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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.


Venn Diagram of differentially expressed genes (DEGs) in leaves of the two pairs of rice NILs and IR64. Number of (a) up- and (b) down-regulated genes under severe (0.2 FTSW) WD treatment; number of (c) up- and (d) down- regulated genes under mild (0.5 FTSW) WD treatment
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Fig1: Venn Diagram of differentially expressed genes (DEGs) in leaves of the two pairs of rice NILs and IR64. Number of (a) up- and (b) down-regulated genes under severe (0.2 FTSW) WD treatment; number of (c) up- and (d) down- regulated genes under mild (0.5 FTSW) WD treatment

Mentions: To obtain insight into changes in rice leaf gene-expression profiles under WD treatments and therefore to provide a global overview of the mechanism underlying drought tolerance in the leaf, we examined the effects of two WD treatments, 0.5 and 0.2 FTSW, on the gene-expression profiles of two pairs of rice NILs and the parent IR64 at the reproductive stage, using Agilent rice oligoarrays (4×44K). Fig. 1 shows the number of genes that were differentially expressed, up- and down-regulated, in the leaves of the rice NILs and IR64 under different WD treatments. Overall, a total of 19,033 (43.8 %) transcripts out of 43,494 were differentially expressed in one or both WD treatments, with 16,566 (38.1 %) and 9019 (20.7 %) transcripts up- and down-regulated at 0.2 and 0.5 FTSW between the rice NILs, respectively (adjusted P < 0.05). Genes encoding hypothetical proteins were classified as genes of unknown function. Among the 19,033 genes that were differentially expressed, 17.9 % of the genes belonged to the unknown function. A dissection of the gene-expression profiles of the leaves of the rice NILs indicated that the number of DEGs at 0.2 FTSW was higher than that at 0.5 FTSW (2–3 times). The high DTN, IR77298-14-1-2-B-10, displayed a greater number of up- and down-regulated genes (17,633) than other NILs and IR64 during both WD treatments. The number of differentially expressed common genes under severe WD (0.2 FTSW) was also significantly higher in IR77298-14-1-2-B-10 than that under mild WD.Fig. 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)

Venn Diagram of differentially expressed genes (DEGs) in leaves of the two pairs of rice NILs and IR64. Number of (a) up- and (b) down-regulated genes under severe (0.2 FTSW) WD treatment; number of (c) up- and (d) down- regulated genes under mild (0.5 FTSW) WD treatment
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Venn Diagram of differentially expressed genes (DEGs) in leaves of the two pairs of rice NILs and IR64. Number of (a) up- and (b) down-regulated genes under severe (0.2 FTSW) WD treatment; number of (c) up- and (d) down- regulated genes under mild (0.5 FTSW) WD treatment
Mentions: To obtain insight into changes in rice leaf gene-expression profiles under WD treatments and therefore to provide a global overview of the mechanism underlying drought tolerance in the leaf, we examined the effects of two WD treatments, 0.5 and 0.2 FTSW, on the gene-expression profiles of two pairs of rice NILs and the parent IR64 at the reproductive stage, using Agilent rice oligoarrays (4×44K). Fig. 1 shows the number of genes that were differentially expressed, up- and down-regulated, in the leaves of the rice NILs and IR64 under different WD treatments. Overall, a total of 19,033 (43.8 %) transcripts out of 43,494 were differentially expressed in one or both WD treatments, with 16,566 (38.1 %) and 9019 (20.7 %) transcripts up- and down-regulated at 0.2 and 0.5 FTSW between the rice NILs, respectively (adjusted P < 0.05). Genes encoding hypothetical proteins were classified as genes of unknown function. Among the 19,033 genes that were differentially expressed, 17.9 % of the genes belonged to the unknown function. A dissection of the gene-expression profiles of the leaves of the rice NILs indicated that the number of DEGs at 0.2 FTSW was higher than that at 0.5 FTSW (2–3 times). The high DTN, IR77298-14-1-2-B-10, displayed a greater number of up- and down-regulated genes (17,633) than other NILs and IR64 during both WD treatments. The number of differentially expressed common genes under severe WD (0.2 FTSW) was also significantly higher in IR77298-14-1-2-B-10 than that under mild WD.Fig. 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.