New insights on key genes involved in drought stress response of barley: gene networks reconstruction, hub, and promoter analysis
Abstract Background Barley (Hordeum vulgare L.) is one of the most important cereals worldwide. Although this crop is drought-tolerant, water deficiency negatively affects its growth and production. To detect key genes involved in drought tolerance in barley, a reconstruction of the related gene net...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2021-01-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s43141-020-00104-z |
| _version_ | 1797204301152518144 |
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| author | Seyedeh Mehri Javadi Zahra-Sadat Shobbar Asa Ebrahimi Maryam Shahbazi |
| author_facet | Seyedeh Mehri Javadi Zahra-Sadat Shobbar Asa Ebrahimi Maryam Shahbazi |
| author_sort | Seyedeh Mehri Javadi |
| collection | DOAJ |
| description | Abstract Background Barley (Hordeum vulgare L.) is one of the most important cereals worldwide. Although this crop is drought-tolerant, water deficiency negatively affects its growth and production. To detect key genes involved in drought tolerance in barley, a reconstruction of the related gene network and discovery of the hub genes would help. Here, drought-responsive genes in barley were collected through analysis of the available microarray datasets (− 5 ≥ Fold change ≥ 5, adjusted p value ≤ 0.05). Protein-protein interaction (PPI) networks were reconstructed. Results The hub genes were identified by Cytoscape software using three Cyto-hubba algorithms (Degree, Closeness, and MNC), leading to the identification of 17 and 16 non-redundant genes at vegetative and reproductive stages, respectively. These genes consist of some transcription factors such as HvVp1, HvERF4, HvFUS3, HvCBF6, DRF1.3, HvNAC6, HvCO5, and HvWRKY42, which belong to AP2, NAC, Zinc-finger, and WRKY families. In addition, the expression pattern of four hub genes was compared between the two studied cultivars, i.e., “Yousef” (drought-tolerant) and “Morocco” (susceptible). The results of real-time PCR revealed that the expression patterns corresponded well with those determined by the microarray. Also, promoter analysis revealed that some TF families, including AP2, NAC, Trihelix, MYB, and one modular (composed of two HD-ZIP TFs), had a binding site in 85% of promoters of the drought-responsive genes and of the hub genes in barley. Conclusions The identified hub genes, especially those from AP2 and NAC families, might be among key TFs that regulate drought-stress response in barley and are suggested as promising candidate genes for further functional analysis. |
| first_indexed | 2024-04-24T08:33:03Z |
| format | Article |
| id | doaj.art-1265417b47fe43d08a21af8ce3fa1e89 |
| institution | Directory Open Access Journal |
| issn | 2090-5920 |
| language | English |
| last_indexed | 2024-04-24T08:33:03Z |
| publishDate | 2021-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj.art-1265417b47fe43d08a21af8ce3fa1e892024-04-16T18:17:28ZengElsevierJournal of Genetic Engineering and Biotechnology2090-59202021-01-0119111210.1186/s43141-020-00104-zNew insights on key genes involved in drought stress response of barley: gene networks reconstruction, hub, and promoter analysisSeyedeh Mehri Javadi0Zahra-Sadat Shobbar1Asa Ebrahimi2Maryam Shahbazi3Department of Biotechnology and Plant Breeding, Science and Research Branch, Islamic Azad UniversityDepartment of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO)Department of Biotechnology and Plant Breeding, Science and Research Branch, Islamic Azad UniversityGorgan University of Agricultural Sciences and Natural ResourcesAbstract Background Barley (Hordeum vulgare L.) is one of the most important cereals worldwide. Although this crop is drought-tolerant, water deficiency negatively affects its growth and production. To detect key genes involved in drought tolerance in barley, a reconstruction of the related gene network and discovery of the hub genes would help. Here, drought-responsive genes in barley were collected through analysis of the available microarray datasets (− 5 ≥ Fold change ≥ 5, adjusted p value ≤ 0.05). Protein-protein interaction (PPI) networks were reconstructed. Results The hub genes were identified by Cytoscape software using three Cyto-hubba algorithms (Degree, Closeness, and MNC), leading to the identification of 17 and 16 non-redundant genes at vegetative and reproductive stages, respectively. These genes consist of some transcription factors such as HvVp1, HvERF4, HvFUS3, HvCBF6, DRF1.3, HvNAC6, HvCO5, and HvWRKY42, which belong to AP2, NAC, Zinc-finger, and WRKY families. In addition, the expression pattern of four hub genes was compared between the two studied cultivars, i.e., “Yousef” (drought-tolerant) and “Morocco” (susceptible). The results of real-time PCR revealed that the expression patterns corresponded well with those determined by the microarray. Also, promoter analysis revealed that some TF families, including AP2, NAC, Trihelix, MYB, and one modular (composed of two HD-ZIP TFs), had a binding site in 85% of promoters of the drought-responsive genes and of the hub genes in barley. Conclusions The identified hub genes, especially those from AP2 and NAC families, might be among key TFs that regulate drought-stress response in barley and are suggested as promising candidate genes for further functional analysis.https://doi.org/10.1186/s43141-020-00104-zBarleyDrought stressBiological networksHub genePromoter analysis |
| spellingShingle | Seyedeh Mehri Javadi Zahra-Sadat Shobbar Asa Ebrahimi Maryam Shahbazi New insights on key genes involved in drought stress response of barley: gene networks reconstruction, hub, and promoter analysis Journal of Genetic Engineering and Biotechnology Barley Drought stress Biological networks Hub gene Promoter analysis |
| title | New insights on key genes involved in drought stress response of barley: gene networks reconstruction, hub, and promoter analysis |
| title_full | New insights on key genes involved in drought stress response of barley: gene networks reconstruction, hub, and promoter analysis |
| title_fullStr | New insights on key genes involved in drought stress response of barley: gene networks reconstruction, hub, and promoter analysis |
| title_full_unstemmed | New insights on key genes involved in drought stress response of barley: gene networks reconstruction, hub, and promoter analysis |
| title_short | New insights on key genes involved in drought stress response of barley: gene networks reconstruction, hub, and promoter analysis |
| title_sort | new insights on key genes involved in drought stress response of barley gene networks reconstruction hub and promoter analysis |
| topic | Barley Drought stress Biological networks Hub gene Promoter analysis |
| url | https://doi.org/10.1186/s43141-020-00104-z |
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