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Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [RNA-seq]

ABSTRACT: Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [RNA-seq]

PROVIDER: PRJNA437000 | ENA |

REPOSITORIES: ENA

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Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [Degradome]

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.

2020-09-30 | GSE118702 | GEO

Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [ncRNA-seq]

2018-04-25 | GSE111440 | GEO

Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [RNA-seq]

2018-04-25 | GSE111438 | GEO

Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits

Project description:Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits

| PRJNA437134 | ENA

Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [Degradome]

Project description:Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [Degradome]

| PRJNA486509 | ENA

Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [ncRNA-seq]

Project description:Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [ncRNA-seq]

| PRJNA437123 | ENA

Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-04-25 | GSE111472 | GEO

Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa

Project description:Laccases were proposed to catalyze the oxidative polymerization of monolignols. We identified 49 laccase gene models in Populus trichocarpa, of which 29 were predicted to be targets of ptr-miR397a. We overexpressed Ptr-MIR397a in transgenic P. trichocarpa. In each of all 9 transgenic lines tested, 17 PtrLACs were down-regulated as analyzed by RNA-seq. Transgenic lines with severe reduction in the expression of these laccase genes resulted in an approximately 40% decrease in the total laccase activity. Overexpression of Ptr-MIR397a in these transgenic lines also reduced lignin content, whereas levels of all monolignol biosynthetic gene transcripts remained unchanged. A hierarchical genetic regulatory network (GRN) built by a bottom-up Graphic Gaussian Model algorithm provides additional support for a role of ptr-miR397a as a negative regulator of laccases for lignin biosynthesis. Full transcriptome based differential gene expression in the overexpressed transgenics and protein domain analyses implicate previously unidentified transcription factors and their targets in an extended hierarchical GRN including ptr-miR397a and laccases that coregulate lignin biosynthesis in wood formation. Ptr-miR397a, laccases and other regulatory components of this network may provide additional strategies for genetic manipulation of lignin content. Total twelve trees were used. Those include nine individual transgenic trees for overexpressing Ptr-miR397a, as nine biological replicates, and three wild-type trees.

2014-01-17 | E-GEOD-54153 | biostudies-arrayexpress

Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa

2014-01-17 | GSE54153 | GEO

Genomic and transcriptomic analyses of valencia orange provide insights into its domestication and traits formation

Project description:Valencia orange (Citrus sinensis Osbeck), namely summer orange (SO), is a type of late-ripening sweet oranges, the ripening time of which is 4 to 5 months later than that of the middle-ripening common sweet orange (CO). The mastication of SO fruit pulp is worse than that of CO. To date, how the late-ripening and poor pulp mastication traits were domesticated in SO is unknown. In this study, 13 SO cultivars and 12 CO cultivars were used for whole-genome resequencing. Population genetic diversity analysis divided these 25 samples into SO and CO subgroups, respectively. There were 144 and 141 genes identified by selective sweep analysis to be strongly selected during SO and CO evolutionary processes, respectively. Based on gene functional annotation and pathway enrichment analysis, most of these selected genes in SO were related to resistance and lignin biosynthesis. Simultaneously, we comparatively analyzed the transcriptome profiles of the peel and pulp tissues among three SO cultivars and three CO cultivars, which also revealed the difference of lignin synthesis between SO and CO fruits. Moreover, according to the comparative analysis of the lignin content and the expressions of the genes related to lignin biosynthesis in SO and CO fruits, we suggested that lignin may play an important role in the pulp mastication trait of SO. In addition, a SNP molecular marker was developed to distinguish SO and CO. This study reveals that the mastication trait may be formed in the process of SO domestication, while the late-ripening trait may be formed in a genetic mutation event.

2021-08-26 | GSE164142 | GEO

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