Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress
Abstract Background Broomcorn millet is a drought-tolerant cereal that is widely cultivated in the semiarid regions of Asia, Europe, and other continents; however, the mechanisms underlying its drought-tolerance are poorly understood. The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a lar...
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| Format: | Article |
| Language: | English |
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BMC
2020-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-020-6479-2 |
| _version_ | 1818934342386188288 |
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| author | Zhongying Shan Yanmiao Jiang Haiquan Li Jinjie Guo Ming Dong Jianan Zhang Guoqing Liu |
| author_facet | Zhongying Shan Yanmiao Jiang Haiquan Li Jinjie Guo Ming Dong Jianan Zhang Guoqing Liu |
| author_sort | Zhongying Shan |
| collection | DOAJ |
| description | Abstract Background Broomcorn millet is a drought-tolerant cereal that is widely cultivated in the semiarid regions of Asia, Europe, and other continents; however, the mechanisms underlying its drought-tolerance are poorly understood. The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family that is involved in the regulation of tissue development and abiotic stress. To date, NAC transcription factors have not been systematically researched in broomcorn millet. Results In the present study, a total of 180 NAC (PmNAC) genes were identified from the broomcorn millet genome and named uniformly according to their chromosomal distribution. Phylogenetic analysis demonstrated that the PmNACs clustered into 12 subgroups, including the broomcorn millet-specific subgroup Pm_NAC. Gene structure and protein motif analyses indicated that closely clustered PmNAC genes were relatively conserved within each subgroup, while genome mapping analysis revealed that the PmNAC genes were unevenly distributed on broomcorn millet chromosomes. Transcriptome analysis revealed that the PmNAC genes differed greatly in expression in various tissues and under different drought stress durations. The expression of 10 selected genes under drought stress was analyzed using quantitative real-time PCR. Conclusion In this study, 180 NAC genes were identified in broomcorn millet, and their phylogenetic relationships, gene structures, protein motifs, chromosomal distribution, duplication, expression patterns in different tissues, and responses to drought stress were studied. These results will be useful for the further study of the functional characteristics of PmNAC genes, particularly with regards to drought resistance. |
| first_indexed | 2024-12-20T05:02:45Z |
| format | Article |
| id | doaj.art-10a93b6229c14150b5dd80ecc2ae9208 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-20T05:02:45Z |
| publishDate | 2020-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-10a93b6229c14150b5dd80ecc2ae92082022-12-21T19:52:29ZengBMCBMC Genomics1471-21642020-01-0121111310.1186/s12864-020-6479-2Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stressZhongying Shan0Yanmiao Jiang1Haiquan Li2Jinjie Guo3Ming Dong4Jianan Zhang5Guoqing Liu6Institute of Millet Crops, Hebei Academy of Agriculture and Forestry SciencesInstitute of Millet Crops, Hebei Academy of Agriculture and Forestry SciencesInstitute of Millet Crops, Hebei Academy of Agriculture and Forestry SciencesInstitute of Millet Crops, Hebei Academy of Agriculture and Forestry SciencesInstitute of Millet Crops, Hebei Academy of Agriculture and Forestry SciencesInstitute of Millet Crops, Hebei Academy of Agriculture and Forestry SciencesInstitute of Millet Crops, Hebei Academy of Agriculture and Forestry SciencesAbstract Background Broomcorn millet is a drought-tolerant cereal that is widely cultivated in the semiarid regions of Asia, Europe, and other continents; however, the mechanisms underlying its drought-tolerance are poorly understood. The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family that is involved in the regulation of tissue development and abiotic stress. To date, NAC transcription factors have not been systematically researched in broomcorn millet. Results In the present study, a total of 180 NAC (PmNAC) genes were identified from the broomcorn millet genome and named uniformly according to their chromosomal distribution. Phylogenetic analysis demonstrated that the PmNACs clustered into 12 subgroups, including the broomcorn millet-specific subgroup Pm_NAC. Gene structure and protein motif analyses indicated that closely clustered PmNAC genes were relatively conserved within each subgroup, while genome mapping analysis revealed that the PmNAC genes were unevenly distributed on broomcorn millet chromosomes. Transcriptome analysis revealed that the PmNAC genes differed greatly in expression in various tissues and under different drought stress durations. The expression of 10 selected genes under drought stress was analyzed using quantitative real-time PCR. Conclusion In this study, 180 NAC genes were identified in broomcorn millet, and their phylogenetic relationships, gene structures, protein motifs, chromosomal distribution, duplication, expression patterns in different tissues, and responses to drought stress were studied. These results will be useful for the further study of the functional characteristics of PmNAC genes, particularly with regards to drought resistance.https://doi.org/10.1186/s12864-020-6479-2Broomcorn milletNAC genesGene expressionDrought stress |
| spellingShingle | Zhongying Shan Yanmiao Jiang Haiquan Li Jinjie Guo Ming Dong Jianan Zhang Guoqing Liu Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress BMC Genomics Broomcorn millet NAC genes Gene expression Drought stress |
| title | Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress |
| title_full | Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress |
| title_fullStr | Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress |
| title_full_unstemmed | Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress |
| title_short | Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress |
| title_sort | genome wide analysis of the nac transcription factor family in broomcorn millet panicum miliaceum l and expression analysis under drought stress |
| topic | Broomcorn millet NAC genes Gene expression Drought stress |
| url | https://doi.org/10.1186/s12864-020-6479-2 |
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