Tissue-Specific Expression Analysis and Functional Validation of <i>SiSCR</i> Genes in Foxtail Millet (<i>Setaria italica</i>) Under Hormone and Drought Stresses, and Heterologous Expression in <i>Arabidopsis</i>
The SCARECROW (SCR) transcription factor governs cell-type patterning in plant roots and Kranz anatomy of leaves, serving as a master regulator of root and shoot morphogenesis. Foxtail millet (<i>Setaria italica</i>), characterized by a compact genome, self-pollination, and a short growt...
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2025-07-01
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| author | Yingying Qin Ruifu Wang Shuwan Chen Qian Gao Yiru Zhao Shuo Chang Mao Li Fangfang Ma Xuemei Ren |
| author_facet | Yingying Qin Ruifu Wang Shuwan Chen Qian Gao Yiru Zhao Shuo Chang Mao Li Fangfang Ma Xuemei Ren |
| author_sort | Yingying Qin |
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| description | The SCARECROW (SCR) transcription factor governs cell-type patterning in plant roots and Kranz anatomy of leaves, serving as a master regulator of root and shoot morphogenesis. Foxtail millet (<i>Setaria italica</i>), characterized by a compact genome, self-pollination, and a short growth cycle, has emerged as a C<sub>4</sub> model plant. Here, we revealed two <i>SCR</i> paralogs in foxtail millet—<i>SiSCR1</i> and <i>SiSCR2</i>—which exhibit high sequence conservation with <i>ZmSCR1/1h</i> (<i>Zea mays</i>), <i>OsSCR1/2</i> (<i>Oryza sativa</i>), and <i>AtSCR</i> (<i>Arabidopsis thaliana</i>), particularly within the C-terminal GRAS domain. Both <i>SiSCR</i> genes exhibited nearly identical secondary structures and physicochemical profiles, with promoter analyses revealing five conserved <i>cis</i>-regulatory elements. Robust phylogenetic reconstruction resolved <i>SCR</i> orthologs into monocot- and dicot-specific clades, with <i>SiSCR</i> genes forming a sister branch to <i>SvSCR</i> from its progenitor species <i>Setaria viridis</i>. Spatiotemporal expression profiling demonstrated ubiquitous <i>SiSCR</i> gene transcription across developmental stages, with notable enrichment in germinated seeds, plants at the one-tip-two-leaf stage, leaf 1 (two days after heading), and roots during the seedling stage. Co-expression network analysis revealed that there is a correlation between <i>SiSCR</i> genes and other functional genes. Abscisic acid (ABA) treatment led to a significant downregulation of the expression level of <i>SiSCR</i> genes in Yugu1 roots, and the expression of the <i>SiSCR</i> genes in the roots of An04 is more sensitive to PEG6000 treatment. Drought treatment significantly upregulated <i>SiSCR2</i> expression in leaves, demonstrating its pivotal role in plant adaptation to abiotic stress. Analysis of heterologous expression under the control of the 35S promoter revealed that <i>SiSCR</i> genes were expressed in root cortical/endodermal initial cells, endodermal cells, cortical cells, and leaf stomatal complexes. Strikingly, ectopic expression of <i>SiSCR</i> genes in <i>Arabidopsis</i> led to hypersensitivity to ABA, and ABA treatment resulted in a significant reduction in the length of the meristematic zone. These data delineate the functional divergence and evolutionary conservation of <i>SiSCR</i> genes, providing critical insights into their roles in root/shoot development and abiotic stress signaling in foxtail millet. |
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| spelling | doaj-art-956175877e344714a3f797f165deb5782025-08-20T02:47:07ZengMDPI AGPlants2223-77472025-07-011414215110.3390/plants14142151Tissue-Specific Expression Analysis and Functional Validation of <i>SiSCR</i> Genes in Foxtail Millet (<i>Setaria italica</i>) Under Hormone and Drought Stresses, and Heterologous Expression in <i>Arabidopsis</i>Yingying Qin0Ruifu Wang1Shuwan Chen2Qian Gao3Yiru Zhao4Shuo Chang5Mao Li6Fangfang Ma7Xuemei Ren8Houji Laboratory in Shanxi Province, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, ChinaHouji Laboratory in Shanxi Province, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, ChinaHouji Laboratory in Shanxi Province, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, ChinaDepartment of Basic Sciences, Shanxi Agricultural University, Jinzhong 030801, ChinaCollege of Agriculture, Shanxi Agricultural University, Jinzhong 030801, ChinaHouji Laboratory in Shanxi Province, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, ChinaHouji Laboratory in Shanxi Province, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, ChinaCollege of Agriculture, Shanxi Agricultural University, Jinzhong 030801, ChinaHouji Laboratory in Shanxi Province, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, ChinaThe