An Integration of MicroRNA and Transcriptome Sequencing Analysis Reveal Regulatory Roles of miRNAs in Response to Chilling Stress in Wild Rice
A chromosome single segment substitution line (CSSL) DC90, which was generated by introgressing <i>CTS-12</i>, a locus derived from common wild rice (<i>Oryza rufipogon</i> Griff.), into the 9311 (<i>Oryza sativa</i> L. ssp. <i>indica</i>) background,...
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MDPI AG
2022-04-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/7/977 |
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| author | Wenlong Zhao Weiyu Xiao Jinliang Sun Mingxin Chen Mingqing Ma Yaqi Cao Weijian Cen Rongbai Li Jijing Luo |
| author_facet | Wenlong Zhao Weiyu Xiao Jinliang Sun Mingxin Chen Mingqing Ma Yaqi Cao Weijian Cen Rongbai Li Jijing Luo |
| author_sort | Wenlong Zhao |
| collection | DOAJ |
| description | A chromosome single segment substitution line (CSSL) DC90, which was generated by introgressing <i>CTS-12</i>, a locus derived from common wild rice (<i>Oryza rufipogon</i> Griff.), into the 9311 (<i>Oryza sativa</i> L. ssp. <i>indica</i>) background, exhibits a chilling tolerance phenotype under chilling stress. Here, an integration of microRNA (miRNA) deep sequencing and transcriptomic sequencing analysis was performed to explore the expression profiles of miRNAs and their target genes mediated by <i>CTS-12</i> under chilling stress, and to reveal the possible regulatory mechanisms of miRNAs that are involved in chilling tolerance. Integration analysis revealed that a number of differentially expressed miRNAs (DEMs) and putative target genes with different expression patterns and levels were identified in 9311 and DC90 under chilling stress. KEGG enrichment analysis revealed that the target genes that are regulated by chilling-induced miRNAs are involved in the regulation of various biological processes/pathways, including protein biosynthesis, redox process, photosynthetic process, and chloroplast development in two genotypes. CRISPR/Cas9 editing of the target genes of the key DEMs in a chilling tolerant rice variety Zhonghua 11 (ZH11) found that <i>LOC_Os11g48020</i> (<i>OsGL1-11</i>), one of the putative target genes of osa-miR1846a/b-5p and encoding a wax synthesis protein, is correlated with a chilling stress tolerance phenotype, implying osa-miR1846a/b-5p/<i>OsGL1-11</i> plays an important role in <i>CTS-12</i>-mediated chilling stress tolerance regulatory pathway(s). Therefore, we speculate that the <i>CTS-12</i> may regulate the key miRNA target genes in response to chilling stress by differential regulation of miRNAs in wild rice, thereby resulting in the variation of chilling tolerance phenotype between 9311 and DC90. |
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| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T11:30:47Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
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| series | Plants |
| spelling | doaj.art-ab261a0eea884fcc81f4c4d2fcd49e742023-11-30T23:51:44ZengMDPI AGPlants2223-77472022-04-0111797710.3390/plants11070977An Integration of MicroRNA and Transcriptome Sequencing Analysis Reveal Regulatory Roles of miRNAs in Response to Chilling Stress in Wild RiceWenlong Zhao0Weiyu Xiao1Jinliang Sun2Mingxin Chen3Mingqing Ma4Yaqi Cao5Weijian Cen6Rongbai Li7Jijing Luo8College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, ChinaCollege of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, ChinaCollege of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, ChinaCollege of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, ChinaCollege of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, ChinaCollege of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, ChinaCollege of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, ChinaAgriculture College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, ChinaCollege of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, ChinaA chromosome single segment substitution line (CSSL) DC90, which was generated by introgressing <i>CTS-12</i>, a locus derived from common wild rice (<i>Oryza rufipogon</i> Griff.), into the 9311 (<i>Oryza sativa</i> L. ssp. <i>indica</i>) background, exhibits a chilling tolerance phenotype under chilling stress. Here, an integration of microRNA (miRNA) deep sequencing and transcriptomic sequencing analysis was performed to explore the expression profiles of miRNAs and their target genes mediated by <i>CTS-12</i> under chilling stress, and to reveal the possible regulatory mechanisms of miRNAs that are involved in chilling tolerance. Integration analysis revealed that a number of differentially expressed miRNAs (DEMs) and putative target genes with different expression patterns and levels were identified in 9311 and DC90 under chilling stress. KEGG enrichment analysis revealed that the target genes that are regulated by chilling-induced miRNAs are involved in the regulation of various biological processes/pathways, including protein biosynthesis, redox process, photosynthetic process, and chloroplast development in two genotypes. CRISPR/Cas9 editing of the target genes of the key DEMs in a chilling tolerant rice variety Zhonghua 11 (ZH11) found that <i>LOC_Os11g48020</i> (<i>OsGL1-11</i>), one of the putative target genes of osa-miR1846a/b-5p and encoding a wax synthesis protein, is correlated with a chilling stress tolerance phenotype, implying osa-miR1846a/b-5p/<i>OsGL1-11</i> plays an important role in <i>CTS-12</i>-mediated chilling stress tolerance regulatory pathway(s). Therefore, we speculate that the <i>CTS-12</i> may regulate the key miRNA target genes in response to chilling stress by differential regulation of miRNAs in wild rice, thereby resulting in the variation of chilling tolerance phenotype between 9311 and DC90.https://www.mdpi.com/2223-7747/11/7/977wild ricechilling stresschilling tolerance locusmiRNA deep sequencingtranscriptomic profilingtarget genes |
| spellingShingle | Wenlong Zhao Weiyu Xiao Jinliang Sun Mingxin Chen Mingqing Ma Yaqi Cao Weijian Cen Rongbai Li Jijing Luo An Integration of MicroRNA and Transcriptome Sequencing Analysis Reveal Regulatory Roles of miRNAs in Response to Chilling Stress in Wild Rice Plants wild rice chilling stress chilling tolerance locus miRNA deep sequencing transcriptomic profiling target genes |
| title | An Integration of MicroRNA and Transcriptome Sequencing Analysis Reveal Regulatory Roles of miRNAs in Response to Chilling Stress in Wild Rice |
| title_full | An Integration of MicroRNA and Transcriptome Sequencing Analysis Reveal Regulatory Roles of miRNAs in Response to Chilling Stress in Wild Rice |
| title_fullStr | An Integration of MicroRNA and Transcriptome Sequencing Analysis Reveal Regulatory Roles of miRNAs in Response to Chilling Stress in Wild Rice |
| title_full_unstemmed | An Integration of MicroRNA and Transcriptome Sequencing Analysis Reveal Regulatory Roles of miRNAs in Response to Chilling Stress in Wild Rice |
| title_short | An Integration of MicroRNA and Transcriptome Sequencing Analysis Reveal Regulatory Roles of miRNAs in Response to Chilling Stress in Wild Rice |
| title_sort | integration of microrna and transcriptome sequencing analysis reveal regulatory roles of mirnas in response to chilling stress in wild rice |
| topic | wild rice chilling stress chilling tolerance locus miRNA deep sequencing transcriptomic profiling target genes |
| url | https://www.mdpi.com/2223-7747/11/7/977 |
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