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Comparative Analysis of the Brassica napus Root and Leaf Transcript Profiling in Response to Drought Stress.

Liu C, Zhang X, Zhang K, An H, Hu K, Wen J, Shen J, Ma C, Yi B, Tu J, Fu T - Int J Mol Sci (2015)

Bottom Line: The gene ontology (GO) enrichment test indicated that up-regulated genes in root were mostly involved in "stimulus" "stress" biological process, and activated genes in leaf mainly functioned in "cell" "cell part" components.Furthermore, a comparative network related to plant hormone signal transduction and AREB/ABF, AP2/EREBP, NAC, WRKY and MYC/MYB transcription factors (TFs) provided a view of different stress tolerance mechanisms between root and leaf.Some of the DEGs identified may be candidates for future research aimed at detecting drought-responsive genes and will be useful for understanding the molecular mechanisms of drought tolerance in root and leaf of B. napus.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China. liuchunqingaixin@126.com.

ABSTRACT
Drought stress is one of the major abiotic factors affecting Brassica napus (B. napus) productivity. In order to identify genes of potential importance to drought stress and obtain a deeper understanding of the molecular mechanisms regarding the responses of B. napus to dehydration stress, we performed large-scale transcriptome sequencing of B. napus plants under dehydration stress using the Illumina sequencing technology. In this work, a relatively drought tolerant B. napus line, Q2, identified in our previous study, was used. Four cDNA libraries constructed from mRNAs of control and dehydration-treated root and leaf were sequenced by Illumina technology. A total of 6018 and 5377 differentially expressed genes (DEGs) were identified in root and leaf. In addition, 1745 genes exhibited a coordinated expression profile between the two tissues under drought stress, 1289 (approximately 74%) of which showed an inverse relationship, demonstrating different regulation patterns between the root and leaf. The gene ontology (GO) enrichment test indicated that up-regulated genes in root were mostly involved in "stimulus" "stress" biological process, and activated genes in leaf mainly functioned in "cell" "cell part" components. Furthermore, a comparative network related to plant hormone signal transduction and AREB/ABF, AP2/EREBP, NAC, WRKY and MYC/MYB transcription factors (TFs) provided a view of different stress tolerance mechanisms between root and leaf. Some of the DEGs identified may be candidates for future research aimed at detecting drought-responsive genes and will be useful for understanding the molecular mechanisms of drought tolerance in root and leaf of B. napus.

No MeSH data available.


Related in: MedlinePlus

GO annotation of the differentially expressed genes in root (A) and leaf (B). The x-axis indicates the sub-categories, the left y-axis indicates the percentage of a sub-category of genes in that category, and the right y-axis indicates the number of unigenes in a sub-category.
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ijms-16-18752-f004: GO annotation of the differentially expressed genes in root (A) and leaf (B). The x-axis indicates the sub-categories, the left y-axis indicates the percentage of a sub-category of genes in that category, and the right y-axis indicates the number of unigenes in a sub-category.

