Genome-Wide Mining and Identification of Protein Kinase Gene Family Impacts Salinity Stress Tolerance in Highly Dense Genetic Map Developed from Interspecific Cross between G. hirsutum L. and G. darwinii G. Watt
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Gene Mining within SSR Markers
2.3. Phylogenetic Analysis
2.4. Subcellular Localization and Structure Analysis
2.5. Gene Ontology (GO) Annotation
2.6. Syntenic Analysis and Duplication of Genes
2.7. Prediction of miRNA Target and Transcription Factor Binding Sites (TFBS) Analysis
2.8. Plant Material and Hydroponic Culture
2.9. RNA Sequence and RT-qPCR Analysis
3. Results
3.1. Genetic Linkage Map Features
3.2. Assessment of Collinearity of the Genetic and Physical Map of G. hirsutum
3.3. Phylogenetic Analysis
3.4. Chromosomal Distribution of Pkinase Genes
3.5. Structural Analysis and Localization of Genes
3.6. Gene Annotation by GO Analysis
3.7. Duplication and Syntenic Analysis of Genes
3.8. Prediction of Transcription Factor Binding Sites
3.9. miRNA Target Analysis of Genes
3.10. RNA Sequence Data of Salt Tolerant Genes
3.11. RT-qPCR Analysis of the Candidate Genes under Salt Stress
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
ATP | Adenosine Triphosphate |
BP | Biological Process |
CDS | Coding Sequence |
CF | Cellular Function |
CIRCOS | Circular Genome Data Visualization |
GO | Gene Ontology |
GSDS | Gene Structure Display Server |
MF | Molecular Function |
MYA | Million Years Ago |
NaCl | Sodium Chloride |
NCBI | National Centre for Biotechnology Information |
SSR | Simple Sequence Repeat |
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Gossypium genome | Chromosome No. | Total Number of Genes | Gossypium genome | Chromosome No. | Total Number of Genes |
---|---|---|---|---|---|
(AD) Genome | At1 | 6 | A03 | 2 | |
At2 | 5 | A04 | 3 | ||
At5 | 4 | A05 | 1 | ||
At7 | 2 | A07 | 2 | ||
At8 | 1 | A08 | 1 | ||
At9 | 4 | A09 | 5 | ||
At10 | 1 | A10 | 1 | ||
At11 | 8 | A11 | 7 | ||
At12 | 3 | A12 | 3 | ||
Dt14 | 1 | Scaffolds | 1 | ||
Dt15 | 9 | Total | 35 | ||
Dt16 | 2 | (D) Genome | D01 | 2 | |
Dt17 | 3 | D02 | 10 | ||
Dt18 | 2 | D03 | 4 | ||
Dt19 | 2 | D04 | 1 | ||
Dt20 | 2 | D05 | 1 | ||
Dt21 | 7 | D06 | 6 | ||
Dt22 | 2 | D07 | 6 | ||
Dt23 | 5 | D08 | 4 | ||
Dt24 | 1 | D09 | 2 | ||
Dt26 | 4 | D11 | 1 | ||
Scaffolds | 1 | D12 | 2 | ||
Total | 75 | D13 | 2 | ||
(A) Genome | A01 | 7 | Total | 41 | |
A02 | 2 |
Factor Name | Signal Sequence | Function | No. of Genes |
---|---|---|---|
Box 4 | ATTAAT | Involved in light responsiveness | 40 |
TATC-box | TATCCCA | Involved in gibberellin-responsiveness | 38 |
MYC | CAATTG | Role in cell proliferation | 50 |
MYBS | CAACTG | Abiotic stress tolerance | 55 |
CAAT-box | CAAT | Binding factors | 60 |
AT-rich element | ATAGAAATCAA | AT-rich DNA binding protein (ATBP-1) | 49 |
G-Box | CACGTT | In network regulating flag leaf senescence process | 40 |
TATA-box | TATA | Core promoter element | 55 |
ARE | AAACCA | Essential for the anaerobic induction | 41 |
MBS | CAACTG | Involved in drought-inducibility | 53 |
ABRE | CGCACGTGTC | Involved in the abscisic acid responsiveness | 54 |
Myb-binding site | CAACAG | Plant Myb-binding site | 50 |
TGACG-motif | TGACG | MeJA responsiveness | 40 |
HD-Zip 1 | CAAT(A/T) ATG | Differentiation of palisade mesophyll cell | 20 |
TGA-element | AACGAC | Auxin-responsive element | 35 |
CCAAT-box | CAACGG | Plant MYBHv1 binding site | 39 |
TCA-element | CCATCTTTTT | Salicylic acid responsiveness | 52 |
P-box | CCTTTTG | Gibberellin-responsive element | 28 |
DRE | GCCGAC | Stress responsiveness | 25 |
3-AF1 binding site | TAAGAGAGGAA | Light responsive element | 4 |
O2-site | GATGATGTGG | Involved in zinc metabolism regulation | 30 |
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Shehzad, M.; Zhou, Z.; Ditta, A.; Cai, X.; Khan, M.; Xu, Y.; Hou, Y.; Peng, R.; Hao, F.; Shafeeq-ur-rahman; et al. Genome-Wide Mining and Identification of Protein Kinase Gene Family Impacts Salinity Stress Tolerance in Highly Dense Genetic Map Developed from Interspecific Cross between G. hirsutum L. and G. darwinii G. Watt. Agronomy 2019, 9, 560. https://doi.org/10.3390/agronomy9090560
Shehzad M, Zhou Z, Ditta A, Cai X, Khan M, Xu Y, Hou Y, Peng R, Hao F, Shafeeq-ur-rahman, et al. Genome-Wide Mining and Identification of Protein Kinase Gene Family Impacts Salinity Stress Tolerance in Highly Dense Genetic Map Developed from Interspecific Cross between G. hirsutum L. and G. darwinii G. Watt. Agronomy. 2019; 9(9):560. https://doi.org/10.3390/agronomy9090560
Chicago/Turabian StyleShehzad, Muhammad, Zhongli Zhou, Allah Ditta, Xiaoyan Cai, Majid Khan, Yanchao Xu, Yuqing Hou, Renhai Peng, Fushun Hao, Shafeeq-ur-rahman, and et al. 2019. "Genome-Wide Mining and Identification of Protein Kinase Gene Family Impacts Salinity Stress Tolerance in Highly Dense Genetic Map Developed from Interspecific Cross between G. hirsutum L. and G. darwinii G. Watt" Agronomy 9, no. 9: 560. https://doi.org/10.3390/agronomy9090560