Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)
Abstract Background Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human health. However, research on the foxtail millet SPL (SQUAMOSA PROMOTE...
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| Format: | Article |
| Language: | English |
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BMC
2022-05-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08633-2 |
| _version_ | 1818240873837625344 |
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| author | Dili Lai Yue Fan Guoxing Xue Ailing He Hao Yang Chunlin He Yijing Li Jingjun Ruan Jun Yan Jianping Cheng |
| author_facet | Dili Lai Yue Fan Guoxing Xue Ailing He Hao Yang Chunlin He Yijing Li Jingjun Ruan Jun Yan Jianping Cheng |
| author_sort | Dili Lai |
| collection | DOAJ |
| description | Abstract Background Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human health. However, research on the foxtail millet SPL (SQUAMOSA PROMOTER BINDING-LIKE) gene family is limited. Results In this study, a total of 18 SPL genes were identified for the comprehensive analysis of the whole genome of foxtail millet. These SiSPL genes were divided into seven subfamilies (I, II, III, V, VI, VII, and VIII) according to the classification of the Arabidopsis thaliana SPL gene family. Structural analysis of the SiSPL genes showed that the number of introns in subfamilies I and II were much larger than others, and the promoter regions of SiSPL genes were rich in different cis-acting elements. Among the 18 SiSPL genes, nine genes had putative binding sites with foxtail millet miR156. No tandem duplication events were found between the SiSPL genes, but four pairs of segmental duplications were detected. The SiSPL genes expression were detected in different tissues, which was generally highly expressed in seeds development process, especially SiSPL6 and SiSPL16, which deserve further study. The results of the expression levels of SiSPL genes under eight types of abiotic stresses showed that many stress responsive genes, especially SiSPL9, SiSPL10, and SiSPL16, were highly expressed under multiple stresses, which deserves further attention. Conclusions In this research, 18 SPL genes were identified in foxtail millet, and their phylogenetic relationships, gene structural features, duplication events, gene expression and potential roles in foxtail millet development were studied. The findings provide a new perspective for the mining of the excellent SiSPL gene and the molecular breeding of foxtail millet. |
| first_indexed | 2024-12-12T13:20:22Z |
| format | Article |
| id | doaj.art-f79f87092d324777aa37504c613476a1 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T13:20:22Z |
| publishDate | 2022-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-f79f87092d324777aa37504c613476a12022-12-22T00:23:20ZengBMCBMC Genomics1471-21642022-05-0123112010.1186/s12864-022-08633-2Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)Dili Lai0Yue Fan1Guoxing Xue2Ailing He3Hao Yang4Chunlin He5Yijing Li6Jingjun Ruan7Jun Yan8Jianping Cheng9College of Agriculture, Guizhou UniversityCollege of Food Science and Engineering, Xinjiang Institute of TechnologyCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Coastal Agricultural Sciences, Guangdong Ocean UniversityHenan Cancer HospitalCollege of Agriculture, Guizhou UniversitySchool of Food and Biological Engineering, Chengdu UniversityCollege of Agriculture, Guizhou UniversityAbstract Background Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human health. However, research on the foxtail millet SPL (SQUAMOSA PROMOTER BINDING-LIKE) gene family is limited. Results In this study, a total of 18 SPL genes were identified for the comprehensive analysis of the whole genome of foxtail millet. These SiSPL genes were divided into seven subfamilies (I, II, III, V, VI, VII, and VIII) according to the classification of the Arabidopsis thaliana SPL gene family. Structural analysis of the SiSPL genes showed that the number of introns in subfamilies I and II were much larger than others, and the promoter regions of SiSPL genes were rich in different cis-acting elements. Among the 18 SiSPL genes, nine genes had putative binding sites with foxtail millet miR156. No tandem duplication events were found between the SiSPL genes, but four pairs of segmental duplications were detected. The SiSPL genes expression were detected in different tissues, which was generally highly expressed in seeds development process, especially SiSPL6 and SiSPL16, which deserve further study. The results of the expression levels of SiSPL genes under eight types of abiotic stresses showed that many stress responsive genes, especially SiSPL9, SiSPL10, and SiSPL16, were highly expressed under multiple stresses, which deserves further attention. Conclusions In this research, 18 SPL genes were identified in foxtail millet, and their phylogenetic relationships, gene structural features, duplication events, gene expression and potential roles in foxtail millet development were studied. The findings provide a new perspective for the mining of the excellent SiSPL gene and the molecular breeding of foxtail millet.https://doi.org/10.1186/s12864-022-08633-2Setaria italicaSPLGenome-wideAbiotic stress |
| spellingShingle | Dili Lai Yue Fan Guoxing Xue Ailing He Hao Yang Chunlin He Yijing Li Jingjun Ruan Jun Yan Jianping Cheng Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica) BMC Genomics Setaria italica SPL Genome-wide Abiotic stress |
| title | Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica) |
| title_full | Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica) |
| title_fullStr | Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica) |
| title_full_unstemmed | Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica) |
| title_short | Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica) |
| title_sort | genome wide identification and characterization of the spl gene family and its expression in the various developmental stages and stress conditions in foxtail millet setaria italica |
| topic | Setaria italica SPL Genome-wide Abiotic stress |
| url | https://doi.org/10.1186/s12864-022-08633-2 |
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