analysis of gene set enrichment (PAGE) method and genes involved in the drought-tolerance mechanism using the singular enrichment analysis (SEA) method [30]. A relatively large number of drought-responsive genes, including 6003 (36.2 %), 1058 (11.7 %) and 854 (5 %), were differentially expressed common genes in the rice NILs at 0.2 FTSW, 0.5 FTSW and both WDs, respectively (Table 1). We also conducted K-means clustering on the DEGs to analyze the co-expression setting, and eight clusters with coordinated gene-expression profiles were identified (Fig. 2). These clusters reflected the general distribution of gene-expression profiles in leaves in response to WD treatments in different rice genotypes in this study. The complete list of genes in each cluster, including log2ratio, can be found in Additional files 2a-h. Cluster I contains 5644 genes with fewer changes in different lines at two WDs with drastically down-regulated genes in IR77298-14-1-2-B-13, whereas clusters II and III contained 3346 and 2877 genes that were highly up- and down-regulated in different lines at severe WDTs, respectively. Clusters IV, V, VI, VII and VIII contained a distribution of 1966, 1658, 1503, 1064 and 975 genes, respectively, with various up-egulated genes in IR77298-14-1-2-B-10 and IR77298-5-6-B-11 and down-regulated genes in IR64, IR77298-14-1-2-B-13 and IR77298-5-6-B-18. These sets of DEGs were subjected to further analysis to investigate the biological functions of the two major groups of DEGs, i.e., differentially expressed common- and specific genes in response to water-deficit treatments. The biological functions of the over-represented drought-responsive genes were obtained by performing a GO analysis (FDR; adjusted P < 0.05) of the differentially expressed common genes in the different NILs under the two WDs.Table 1

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.