Insights into Barley Root Transcriptome under Mild Drought Stress with an Emphasis on Gene Expression Regulatory Mechanisms
Abstract
:1. Introduction
2. Results
2.1. An Overview of Root and Leaf Transcriptome Changes in Response to Mild Drought Stress
2.2. The Characteristics of Root Transcriptomes of Barley Genotypes Exposed to Mild Drought Stress
2.3. Root DEGs Involved in the Regulation of Gene Expression
2.4. Target Genes Putatively Regulated by Specific Transcription Factors with Differential Expression in Roots
2.5. A Comparison of DEGs Involved in Gene Expression Regulation in Roots during Mild and Severe Drought Stress
3. Discussion
4. Materials and Methods
4.1. Plant Material and STRESS Treatment
4.2. RNA Isolation
4.3. Preparation of Microarrays and Microarray Data Analysis
4.4. Agilent Barley Gene Expression Microarray Annotation, GO Enrichment and Transcription Factor Encoding Genes Analysis
4.5. Quantitative Reverse Transcription (RT)-qPCR
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
DEG | Differentially expressed gene |
GO | Gene ontology |
PSI | Photosystem I |
PSII | Photosystem II |
ROS | Reactive oxygen species |
TF | Transcription factor |
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Genotype | Organ | No. of Probes | No. of Genes with Known Annotations * | ||
---|---|---|---|---|---|
Down-Regulation | Up-Regulation | Down-Regulation | Up-Regulation | ||
CamB | Roots | 792 | 1019 | 519 | 536 |
CamB | Leaves | 597 | 705 | 354 | 429 |
Maresi | Roots | 999 | 884 | 634 | 452 |
Maresi | Leaves | 602 | 717 | 353 | 436 |
Horvu ID | Expression Change | Family Name | Gene Description | |||
---|---|---|---|---|---|---|
CamB Roots | CamB Leaves | Mar Roots | Mar Leaves | |||
Transcription factors: | ||||||
HORVU4HR1G087580 | up | n/c | n/c | n/c | bHLH | Uncharacterized |
HORVU3Hr1G073470 | up | n/c | n/c | n/c | CPP | Protein tesmin/TSO1-like CXC 5 |
HORVU2Hr1G020140 | up | n/c | n/c | up | GARP-G2-like | Two-component response regulator ARR18 |
HORVU7Hr1G096430 | down | n/c | n/c | n/c | GARP-G2-like | Myb-like transcription factor family protein |
HORVU5Hr1G110960 | up | n/c | n/c | n/c | General TF | Transcription initiation factor IIE subunit beta |
HORVU1Hr1G071620 | up | n/c | n/c | n/c | NF-YB | Nuclear transcription factor Y subunit B |
HORVU5Hr1G062040 | up | n/c | n/c | n/c | SCAI TF family | Protein SCAI |
HORVU3Hr1G061930 | down | down | n/c | down | TUB | Tubby-like F-box protein 1 |
Transcriptional Regulators: | ||||||
HORVU5Hr1G061120 | down | n/c | n/c | n/c | BAH domain | Bromo-adjacent homology (BAH) domain-containing protein |
HORVU6Hr1G034680 | up | n/c | n/c | n/c | PHD | methyl-CPG-binding domain 9 |
Horvu ID | Expression change | Family Name | Gene Description | |||
---|---|---|---|---|---|---|
CamB Roots | CamB Leaves | Mar Roots | Mar Leaves | |||
Transcription factors: | ||||||
HORVU2Hr1G050260 | n/c | n/c | up | n/c | AP2/ERF-ERF | Ethylene-responsive transcription factor |
HORVU4Hr1G077310 | n/c | n/c | down | n/c | AP2/ERF-ERF | Ethylene-responsive transcription factor |
HORVU5Hr1G080300 | n/c | n/c | down | down | AP2/ERF-ERF | Dehydration-responsive element-binding protein 1B |
HORVU6Hr1G080340 | n/c | up | up | up | AP2/ERF-ERF | Ethylene-responsive transcription factor 5 |
HORVU3Hr1G105720 | n/c | n/c | down | n/c | B3 | B3 domain-containing protein |
HORVU5Hr1G017450 | n/c | n/c | up | n/c | B3 | B3 domain-containing protein |
HORVU3Hr1G108680 | n/c | n/c | up | n/c | bHLH | Transcription factor ORG2 |
HORVU5Hr1G002090 | n/c | n/c | down | n/c | bHLH | Basic helix-loop-helix (bHLH) DNA-binding superfamily protein |
HORVU6Hr1G071950 | n/c | n/c | down | n/c | C2C2-CO-like | Zinc finger protein CONSTANS-LIKE 10 |
HORVU4Hr1G088280 | n/c | up | up | up | C2C2-GATA | GATA transcription factor 2 |
HORVU3Hr1G085720 | n/c | n/c | down | n/c | HB-BELL | BEL1-like homeodomain 8 |
HORVU5Hr1G067010 | n/c | n/c | down | n/c | HB-HD-ZIP | Homeobox-leucine zipper protein family |
HORVU2Hr1G061320 | n/c | n/c | down | n/c | HB-KNOX | Homeobox protein knotted-1-like 12 |
HORVU5Hr1G098570 | n/c | n/c | down | n/c | HB-KNOX | Homeobox protein knotted-1-like 12 |
HORVU0Hr1G003020 | n/c | n/c | down | n/c | MADS-M-type | MADS-box transcription factor 18 |
