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| Status |
Public on Apr 25, 2018 |
| Title |
Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [RNA-seq] |
| Organisms |
Oryza rufipogon; Oryza sativa; Oryza nivara; Oryza sativa Indica Group; Oryza sativa aus subgroup |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
MicroRNAs (miRNAs) are a class of 21 nt non-coding small RNAs (sRNAs) produced from endogenously expressed MIR genes. MiRNAs are mostly involved in development and disease resistance. To know the involvement of miRNAs during domestication of rice, sRNA sequencing of two wild species (O. nivara and O. rufipogon), one landrace (O. sativa chomala) and one cultivated species of rice (O. sativa indica Pusa Basmati-1) was carried out. Analysis of sRNA datasets revealed a surprisingly higher abundance of 22nt sRNAs originating from a loci on Chromosome 2 in wild rice species. This locus codes for a 22 nt miRNA named as miR397. Studies in Arabidopsis and O. sativa japonica nipponbare have shown that miR397 targets a group of proteins called laccases, which are involved in secondary metabolite (lignin) production. The expression of these targets also differs across the species shown through RNA-Seq analysis. Although a functional significance of this interaction between the miRNA and laccase has not been understood. In the current study we attempt to explain the functional relevance of the miRNA in domestication of rice.
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| Overall design |
We have performed RNA seq analysis using reproductive tissues (flagleaf and panicle) of various rice species. Libraries were prepared from total RNA isolated from the tissues mentioned.
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| Contributor(s) |
Shivaprasad PV, Chenna S |
| Citation(s) |
30341147 |
| |
| Submission date |
Mar 05, 2018 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Shivaprasad Padubidri V. |
| E-mail(s) |
[email protected]
|
| Phone |
+91 80 2366 6511
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| Organization name |
National Center for Biological Sciences
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| Department |
Plant epigenetics
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| Street address |
GKVK Campus, Bellary road
|
| City |
Bangalore |
| ZIP/Postal code |
560065 |
| Country |
India |
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| Platforms (5)
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| GPL21087 |
Illumina NextSeq 500 (Oryza sativa) |
| GPL24693 |
Illumina NextSeq 500 (Oryza nivara) |
| GPL24694 |
Illumina NextSeq 500 (Oryza rufipogon) |
| GPL24959 |
Illumina NextSeq 500 (Oryza sativa Indica Group) |
| GPL24960 |
Illumina NextSeq 500 (Oryza sativa aus subgroup) |
|
| Samples (20)
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| This SubSeries is part of SuperSeries: |
| GSE111472 |
Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits |
|
| Relations |
| BioProject |
PRJNA437000 |
| SRA |
SRP133966 |
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