Mentions: Gene ontology (GO) is widely applied to understand the functional classification of differential gene expression data [49]. This analysis was performed to determine the major molecular functions, biological processes, and cellular components with which the DEGs were associated. A total of 6018 DEGs in root and 5377 DEGs in leaf of B. rapa were analyzed for GO category annotations using Blast2GO [50]. A GO term with p ≤ 0.001 and /log2/ > 2 was defined as a significantly DEG-enriched GO term (Figure 3). Twelve GO terms were found as enriched biological processes based on the DEGs in root (Figure 3A): “response to stress”, “response to stimulus”, and “response to chemical stimulus”, which were the major GO terms. Simultaneously, more down-regulated genes were shown in “cell cycle”, “cell wall”, “external encapsulating structure” and “cell periphery” terms. However, 37 GO terms for the DEGs were found in leaf (Figure 3B): “cell”, “cell part”, and “organelle” were the major GO terms. Also comparatively higher contents of down-regulated genes were found in “response to stress” (63.0%), “response to chemical stimulus” (73.7%), and “response to stimulus” (52.7%) terms. Overall, most stress-related biological processes were up-regulated in root but down-regulated in leaf, and cellular components were mostly down-regulated in root but up-regulated in leaf. This GO terms enrichment analysis showed the critical biological processes in response to drought stress. We concluded from this result that B. napus seedlings mostly used the same terms and pathways, but different models of gene regulation were present in different tissue types in response to drought-stress conditions. In addition, GO (Gene ontology) classifications were also obtained to investigate the functions of the unigenes (Figure 4). A total of 6018 DEGs in root and 5377 DEGs in leaf were classified into 42 groups, and all could be categorized into three main classifications: “cellular component”, “molecular function”, and “biological process.” Among the biological process category, “cell” (approximately 59.3% in root and 60.8% in leaf) and “cell part” (approximately 59.3% in root and 60.8% in leaf) were the most dominant groups. GO enrichment analysis was also carried out in root (Supplementary Table S1) and leaf (Supplementary Table S2). Among the biological process category, response to stimulus process (about 44.6%) was the most dominant group in root, followed by response to stress (about 23.2%), biosynthetic process (about 23.2%), cellular biosynthetic process (about 22.6%), and response to chemical stimulus (about 22.1%). Regarding molecular functions, 12.3% of the unigenes were assigned to nucleic acid binding transcription factor activity, followed by phosphotransferase activity, alcohol group as acceptor (about 9.8%) and protein kinase activity (about 9.4%). In the cellular component category, intrinsic to membrane (12.8% for both) was the dominant group, followed by cell periphery (about 9.7%). In leaf, response to stimulus (about 44%) was also the most dominant group, followed by response to stress (about 23.6%), response to abiotic stimulus (about 16.2%), cellular component organization or biogenesis (about 13.7%) in the biological process category. Regarding molecular functions in leaf, 11.1% of the unigenes were assigned to nucleic acid binding transcription factor activity, followed by structural molecule activity (about 5.4%). In the cellular component category, membrane (about 36.3%) was the dominant group, followed by organelle part (about 24.3%), intracellular organelle part (about 20.8%).


Comparative Analysis of the Brassica napus Root and Leaf Transcript Profiling in Response to Drought Stress.

Liu C, Zhang X, Zhang K, An H, Hu K, Wen J, Shen J, Ma C, Yi B, Tu J, Fu T - Int J Mol Sci (2015)

GO annotation of the differentially expressed genes in root (A) and leaf (B). The x-axis indicates the sub-categories, the left y-axis indicates the percentage of a sub-category of genes in that category, and the right y-axis indicates the number of unigenes in a sub-category.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4581270&req=5

