Genome-wide identification of MAPK cascade genes reveals the GhMAP3K14–GhMKK11–GhMPK31 pathway is involved in the drought response in cotton

2020 ◽  
Vol 103 (1-2) ◽  
pp. 211-223 ◽  
Author(s):  
Lin Chen ◽  
Heng Sun ◽  
Fengjiao Wang ◽  
Dandan Yue ◽  
Xiankun Shen ◽  
...  
Keyword(s):  
Mapk Cascade ◽  
Drought Response ◽  
Genome Wide

scholarly journals Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

2019 ◽  
Author(s):  
Licao Cui ◽  
Guang Yang ◽  
Jali Yan ◽  
Yan Pan ◽  
Xiaojun Nie
Keyword(s):  
Regulatory Network ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Mapk Cascade ◽  
Mitogen Activated Protein Kinase ◽  
Systematic Analysis ◽  
Functional Studies ◽  
Genome Wide ◽  
A Genome ◽  
Duplication Events

Abstract Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organism. Although it has been well characterized in many plants, no systematic analysis has been conducted in the model cereal crop barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs through a genome-wide search method using the latest published barley genomic data. Phylogenetic analysis assigned all the MAPK cascade genes into three groups in accordance to MAPK, MAPKK and MAPKKK family. Gene duplication revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of the HvMAPK, HvMAPKK and HvMAPKKKs were then investigated in different organs and under diverse stresses using the available 132 RNA-seq datasets, and then the tissue-specific and stress-responsive ones were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs. Conclusion This study provides the candidates for further functional studies and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

scholarly journals Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

2019 ◽  
Author(s):  
Licao Cui ◽  
Guang Yang ◽  
Jali Yan ◽  
Yan Pan ◽  
Xiaojun Nie
Keyword(s):  
Regulatory Network ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Mapk Cascade ◽  
Mitogen Activated Protein Kinase ◽  
Functional Study ◽  
Systematic Analysis ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome

Abstract Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been conducted in barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs in barley through a genome-wide search against the updated reference genome. Then, phylogenetic relationship, gene structure and conserved protein motifs organization of them were systematically analyzed and results supported the predictions. Gene duplication analysis revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of them were further investigated in different organs and under diverse abiotic stresses using the available 173 RNA-seq datasets, and then the tissue-specific and stress-responsive candidates were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs. Conclusion This study provides the targets for further functional study and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

scholarly journals Genome-wide transcriptome and physiological analyses provide new insights into peanut drought response mechanisms

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sailaja Bhogireddy ◽  
Abishek Xavier ◽  
Vanika Garg ◽  
Nancy Layland ◽  
Renee Arias ◽  
...  
Keyword(s):  
Drought Response ◽  
Genome Wide

scholarly journals Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response

2014 ◽  
Vol 290 (3) ◽  
pp. 1095-1115 ◽  
Author(s):  
Truyen N. Quach ◽  
Hanh T. M. Nguyen ◽  
Babu Valliyodan ◽  
Trupti Joshi ◽  
Dong Xu ◽  
...  
Keyword(s):  
Potential Function ◽  
Expression Analysis ◽  
Drought Response ◽  
Genome Wide ◽  
Genome Wide Expression

scholarly journals Genome-Wide Identification of SNAC1-Targeted Genes Involved in Drought Response in Rice

2019 ◽  
Vol 10 ◽  
Author(s):  
Xu Li ◽  
Yu Chang ◽  
Siqi Ma ◽  
Jianqiang Shen ◽  
Honghong Hu ◽  
...  
Keyword(s):  
Drought Response ◽  
Genome Wide

scholarly journals Genome-Wide Associations of Chlorophyll Fluorescence OJIP Transient Parameters Connected With Soil Drought Response in Barley

2019 ◽  
Vol 10 ◽  
Author(s):  
Marcin Rapacz ◽  
Magdalena Wójcik-Jagła ◽  
Anna Fiust ◽  
Hazem M. Kalaji ◽  
Janusz Kościelniak
Keyword(s):  
Chlorophyll Fluorescence ◽  
Soil Drought ◽  
Drought Response ◽  
Ojip Transient ◽  
Genome Wide

Genome-Wide Identification of Drought Response Genes in Soybean Seedlings and Development of Biomarkers for Early Diagnoses

2018 ◽  
Vol 36 (2) ◽  
pp. 350-362 ◽  
Author(s):  
Lei Hua ◽  
Ghana Shyam Challa ◽  
Senthil Subramanian ◽  
Xingyou Gu ◽  
Wanlong Li
Keyword(s):  
Drought Response ◽  
Soybean Seedlings ◽  
Genome Wide

scholarly journals Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Licao Cui ◽  
Guang Yang ◽  
Jiali Yan ◽  
Yan Pan ◽  
Xiaojun Nie
Keyword(s):  
Regulatory Network ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Mapk Cascade ◽  
Mitogen Activated Protein Kinase ◽  
Functional Study ◽  
Systematic Analysis ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome

Abstract Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been conducted in barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs in barley through a genome-wide search against the updated reference genome. Then, phylogenetic relationship, gene structure and conserved protein motifs organization of them were systematically analyzed and results supported the predictions. Gene duplication analysis revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of them were further investigated in different organs and under diverse abiotic stresses using the available 173 RNA-seq datasets, and then the tissue-specific and stress-responsive candidates were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs. Conclusion This study provides the targets for further functional study and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

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