SCARECROW (SCR) transcription factor governs cell-type patterning in plant roots and Kranz anatomy of leaves, serving as a master regulator of root and shoot morphogenesis. Foxtail millet (<i>Setaria italica</i>), characterized by a compact genome, self-pollination, and a short growth cycle, has emerged as a C<sub>4</sub> model plant. Here, we revealed two <i>SCR</i> paralogs in foxtail millet—<i>SiSCR1</i> and <i>SiSCR2</i>—which exhibit high sequence conservation with <i>ZmSCR1/1h</i> (<i>Zea mays</i>), <i>OsSCR1/2</i> (<i>Oryza sativa</i>), and <i>AtSCR</i> (<i>Arabidopsis thaliana</i>), particularly within the C-terminal GRAS domain. Both <i>SiSCR</i> genes exhibited nearly identical secondary structures and physicochemical profiles, with promoter analyses revealing five conserved <i>cis</i>-regulatory elements. Robust phylogenetic reconstruction resolved <i>SCR</i> orthologs into monocot- and dicot-specific clades, with <i>SiSCR</i> genes forming a sister branch to <i>SvSCR</i> from its progenitor species <i>Setaria viridis</i>. Spatiotemporal expression profiling demonstrated ubiquitous <i>SiSCR</i> gene transcription across developmental stages, with notable enrichment in germinated seeds, plants at the one-tip-two-leaf stage, leaf 1 (two days after heading), and roots during the seedling stage. Co-expression network analysis revealed that there is a correlation between <i>SiSCR</i> genes and other functional genes. Abscisic acid (ABA) treatment led to a significant downregulation of the expression level of <i>SiSCR</i> genes in Yugu1 roots, and the expression of the <i>SiSCR</i> genes in the roots of An04 is more sensitive to PEG6000 treatment. Drought treatment significantly upregulated <i>SiSCR2</i> expression in leaves, demonstrating its pivotal role in plant adaptation to abiotic stress. Analysis of heterologous expression under the control of the 35S promoter revealed that <i>SiSCR</i> genes were expressed in root cortical/endodermal initial cells, endodermal cells, cortical cells, and leaf stomatal complexes. Strikingly, ectopic expression of <i>SiSCR</i> genes in <i>Arabidopsis</i> led to hypersensitivity to ABA, and ABA treatment resulted in a significant reduction in the length of the meristematic zone. These data delineate the functional divergence and evolutionary conservation of <i>SiSCR</i> genes, providing critical insights into their roles in root/shoot development and abiotic stress signaling in foxtail millet.https://www.mdpi.com/2223-7747/14/14/2151<i>Setaria italica</i>SCARECROWexpression patternabiotic stress signalingABA signalingbioinformatic analysis |
| spellingShingle | Yingying Qin Ruifu Wang Shuwan Chen Qian Gao Yiru Zhao Shuo Chang Mao Li Fangfang Ma Xuemei Ren Tissue-Specific Expression Analysis and Functional Validation of <i>SiSCR</i> Genes in Foxtail Millet (<i>Setaria italica</i>) Under Hormone and Drought Stresses, and Heterologous Expression in <i>Arabidopsis</i> Plants <i>Setaria italica</i> SCARECROW expression pattern abiotic stress signaling ABA signaling bioinformatic analysis |
| title | Tissue-Specific Expression Analysis and Functional Validation of <i>SiSCR</i> Genes in Foxtail Millet (<i>Setaria italica</i>) Under Hormone and Drought Stresses, and Heterologous Expression in <i>Arabidopsis</i> |
| title_full | Tissue-Specific Expression Analysis and Functional Validation of <i>SiSCR</i> Genes in Foxtail Millet (<i>Setaria italica</i>) Under Hormone and Drought Stresses, and Heterologous Expression in <i>Arabidopsis</i> |
| title_fullStr | Tissue-Specific Expression Analysis and Functional Validation of <i>SiSCR</i> Genes in Foxtail Millet (<i>Setaria italica</i>) Under Hormone and Drought Stresses, and Heterologous Expression in <i>Arabidopsis</i> |
| title_full_unstemmed | Tissue-Specific Expression Analysis and Functional Validation of <i>SiSCR</i> Genes in Foxtail Millet (<i>Setaria italica</i>) Under Hormone and Drought Stresses, and Heterologous Expression in <i>Arabidopsis</i> |
| title_short | Tissue-Specific Expression Analysis and Functional Validation of <i>SiSCR</i> Genes in Foxtail Millet (<i>Setaria italica</i>) Under Hormone and Drought Stresses, and Heterologous Expression in <i>Arabidopsis</i> |
| title_sort | tissue specific expression analysis and functional validation of i siscr i genes in foxtail millet i setaria italica i under hormone and drought stresses and heterologous expression in i arabidopsis i |
| topic | <i>Setaria italica</i> SCARECROW expression pattern abiotic stress signaling ABA signaling bioinformatic analysis |
| url | https://www.mdpi.com/2223-7747/14/14/2151 |
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