Identification, characterization, and validation of NBS-encoding genes in grass pea
Grass pea is a promising crop with the potential to provide food and fodder, but its genomics has not been adequately explored. Identifying genes for desirable traits, such as drought tolerance and disease resistance, is critical for improving the plant. Grass pea currently lacks known R-genes, incl...
| Autores principales: | , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media S.A.
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/132671 |
| _version_ | 1855521765799755776 |
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| author | Alsamman, Alsamman M. Mousa, Khaled H. Nassar, Ahmed E. M. Faheem, Mostafa Radwan, Khaled Adly, Monica Ahmed, Ahmed Istanbuli, Tawffiq Mokhtar, Morad M. Ahmed Elakkad, Tamer Kehel, Zakaria Hamwieh, Aladdin Abdelsattar, Mohamed El Allali, Achraf |
| author_browse | Abdelsattar, Mohamed Adly, Monica Ahmed Elakkad, Tamer Ahmed, Ahmed Alsamman, Alsamman M. El Allali, Achraf Hamwieh, Aladdin Istanbuli, Tawffiq Kehel, Zakaria M. Faheem, Mostafa Mokhtar, Morad M. Mousa, Khaled H. Nassar, Ahmed E. Radwan, Khaled |
| author_facet | Alsamman, Alsamman M. Mousa, Khaled H. Nassar, Ahmed E. M. Faheem, Mostafa Radwan, Khaled Adly, Monica Ahmed, Ahmed Istanbuli, Tawffiq Mokhtar, Morad M. Ahmed Elakkad, Tamer Kehel, Zakaria Hamwieh, Aladdin Abdelsattar, Mohamed El Allali, Achraf |
| author_sort | Alsamman, Alsamman M. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Grass pea is a promising crop with the potential to provide food and fodder, but its genomics has not been adequately explored. Identifying genes for desirable traits, such as drought tolerance and disease resistance, is critical for improving the plant. Grass pea currently lacks known R-genes, including the nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family, which plays a key role in protecting the plant from biotic and abiotic stresses. In our study, we used the recently published grass pea genome and available transcriptomic data to identify 274 NBS-LRR genes. The evolutionary relationships between the classified genes on the reported plants and LsNBS revealed that 124 genes have TNL domains, while 150 genes have CNL domains. All genes contained exons, ranging from 1 to 7. Ten conserved motifs with lengths ranging from 16 to 30 amino acids were identified. We found TIR-domain-containing genes in 132 LsNBSs, with 63 TIR-1 and 69 TIR-2, and RX-CCLike in 84 LsNBSs. We also identified several popular motifs, including P-loop, Uup, kinase-GTPase, ABC, ChvD, CDC6, Rnase_H, Smc, CDC48, and SpoVK. According to the gene enrichment analysis, the identified genes undergo several biological processes such as plant defense, innate immunity, hydrolase activity, and DNA binding. In the upstream regions, 103 transcription factors were identified that govern the transcription of nearby genes affecting the plant excretion of salicylic acid, methyl jasmonate, ethylene, and abscisic acid. According to RNA-Seq expression analysis, 85% of the encoded genes have high expression levels. Nine LsNBS genes were selected for qPCR under salt stress conditions. The majority of the genes showed upregulation at 50 and 200 μM NaCl. However, LsNBS-D18, LsNBS-D204, and LsNBS-D180 showed reduced or drastic downregulation compared to their respective expression levels, providing further insights into the potential functions of LsNBSs under salt stress conditions. They provide valuable insights into the potential functions of LsNBSs under salt stress conditions. Our findings also shed light on the evolution and classification of NBS-LRR genes in legumes, highlighting the potential of grass pea. Further research could focus on the functional analysis of these genes, and their potential use in breeding programs to improve the salinity, drought, and disease resistance of this important crop. |
| format | Journal Article |
| id | CGSpace132671 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Frontiers Media S.A. |
| publisherStr | Frontiers Media S.A. |
| record_format | dspace |