HORVU3Hr1G095090 | n/c | n/c | down | n/c | MADS-M-type | MADS-box transcription factor family protein |
HORVU3Hr1G052710 | n/c | n/c | down | n/c | MYB-related | Myb-like transcription factor family protein |
HORVU6Hr1G066000 | n/c | down | down | n/c | MYB-related | Myb-like transcription factor family protein |
HORVU5Hr1G045640 | n/c | n/c | down | down | NAC | NAC domain protein, |
HORVU2Hr1G072420 | n/c | n/c | down | n/c | S1Fa-like | DNA-binding protein S1FA2 |
HORVU3Hr1G094730 | n/c | n/c | down | n/c | SBP | Squamosa promoter-binding-like protein 2 |
HORVU1Hr1G054620 | n/c | n/c | down | n/c | STAT | SH2 domain protein B |
HORVU3Hr1G095400 | n/c | n/c | down | down | TCP | TCP family transcription factor |
HORVU6Hr1G093960 | n/c | n/c | down | n/c | TCP | TCP family transcription factor |
HORVU7Hr1G038130 | n/c | n/c | down | n/c | TCP | TCP family transcription factor |
HORVU7Hr1G041230 | n/c | n/c | down | up | Tify | Protein TIFY 3A |
HORVU1Hr1G069620 | n/c | n/c | down | n/c | WRKY | WRKY DNA-binding protein 54 |
HORVU3Hr1G050590 | n/c | n/c | down | n/c | WRKY | WRKY DNA-binding protein 50 |
Transcriptional regulators: | ||||||
HORVU6Hr1G091700 | n/c | n/c | down | n/c | Others | Ethylene receptor 3 |
HORVU2Hr1G017680 | n/c | up | down | up | PHD | E3 ubiquitin-protein ligase SHPRH |
HORVU4Hr1G003040 | n/c | n/c | down | n/c | TRAF | Regulatory protein (NPR1) |
Horvu ID | MLOC ID | Background-All 1 | Background-Bind 2 | Query-All 3 | Query-Bind 4 | p-Value | q-Value | Description (IPK) |
---|---|---|---|---|---|---|---|---|
HORVU1Hr1G090030 | MLOC_6711 | 24306 | 470 | 546 | 21 | 1.059 × 10−3 | 3.352 × 10−2 | G-box binding factor 2 |
HORVU5Hr1G014170 | MLOC_81003 | 24306 | 388 | 546 | 16 | 7.159 × 10−3 | 9.715 × 10−2 | Basic-leucine zipper (bZIP) TF family protein |
HORVU7Hr1G056820 | MLOC_75166 | 24306 | 368 | 546 | 15 | 9.549 × 10−3 | 1.210 × 10−1 | Heat stress transcription factor B-2b |
HORVU6Hr1G068100 | MLOC_14844 | 24306 | 386 | 546 | 14 | 2.906 × 10−2 | 2.301 × 10−1 | Myb-like TF family protein |
Horvu ID | MLOC ID | Family Name | Mild Drought | Severe Drought | Description | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Roots | Leaves | Roots | Leaves | ||||||||
CamB | Mar | CamB | Mar | CamB | Mar | CamB | Mar | ||||
HORVU7Hr1G089930 | MLOC_59305 | AP2/ERF-ERF | up | up | n/c | n/c | down | down | n/c | n/c | Ethylene-responsive transcription factor 1 |
HORVU5Hr1G047610 | MLOC_5148 | LOB | up | up | n/c | n/c | n/c | down | n/c | n/c | LOB domain-containing protein 4 |
HORVU2Hr1G017460 | MLOC_65101 | NAC | up | up | n/c | up | down | down | up | NAC domain protein | |
HORVU1Hr1G081570 | MLOC_32433 | WRKY | up | up | n/c | n/c | down | n/c | n/c | n/c | WRKY DNA-binding protein 24 |
HORVU3Hr1G108680 | MLOC_36351 | bHLH | n/c | up | n/c | n/c | down | down | n/c | n/c | Transcription factor ORG2 |
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Janiak, A.; Kwasniewski, M.; Sowa, M.; Kuczyńska, A.; Mikołajczak, K.; Ogrodowicz, P.; Szarejko, I. Insights into Barley Root Transcriptome under Mild Drought Stress with an Emphasis on Gene Expression Regulatory Mechanisms. Int. J. Mol. Sci. 2019, 20, 6139. https://doi.org/10.3390/ijms20246139
Janiak A, Kwasniewski M, Sowa M, Kuczyńska A, Mikołajczak K, Ogrodowicz P, Szarejko I. Insights into Barley Root Transcriptome under Mild Drought Stress with an Emphasis on Gene Expression Regulatory Mechanisms. International Journal of Molecular Sciences. 2019; 20(24):6139. https://doi.org/10.3390/ijms20246139
Chicago/Turabian StyleJaniak, Agnieszka, Miroslaw Kwasniewski, Marta Sowa, Anetta Kuczyńska, Krzysztof Mikołajczak, Piotr Ogrodowicz, and Iwona Szarejko. 2019. "Insights into Barley Root Transcriptome under Mild Drought Stress with an Emphasis on Gene Expression Regulatory Mechanisms" International Journal of Molecular Sciences 20, no. 24: 6139. https://doi.org/10.3390/ijms20246139
APA StyleJaniak, A., Kwasniewski, M., Sowa, M., Kuczyńska, A., Mikołajczak, K., Ogrodowicz, P., & Szarejko, I. (2019). Insights into Barley Root Transcriptome under Mild Drought Stress with an Emphasis on Gene Expression Regulatory Mechanisms. International Journal of Molecular Sciences, 20(24), 6139. https://doi.org/10.3390/ijms20246139