Oryza
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA478144 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7445560_1.fastq.gz | Fastqsanger.gz | |||
| SRR7445560_2.fastq.gz | Fastqsanger.gz | |||
| SRR7445570_1.fastq.gz | Fastqsanger.gz | |||
| SRR7445570_2.fastq.gz | Fastqsanger.gz | |||
| SRR7445580_1.fastq.gz | Fastqsanger.gz |
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Project description:Improving the yield by modifying plant architecture is key to progressive crop domestication. Here, we show that a 110-kb deletion on the short arm of chromosome 7 promotes the critical transition from semi-prostrate growth and low yield in wild rice (Oryza rufipogon), to erect growth and high yield in Asian cultivated rice (O. sativa). The microdeletion harbors a tandem repeat of seven putative Cys2-His2 zinc-finger genes. Three of these genes regulate the plant architecture in O. rufipogon and are closely linked to the previously identified PROSTRATE GROWTH 1 (PROG1) gene. Therefore, we refer to this locus as RICE PLANT ARCHITECTURE DOMESTICATION (RPAD). Furthermore, a similar but independent 113-kb deletion was detected at the RPAD locus in African cultivated rice. These results indicate that the deletions, coupled with the loss of a tandem repeat of zinc-finger genes, drove the parallel domestication of plant architecture in Asian and African rice.
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Project description:Changes in patterns of gene expression are believed to be responsible for the phenotypic differences within and between species. Although the evolutionary significance of functional mutations has been emphasized in rice domestication, little is known about the differences in gene regulation underlying the phenotypic diversification among rice varieties. MicroRNAs (miRNAs) are small regulatory RNAs that play crucial roles in regulating post-transcriptional gene expression. Here, we studied the variation in the expression of both miRNAs and mRNA transcripts in three indica and three japonica rice varieties using RNA sequencing (RNA-seq) to examine the miRNA regulatory effect on target gene expression in rice. In total, 71.0%, 9.2%, and 1.5% of the expressed mature miRNAs showed tissue, subspecies, and tissue-subspecies interaction-biased expression. Most of these differentially expressed miRNAs are evolutionarily weakly conserved. To examine the miRNA regulatory effect on global gene expression under endogenous conditions, we performed pair-wise correlation coefficient analyses on the expression levels of 240 mature miRNAs and 1178 messenger RNAs (mRNAs) both globally and for each specific miRNA-mRNA pair. We found that the deeply conserved miRNAs can significantly decrease the target mRNA abundance. In addition, a total of 109 miRNA-mRNA pairs were identified as significantly correlated pairs (Adjusted p<0.01). Of those, 41 pairs showed positive correlations, while 68 pairs showed negative correlations. Functional analysis elucidated that these mRNAs belonged to different biological pathways that could regulate the stress response, metabolic processes, and rice development. In conclusion, the joint interrogation of miRNA and mRNA expression profiles in this study proved useful for the study of the role of miRNA expression and regulation in the plant transcriptome.
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Project description: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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