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. 2016 Jan 18;6:19349.
doi: 10.1038/srep19349.

Comparative Transcriptome Analysis Highlights the Crucial Roles of Photosynthetic System in Drought Stress Adaptation in Upland Rice

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Comparative Transcriptome Analysis Highlights the Crucial Roles of Photosynthetic System in Drought Stress Adaptation in Upland Rice

Zheng-Feng Zhang et al. Sci Rep. .
Free PMC article

Abstract

Drought stress is one of the major adverse environmental factors reducing plant growth. With the aim to elucidate the underlying molecular basis of rice response to drought stress, comparative transcriptome analysis was conducted between drought susceptible rice cultivar Zhenshan97 and tolerant cultivar IRAT109 at the seedling stage. 436 genes showed differential expression and mainly enriched in the Gene Ontology (GO) terms of stress defence. A large number of variations exist between these two genotypes including 2564 high-quality insertion and deletions (INDELs) and 70,264 single nucleotide polymorphism (SNPs). 1041 orthologous gene pairs show the ratio of nonsynonymous nucleotide substitution rate to synonymous nucleotide substitutions rate (Ka/Ks) larger than 1.5, indicating the rapid adaptation to different environments during domestication. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of positive selection genes suggested that photosynthesis represents the most significant category. The collocation of positively selected genes with the QTLs of photosynthesis and the different photosynthesis performance of these two cultivars further illuminate the crucial function of photosynthesis in rice adaptation to drought stress. Our results also provide fruitful functional markers and candidate genes for future genetic research and improvement of drought tolerance in rice.

Figures

Figure 1
Figure 1. GO enrichment of DEGs between the upland and paddy rice.
(A) Significant GO terms of genes up-regulated or specific expressed in Zhenshan97. (B) Significant GO terms of genes up-regulated or specific expressed in IRAT109. The blue bar indicate the percent of query genes in a specific GO terms to the total query genes and the purple bar indicate that for the background. The left and right of the vertical line indicate the biological process and molecular function GO terms, respectively.
Figure 2
Figure 2. Validation of 10 DEGs by qRT-PCR.
qRT-PCR values were calculated as means from all relevant varieties for Lowland rice under Control (LC) and Drought stress (LD) as well as for Upland rice under Control (UC) and Drought stress (UD). Error bars indicate the standard deviation. The X-axis indicates the rice materials and growth condition. Y axis indicates the relative expression level.
Figure 3
Figure 3. The distribution of sequence variations (SNPs and INDELs) and genes along the chromosomes.
The left Y-axis shows the number of sequence variations and genes. The right Y-axis indicates the Ka/Ks value of genes. The X-axis shows the position on the chromosomes with the scale as 100kb. The red and blue lines indicate the numbers of sequence variations and genes in 100kb slide windows, respectively. The black point in the graph represents the genes with Ka/Ks value bigger than 2. The detailed information about the ids and function annotation of these genes were summarized in supplementary table 3. The black vertical lines shows the positions of centromere.
Figure 4
Figure 4. The representative INDELs shown through PAGE and silver staining.
These 2bp-INDELs A-E represents INDEL1_146103_CT, INDEL3_7749032_GT, INDEL7_6809650_AG, INDEL8_14321370_AA and INDEL9_14716537_AG, respectively. For the nomenclature of these INDELs, number after the word INDEL indicates the chromosome, the number after the first underline indicates the position on the corresponding chromosome, and the two nucleotides after the second underline is the INDEL. P1 and P2 on the top of each gel track represents the Zhenshan97 and IRAT109, and the bands after P1 and P2 represent individuals from the RIL population which was originated from Zhenshan97 and IRAT109.
Figure 5
Figure 5. The synonymous, nonsynonymous mutatation rates and Ka/Ks value of orthologs between the upland and lowland rice accessions in the present study.
The 3D scatter plot at the left shows the Ks at X-axis, Ka at Y-axis and Ka/Ks at the Z-axis. The right box plot displays the range of Ka/Ks values and with the mean of about 1.
Figure 6
Figure 6. Go enrichment analysis for genes with Ka/Ks > 1.5.
(a) The significant biological process, cell compartment and molecular function GO terms are shown from left to right. Photosynthesis represents the most significant GO terms in biological process. (b) The categories of biological processes GO terms are shown as a diagram. The darker the box color, the significant level is higher.
Figure 7
Figure 7. The KEGG photosynthesis pathway including many genes with Ka/Ks > 1.5.
The KEGG photosynthesis pathway map can be found online at http://www.kegg.jp/pathway/map00195. The light green boxes indicate the proteins encoded by the genes with Ka/Ks value bigger than 1.5. The detail annotation of these genes were summarized in Supplemental Table 4.
Figure 8
Figure 8. Changes in the photosynthetic machinery in leaves of lowland and upland rice under control and drought stress conditions.
(A) Rates of photosynthesis in leaves of lowland and upland rice under control and drought stress conditions. (B) Stomatal conductance in leaves of lowland and upland rice under control and drought stress conditions. (C) Intercellular CO2 concentration in leaves of lowland and upland rice under control and drought stress conditions. (D) Transpiration rate in leaves of lowland and upland rice under control and drought stress conditions. LC-Lowland rice under control condition; LS-Lowland rice under stress condition; UC-Upland rice under control condition; US-Upland rice under stress condition (Multiple compare test of mean for the four cases was used as a statistical test and the 0.05 statistical significant threshold was chosen.).

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