| spelling | CGSpace1326712026-01-21T02:04:59Z Identification, characterization, and validation of NBS-encoding genes in grass pea Alsamman, Alsamman M. Mousa, Khaled H. Nassar, Ahmed E. M. Faheem, Mostafa Radwan, Khaled Adly, Monica Ahmed, Ahmed Istanbuli, Tawffiq Mokhtar, Morad M. Ahmed Elakkad, Tamer Kehel, Zakaria Hamwieh, Aladdin Abdelsattar, Mohamed El Allali, Achraf legumes gene expression biotic stress abiotic stress identification grass pea (lathyrus sativus) nbs grass pea (lathyrus sativus l) genome wide analysis real time—pcr Grass pea is a promising crop with the potential to provide food and fodder, but its genomics has not been adequately explored. Identifying genes for desirable traits, such as drought tolerance and disease resistance, is critical for improving the plant. Grass pea currently lacks known R-genes, including the nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family, which plays a key role in protecting the plant from biotic and abiotic stresses. In our study, we used the recently published grass pea genome and available transcriptomic data to identify 274 NBS-LRR genes. The evolutionary relationships between the classified genes on the reported plants and LsNBS revealed that 124 genes have TNL domains, while 150 genes have CNL domains. All genes contained exons, ranging from 1 to 7. Ten conserved motifs with lengths ranging from 16 to 30 amino acids were identified. We found TIR-domain-containing genes in 132 LsNBSs, with 63 TIR-1 and 69 TIR-2, and RX-CCLike in 84 LsNBSs. We also identified several popular motifs, including P-loop, Uup, kinase-GTPase, ABC, ChvD, CDC6, Rnase_H, Smc, CDC48, and SpoVK. According to the gene enrichment analysis, the identified genes undergo several biological processes such as plant defense, innate immunity, hydrolase activity, and DNA binding. In the upstream regions, 103 transcription factors were identified that govern the transcription of nearby genes affecting the plant excretion of salicylic acid, methyl jasmonate, ethylene, and abscisic acid. According to RNA-Seq expression analysis, 85% of the encoded genes have high expression levels. Nine LsNBS genes were selected for qPCR under salt stress conditions. The majority of the genes showed upregulation at 50 and 200 μM NaCl. However, LsNBS-D18, LsNBS-D204, and LsNBS-D180 showed reduced or drastic downregulation compared to their respective expression levels, providing further insights into the potential functions of LsNBSs under salt stress conditions. They provide valuable insights into the potential functions of LsNBSs under salt stress conditions. Our findings also shed light on the evolution and classification of NBS-LRR genes in legumes, highlighting the potential of grass pea. Further research could focus on the functional analysis of these genes, and their potential use in breeding programs to improve the salinity, drought, and disease resistance of this important crop. 2023-06-20 2023-11-02T13:27:52Z 2023-11-02T13:27:52Z Journal Article https://hdl.handle.net/10568/132671 en Open Access application/pdf Frontiers Media S.A. Alsamman M. Alsamman, Khaled H. Mousa, Ahmed E. Nassar, Mostafa M. Faheem, Khaled Radwan, Monica Adly, Ahmed Ahmed, Tawffiq Istanbuli, Morad M. Mokhtar, Tamer Ahmed Elakkad, Zakaria Kehel, Aladdin Hamwieh, Mohamed Abdelsattar, Achraf El Allali. (20/6/2023). Identification, characterization, and validation of NBS-encoding genes in grass pea. Frontiers in Genetics, 14. |
| spellingShingle | legumes gene expression biotic stress abiotic stress identification grass pea (lathyrus sativus) nbs grass pea (lathyrus sativus l) genome wide analysis real time—pcr Alsamman, Alsamman M. Mousa, Khaled H. Nassar, Ahmed E. M. Faheem, Mostafa Radwan, Khaled Adly, Monica Ahmed, Ahmed Istanbuli, Tawffiq Mokhtar, Morad M. Ahmed Elakkad, Tamer Kehel, Zakaria Hamwieh, Aladdin Abdelsattar, Mohamed El Allali, Achraf Identification, characterization, and validation of NBS-encoding genes in grass pea |
| title | Identification, characterization, and validation of NBS-encoding genes in grass pea |
| title_full | Identification, characterization, and validation of NBS-encoding genes in grass pea |
| title_fullStr | Identification, characterization, and validation of NBS-encoding genes in grass pea |
| title_full_unstemmed | Identification, characterization, and validation of NBS-encoding genes in grass pea |
| title_short | Identification, characterization, and validation of NBS-encoding genes in grass pea |
| title_sort | identification characterization and validation of nbs encoding genes in grass pea |
| topic | legumes gene expression biotic stress abiotic stress identification grass pea (lathyrus sativus) nbs grass pea (lathyrus sativus l) genome wide analysis real time—pcr |
| url | https://hdl.handle.net/10568/132671 |
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