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| Status |
Public on Jul 30, 2016 |
| Title |
MicroRNA and mRNA expression profiling analysis revealed the regulation of plant height in Gossypium hirsutum |
| Organism |
Gossypium hirsutum |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Background: Dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and also desirable source for breeding the machine harvest varieties. In an effort to uncover the transcripts and miRNA networks involved in plant height, the transcriptome and small RNA sequencing were performed based on dwarf mutant Ari1327 (A1), tall-culm mutant Ari3697 (A3) and wild type Ari971 (A9) in Gossypium hirsutum.
Results: The transcriptome sequencing analysis showed that the enriched pathways of top 3 differentially expressed genes (DEGs) were categorized as carotenoid biosynthesis, plant-pathogen interaction and plant hormone signal transduction in both A1-A9 and A3-A9. The ABA and IAA related factors were differentially expressed in the mutants. Importantly, we found the lower expressed SAUR and elevated expressed GH3, and ABA related genes such as NCED and PP2C maybe relate to reduced growth of the plant height in Ari1327 which is consistent with the higher auxin and ABA content in this mutant. Furthermore, miRNA160 targeted to the auxin response factor (ARF) and miRNA166 (gma-miR166u and gma-miR166h-3p) targeted to ABA responsive element binding factor were related to the mutation in cotton. We have noticed that the cell growth related factors (smg7 targeted by gra-miR482 and 6 novel miRNAs and Pectatelyases targeted by osa-miR159f), the redox reactions related factors (Cytochrome P450 targeted by miR172) and MYB genes targeted by miR828, miR858 and miR159 were also involved in plant height of the cotton mutants. A total of 226 conserved miRNAs representing 32 known miRNA families were obtained, and 38 novel miRNAs corresponding to 23 unique RNA sequences were identified. Total 531 targets for 211 conserved miRNAs were obtained. Using PAREsnip, 27 and 29 miRNA/target conserved interactions were validated in A1-A9 and A3-A9, respectively. Furthermore, miRNA160, miRNA858 and miRNA172 were validated to be up-regulated in A1-A9 but down-regulated in A3-A9, whereas miRNA159 showed the opposite regulation.
Conclusions: This comprehensive interaction of the transcriptome and miRNA at tall-culmand dwarf mutant led to the discovery of regulatory mechanisms in plant height. It also provides the basis for in depth analyses of dwarf mutant genes for further breeding of dwarf cotton.
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| Overall design |
Total RNA was purified from stem apexes of three samples at the fifth true leaf stages and sequenced deeply using Illumina HiSeq 2000 system.
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| Contributor(s) |
Du X, Gong W |
| Citation(s) |
26517985 |
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| Submission date |
Jul 31, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Du Xiongming |
| E-mail(s) |
[email protected]
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| Organization name |
Institute of cotton research of CAAS
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| Street address |
38# Huanghe Avenue
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| City |
Anyang |
| State/province |
Henan |
| ZIP/Postal code |
455000 |
| Country |
China |
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| Platforms (1) |
| GPL16485 |
Illumina HiSeq 2000 (Gossypium hirsutum) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA291612 |
| SRA |
SRP061885 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE71608_RAW.tar |
20.0 Mb |
(http)(custom) |
TAR (of FA, TXT) |
| GSE71608_Unigene.fa.gz |
20.1 Mb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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