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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

Distribution of transcription factor gene families in B. napus. (A) Distribution of transcription factors specially expressed in root; (B) Distribution of transcription factors specially expressed in leaf; (C) Distribution of transcription factors expressed both in root and leaf; (D) Distribution of transcription factors conversely expressed in root and leaf.
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ijms-16-18752-f006: Distribution of transcription factor gene families in B. napus. (A) Distribution of transcription factors specially expressed in root; (B) Distribution of transcription factors specially expressed in leaf; (C) Distribution of transcription factors expressed both in root and leaf; (D) Distribution of transcription factors conversely expressed in root and leaf.

Mentions: To assess the complex network of signaling pathways in drought stress, we further compared the expression profiles of the TFs in root and leaf. Genes (501 genes in root and 400 genes in leaf) encoding putative TFs that were responsive to drought stress in B. napus were identified based on a comparison with their expression of Arabidopsis, and 157 TFs were found to be co-expressed. In addition, 110 TFs (70% of the 157 co-expressed TFs) were conversely expressed in root and leaf. Of the root TFs, 344 TFs that were specifically expressed in root were divided into 16 groups based on a classification of their Arabidopsis homologs (Figure 6A). Also, five of the TF families which comprised 47% of these groups, including MYB (Bra027389, Bra039067, Bra020624, Bra018223), basic helix-loop-helix (bHLH) (Bra019773, Bra033690, Bra031721, Bra027501, Bra038792, Bra024115), C2H2 (Bra008445, Bra003582), AP2/EREBP (Bra037630, Bra006599, Bra009272, Bra026280), and NAC (Bra001596, Bra040152), played important roles in response to drought stress in root (Figure 6A). In addition, 243 TFs specifically expressed in leaf were also divided into 16 groups, in which four TF families, including MYB (Bra013000, Bra003443, Bra015911), HB (Bra024984, Bra028454), AP2/EREBP (Bra019777), and bHLH (Bra003073), accounting for 40% of the total TFs (Figure 6B). Four groups of TFs—AP2/EREBP (Bra024539, Bra010880, Bra022115, Bra024394), bHLH (Bra004489), WRKY (Bra008435, Bra035148, Bra003588, Bra005104), and HB (Bra027050, Bra007920)—were co-expressed in root and leaf (Figure 6C). Moreover, five groups—AP2/EREBP (Bra024539, Bra024394), WRKY (Bra008435, Bra035148, Bra003588, Bra005104), bHLH (Bra004489), C2H2 (Bra017432), and HB (Bra007920, Bra027050)—exhibited converse expressions between root and leaf (con-expression TFs) (Figure 6D). It has been demonstrated that MYB, NAC, C2H2, AP2/EREBP, bHLH, WRKY TFs participate in plant defense and play important roles in crosstalk among abiotic stress responses [19,57].


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)

Distribution of transcription factor gene families in B. napus. (A) Distribution of transcription factors specially expressed in root; (B) Distribution of transcription factors specially expressed in leaf; (C) Distribution of transcription factors expressed both in root and leaf; (D) Distribution of transcription factors conversely expressed in root and leaf.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-18752-f006: Distribution of transcription factor gene families in B. napus. (A) Distribution of transcription factors specially expressed in root; (B) Distribution of transcription factors specially expressed in leaf; (C) Distribution of transcription factors expressed both in root and leaf; (D) Distribution of transcription factors conversely expressed in root and leaf.
Mentions: To assess the complex network of signaling pathways in drought stress, we further compared the expression profiles of the TFs in root and leaf. Genes (501 genes in root and 400 genes in leaf) encoding putative TFs that were responsive to drought stress in B. napus were identified based on a comparison with their expression of Arabidopsis, and 157 TFs were found to be co-expressed. In addition, 110 TFs (70% of the 157 co-expressed TFs) were conversely expressed in root and leaf. Of the root TFs, 344 TFs that were specifically expressed in root were divided into 16 groups based on a classification of their Arabidopsis homologs (Figure 6A). Also, five of the TF families which comprised 47% of these groups, including MYB (Bra027389, Bra039067, Bra020624, Bra018223), basic helix-loop-helix (bHLH) (Bra019773, Bra033690, Bra031721, Bra027501, Bra038792, Bra024115), C2H2 (Bra008445, Bra003582), AP2/EREBP (Bra037630, Bra006599, Bra009272, Bra026280), and NAC (Bra001596, Bra040152), played important roles in response to drought stress in root (Figure 6A). In addition, 243 TFs specifically expressed in leaf were also divided into 16 groups, in which four TF families, including MYB (Bra013000, Bra003443, Bra015911), HB (Bra024984, Bra028454), AP2/EREBP (Bra019777), and bHLH (Bra003073), accounting for 40% of the total TFs (Figure 6B). Four groups of TFs—AP2/EREBP (Bra024539, Bra010880, Bra022115, Bra024394), bHLH (Bra004489), WRKY (Bra008435, Bra035148, Bra003588, Bra005104), and HB (Bra027050, Bra007920)—were co-expressed in root and leaf (Figure 6C). Moreover, five groups—AP2/EREBP (Bra024539, Bra024394), WRKY (Bra008435, Bra035148, Bra003588, Bra005104), bHLH (Bra004489), C2H2 (Bra017432), and HB (Bra007920, Bra027050)—exhibited converse expressions between root and leaf (con-expression TFs) (Figure 6D). It has been demonstrated that MYB, NAC, C2H2, AP2/EREBP, bHLH, WRKY TFs participate in plant defense and play important roles in crosstalk among abiotic stress responses [19,57].

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