ijms-16-18752-f004: GO annotation of the differentially expressed genes in root (A) and leaf (B). The x-axis indicates the sub-categories, the left y-axis indicates the percentage of a sub-category of genes in that category, and the right y-axis indicates the number of unigenes in a sub-category.
Mentions: Gene ontology (GO) is widely applied to understand the functional classification of differential gene expression data [49]. This analysis was performed to determine the major molecular functions, biological processes, and cellular components with which the DEGs were associated. A total of 6018 DEGs in root and 5377 DEGs in leaf of B. rapa were analyzed for GO category annotations using Blast2GO [50]. A GO term with p ≤ 0.001 and /log2/ > 2 was defined as a significantly DEG-enriched GO term (Figure 3). Twelve GO terms were found as enriched biological processes based on the DEGs in root (Figure 3A): “response to stress”, “response to stimulus”, and “response to chemical stimulus”, which were the major GO terms. Simultaneously, more down-regulated genes were shown in “cell cycle”, “cell wall”, “external encapsulating structure” and “cell periphery” terms. However, 37 GO terms for the DEGs were found in leaf (Figure 3B): “cell”, “cell part”, and “organelle” were the major GO terms. Also comparatively higher contents of down-regulated genes were found in “response to stress” (63.0%), “response to chemical stimulus” (73.7%), and “response to stimulus” (52.7%) terms. Overall, most stress-related biological processes were up-regulated in root but down-regulated in leaf, and cellular components were mostly down-regulated in root but up-regulated in leaf. This GO terms enrichment analysis showed the critical biological processes in response to drought stress. We concluded from this result that B. napus seedlings mostly used the same terms and pathways, but different models of gene regulation were present in different tissue types in response to drought-stress conditions. In addition, GO (Gene ontology) classifications were also obtained to investigate the functions of the unigenes (Figure 4). A total of 6018 DEGs in root and 5377 DEGs in leaf were classified into 42 groups, and all could be categorized into three main classifications: “cellular component”, “molecular function”, and “biological process.” Among the biological process category, “cell” (approximately 59.3% in root and 60.8% in leaf) and “cell part” (approximately 59.3% in root and 60.8% in leaf) were the most dominant groups. GO enrichment analysis was also carried out in root (Supplementary Table S1) and leaf (Supplementary Table S2). Among the biological process category, response to stimulus process (about 44.6%) was the most dominant group in root, followed by response to stress (about 23.2%), biosynthetic process (about 23.2%), cellular biosynthetic process (about 22.6%), and response to chemical stimulus (about 22.1%). Regarding molecular functions, 12.3% of the unigenes were assigned to nucleic acid binding transcription factor activity, followed by phosphotransferase activity, alcohol group as acceptor (about 9.8%) and protein kinase activity (about 9.4%). In the cellular component category, intrinsic to membrane (12.8% for both) was the dominant group, followed by cell periphery (about 9.7%). In leaf, response to stimulus (about 44%) was also the most dominant group, followed by response to stress (about 23.6%), response to abiotic stimulus (about 16.2%), cellular component organization or biogenesis (about 13.7%) in the biological process category. Regarding molecular functions in leaf, 11.1% of the unigenes were assigned to nucleic acid binding transcription factor activity, followed by structural molecule activity (about 5.4%). In the cellular component category, membrane (about 36.3%) was the dominant group, followed by organelle part (about 24.3%), intracellular organelle part (about 20.8%).

Bottom Line: The gene ontology (GO) enrichment test indicated that up-regulated genes in root were mostly involved in "stimulus" "stress" biological process, and activated genes in leaf mainly functioned in "cell" "cell part" components.Furthermore, a comparative network related to plant hormone signal transduction and AREB/ABF, AP2/EREBP, NAC, WRKY and MYC/MYB transcription factors (TFs) provided a view of different stress tolerance mechanisms between root and leaf.Some of the DEGs identified may be candidates for future research aimed at detecting drought-responsive genes and will be useful for understanding the molecular mechanisms of drought tolerance in root and leaf of B. napus.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China. liuchunqingaixin@126.com.

ABSTRACT
Drought stress is one of the major abiotic factors affecting Brassica napus (B. napus) productivity. In order to identify genes of potential importance to drought stress and obtain a deeper understanding of the molecular mechanisms regarding the responses of B. napus to dehydration stress, we performed large-scale transcriptome sequencing of B. napus plants under dehydration stress using the Illumina sequencing technology. In this work, a relatively drought tolerant B. napus line, Q2, identified in our previous study, was used. Four cDNA libraries constructed from mRNAs of control and dehydration-treated root and leaf were sequenced by Illumina technology. A total of 6018 and 5377 differentially expressed genes (DEGs) were identified in root and leaf. In addition, 1745 genes exhibited a coordinated expression profile between the two tissues under drought stress, 1289 (approximately 74%) of which showed an inverse relationship, demonstrating different regulation patterns between the root and leaf. The gene ontology (GO) enrichment test indicated that up-regulated genes in root were mostly involved in "stimulus" "stress" biological process, and activated genes in leaf mainly functioned in "cell" "cell part" components. Furthermore, a comparative network related to plant hormone signal transduction and AREB/ABF, AP2/EREBP, NAC, WRKY and MYC/MYB transcription factors (TFs) provided a view of different stress tolerance mechanisms between root and leaf. Some of the DEGs identified may be candidates for future research aimed at detecting drought-responsive genes and will be useful for understanding the molecular mechanisms of drought tolerance in root and leaf of B. napus.

No MeSH data available.


Related in: MedlinePlus