Integrated analysis of transcriptome, sRNAome, and degradome involved in the drought-response of maize Zhengdan958
Drought is a major abiotic stress in restricting the growth, development, and yield of maize. As a significant epigenetic regulator, small RNA also functions in connecting the transcriptional and post-transcriptional regulatory network. Further to help comprehending the molecular mechanisms underlyi...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2025-01-01
|
| Series: | Open Life Sciences |
| Subjects: | |
| Online Access: | https://doi.org/10.1515/biol-2022-1044 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832570515979501568 |
|---|---|
| author | Yang Shuqiong Liu Jiafei Cao Lingling Chen Jibao Duan Pengfei |
| author_facet | Yang Shuqiong Liu Jiafei Cao Lingling Chen Jibao Duan Pengfei |
| author_sort | Yang Shuqiong |
| collection | DOAJ |
| description | Drought is a major abiotic stress in restricting the growth, development, and yield of maize. As a significant epigenetic regulator, small RNA also functions in connecting the transcriptional and post-transcriptional regulatory network. Further to help comprehending the molecular mechanisms underlying drought adaptability and tolerance of maize, an integrated multi-omics analysis of transcriptome, sRNAome, and degradome was performed on the seedling roots of an elite hybrid Zhengdan958 under drought stress. In this study, 2,911 genes, 32 conserved miRNAs, and 12 novel miRNAs showed a significantly differential expression under drought stress. Moreover, 6,340 target genes of 445 miRNAs were validated using degradome sequencing, forming 281 miRNA–mRNA pairs in control (CK) and drought-stressed (DS) library. These target genes were mainly involved in the plant hormone signal transduction and phenylpropanoid biosynthesis pathways. The integrated multi-omics analysis revealed that five DEmiRNA–mRNA pairs displayed negatively correlated expression patterns, which were also verified by qRT-PCR. Tissue-specific expression profile and regulatory network analysis revealed that miR528a/b-Zm00001d021850, miR408a/b-Zm00001d020794, and miR164e-Zm00001d003414 might be essential in root-specific drought stress response of maize Zhengdan958 seedlings. These worthwhile will promote the functional characterization of miRNA–mRNA modules response to drought stress, and potentially contribute to drought-resistance breeding of maize. |
| format | Article |
| id | doaj-art-9c7c6de685f444da91243b3bf4538b42 |
| institution | Kabale University |
| issn | 2391-5412 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Open Life Sciences |
| spelling | doaj-art-9c7c6de685f444da91243b3bf4538b422025-02-02T15:44:51ZengDe GruyterOpen Life Sciences2391-54122025-01-0120165629410.1515/biol-2022-1044Integrated analysis of transcriptome, sRNAome, and degradome involved in the drought-response of maize Zhengdan958Yang Shuqiong0Liu Jiafei1Cao Lingling2Chen Jibao3Duan Pengfei4Henan Provincial Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North Diversion Project, Nanyang Normal University, Nanyang, 473061, ChinaHenan Provincial Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North Diversion Project, Nanyang Normal University, Nanyang, 473061, ChinaHenan Provincial Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North Diversion Project, Nanyang Normal University, Nanyang, 473061, ChinaHenan Provincial Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North Diversion Project, Nanyang Normal University, Nanyang, 473061, ChinaHenan Provincial Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North Diversion Project, Nanyang Normal University, Nanyang, 473061, ChinaDrought is a major abiotic stress in restricting the growth, development, and yield of maize. As a significant epigenetic regulator, small RNA also functions in connecting the transcriptional and post-transcriptional regulatory network. Further to help comprehending the molecular mechanisms underlying drought adaptability and tolerance of maize, an integrated multi-omics analysis of transcriptome, sRNAome, and degradome was performed on the seedling roots of an elite hybrid Zhengdan958 under drought stress. In this study, 2,911 genes, 32 conserved miRNAs, and 12 novel miRNAs showed a significantly differential expression under drought stress. Moreover, 6,340 target genes of 445 miRNAs were validated using degradome sequencing, forming 281 miRNA–mRNA pairs in control (CK) and drought-stressed (DS) library. These target genes were mainly involved in the plant hormone signal transduction and phenylpropanoid biosynthesis pathways. The integrated multi-omics analysis revealed that five DEmiRNA–mRNA pairs displayed negatively correlated expression patterns, which were also verified by qRT-PCR. Tissue-specific expression profile and regulatory network analysis revealed that miR528a/b-Zm00001d021850, miR408a/b-Zm00001d020794, and miR164e-Zm00001d003414 might be essential in root-specific drought stress response of maize Zhengdan958 seedlings. These worthwhile will promote the functional characterization of miRNA–mRNA modules response to drought stress, and potentially contribute to drought-resistance breeding of maize.https://doi.org/10.1515/biol-2022-1044maizedrought stresstransciptomesrnaomedegradome |
| spellingShingle | Yang Shuqiong Liu Jiafei Cao Lingling Chen Jibao Duan Pengfei Integrated analysis of transcriptome, sRNAome, and degradome involved in the drought-response of maize Zhengdan958 Open Life Sciences maize drought stress transciptome srnaome degradome |
| title | Integrated analysis of transcriptome, sRNAome, and degradome involved in the drought-response of maize Zhengdan958 |
| title_full | Integrated analysis of transcriptome, sRNAome, and degradome involved in the drought-response of maize Zhengdan958 |
| title_fullStr | Integrated analysis of transcriptome, sRNAome, and degradome involved in the drought-response of maize Zhengdan958 |
| title_full_unstemmed | Integrated analysis of transcriptome, sRNAome, and degradome involved in the drought-response of maize Zhengdan958 |
| title_short | Integrated analysis of transcriptome, sRNAome, and degradome involved in the drought-response of maize Zhengdan958 |
| title_sort | integrated analysis of transcriptome srnaome and degradome involved in the drought response of maize zhengdan958 |
| topic | maize drought stress transciptome srnaome degradome |
| url | https://doi.org/10.1515/biol-2022-1044 |
| work_keys_str_mv | AT yangshuqiong integratedanalysisoftranscriptomesrnaomeanddegradomeinvolvedinthedroughtresponseofmaizezhengdan958 AT liujiafei integratedanalysisoftranscriptomesrnaomeanddegradomeinvolvedinthedroughtresponseofmaizezhengdan958 AT caolingling integratedanalysisoftranscriptomesrnaomeanddegradomeinvolvedinthedroughtresponseofmaizezhengdan958 AT chenjibao integratedanalysisoftranscriptomesrnaomeanddegradomeinvolvedinthedroughtresponseofmaizezhengdan958 AT duanpengfei integratedanalysisoftranscriptomesrnaomeanddegradomeinvolvedinthedroughtresponseofmaizezhengdan958 |