Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.)
Abstract Background Rice (Oryza sativa L.) is a food crop for humans worldwide. However, temperature has an effect during the vegetative and reproductive stages. In high-latitude regions where rice is cultivated, cold stress is a major cause of yield loss and plant death. Research has identified a g...
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BMC
2021-11-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-08104-0 |
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| author | Jia Liu Qinglin Meng Hongtao Xiang Fengmei Shi Ligong Ma Yichu Li Chunlai Liu Yu Liu Baohua Su |
| author_facet | Jia Liu Qinglin Meng Hongtao Xiang Fengmei Shi Ligong Ma Yichu Li Chunlai Liu Yu Liu Baohua Su |
| author_sort | Jia Liu |
| collection | DOAJ |
| description | Abstract Background Rice (Oryza sativa L.) is a food crop for humans worldwide. However, temperature has an effect during the vegetative and reproductive stages. In high-latitude regions where rice is cultivated, cold stress is a major cause of yield loss and plant death. Research has identified a group of plant-specific transcription factors, DNA binding with one zinc fingers (DOFs), with a diverse range of functions, including stress signaling and stress response during plant growth. The aim of this study was to identify Dof genes in two rice subspecies, indica and japonica, and screen for Dof genes that may be involved in cold tolerance during plant growth. Results A total of 30 rice Dofs (OsDofs) were identified using bioinformatics and genome-wide analyses and phylogenetically analyzed. The 30 OsDOFs were classified into six subfamilies, and 24 motifs were identified based on protein sequence alignment. The chromosome locations of OsDofs were determined and nine gene duplication events were identified. A joint phylogenetic analysis was performed on DOF protein sequences obtained from four monocotyledon species to examine the evolutionary relationship of DOF proteins. Expression profiling of OsDofs from two japonica cultivars (Longdao5, which is cold-tolerant, and Longjing11, which is cold-sensitive) revealed that OsDof1 and OsDof19 are cold-inducible genes. We examined the seed setting rates in OsDof1- and OsDof19-overexpression and RNAi lines and found that OsDof1 showed a response to cold stress. Conclusions Our investigation identified OsDof1 as a potential target for genetic breeding of rice with enhanced cold tolerance. |
| first_indexed | 2024-12-19T08:29:20Z |
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| id | doaj.art-0fa0a1081db8499c94c71079b31c93da |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-19T08:29:20Z |
| publishDate | 2021-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-0fa0a1081db8499c94c71079b31c93da2022-12-21T20:29:13ZengBMCBMC Genomics1471-21642021-11-0122111210.1186/s12864-021-08104-0Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.)Jia Liu0Qinglin Meng1Hongtao Xiang2Fengmei Shi3Ligong Ma4Yichu Li5Chunlai Liu6Yu Liu7Baohua Su8Institute of Plant Protection, Heilongjiang Academy of Agricultural SciencesInstitute of Plant Protection, Heilongjiang Academy of Agricultural SciencesInstitute of Farming and Cultivation, Heilongjiang Academy of Agricultural SciencesInstitute of Plant Protection, Heilongjiang Academy of Agricultural SciencesInstitute of Plant Protection, Heilongjiang Academy of Agricultural SciencesInstitute of Plant Protection, Heilongjiang Academy of Agricultural SciencesInstitute of Plant Protection, Heilongjiang Academy of Agricultural SciencesInstitute of Plant Protection, Heilongjiang Academy of Agricultural SciencesInstitute of Plant Protection, Heilongjiang Academy of Agricultural SciencesAbstract Background Rice (Oryza sativa L.) is a food crop for humans worldwide. However, temperature has an effect during the vegetative and reproductive stages. In high-latitude regions where rice is cultivated, cold stress is a major cause of yield loss and plant death. Research has identified a group of plant-specific transcription factors, DNA binding with one zinc fingers (DOFs), with a diverse range of functions, including stress signaling and stress response during plant growth. The aim of this study was to identify Dof genes in two rice subspecies, indica and japonica, and screen for Dof genes that may be involved in cold tolerance during plant growth. Results A total of 30 rice Dofs (OsDofs) were identified using bioinformatics and genome-wide analyses and phylogenetically analyzed. The 30 OsDOFs were classified into six subfamilies, and 24 motifs were identified based on protein sequence alignment. The chromosome locations of OsDofs were determined and nine gene duplication events were identified. A joint phylogenetic analysis was performed on DOF protein sequences obtained from four monocotyledon species to examine the evolutionary relationship of DOF proteins. Expression profiling of OsDofs from two japonica cultivars (Longdao5, which is cold-tolerant, and Longjing11, which is cold-sensitive) revealed that OsDof1 and OsDof19 are cold-inducible genes. We examined the seed setting rates in OsDof1- and OsDof19-overexpression and RNAi lines and found that OsDof1 showed a response to cold stress. Conclusions Our investigation identified OsDof1 as a potential target for genetic breeding of rice with enhanced cold tolerance.https://doi.org/10.1186/s12864-021-08104-0ColdDofExpression profilingRiceStress responseTranscription factor |
| spellingShingle | Jia Liu Qinglin Meng Hongtao Xiang Fengmei Shi Ligong Ma Yichu Li Chunlai Liu Yu Liu Baohua Su Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.) BMC Genomics Cold Dof Expression profiling Rice Stress response Transcription factor |
| title | Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.) |
| title_full | Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.) |
| title_fullStr | Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.) |
| title_full_unstemmed | Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.) |
| title_short | Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.) |
| title_sort | genome wide analysis of dof transcription factors and their response to cold stress in rice oryza sativa l |
| topic | Cold Dof Expression profiling Rice Stress response Transcription factor |
| url | https://doi.org/10.1186/s12864-021-08104-0 |
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