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Genome-wide lncRNAs identification and meta-analysis for cold-responsive genes at the booting stage in rice (Oryza sativa L)

ABSTRACT: Long non-coding RNAs (lncRNAs) are essential regulators of a broad range of biological processes in plants. Spectacular progress in next-generation sequencing technologies has enabled genome-wide identification of lncRNAs in multiple plant species. In this study, genome-wide lncRNA sequencing technology was used to identify cold-responsive lncRNAs at the booting stage in rice by comparison of a tolerant variety, Kongyu131 (KY131), and a sensitive variety, Dongnong422 (DN422). GO and KEGG enrichment analysis were performed, focusing on the cis- and trans- target genes of differential lncRNAs. To identify cold-responsive genes, a meta-analysis was used to integrate cold-tolerant QTLs at the booting stage. In total, 13 cold-responsive target genes were obtained by KEGG enrichment analysis combined with meta-analysis, as confirmed by qRT-PCR. Finally, three of these genes were identified in response to cold stress. These results sought to provide new insight into cold-resistance research for rice.

ORGANISM(S): Oryza sativa

PROVIDER: GSE123900 | GEO | 2018/12/15

REPOSITORIES: GEO

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Project description:Background: Glyphosate has become the most widely used herbicide in the world. Therefore, the development of new glyphosate-tolerant varieties is a research focus of seed companies and researchers. The glyphosate stress-responsive genes were used for the development of genetically modified crops, while only the EPSPS gene has been used currently in the study on glyphosate-tolerance in rice. Therefore, it is essential and crucial to intensify the exploration of glyphosate stress-responsive genes, to not only acquire otherglyphosate stress-responsive genes with clean intellectual property rights but also obtain non-transgenic glyphosate-tolerant rice varieties. This study is expected to elucidate the responses of miRNAs, lncRNAs, and mRNAs to glyphosate applications and the potential regulatory mechanisms in response to glyphosate stress in rice. Results: Leaves of the non-transgenic glyphosate-tolerant germplasm CA21 sprayed with 2 mg•ml-1 glyphosate (GLY) and CA21 plants with no spray (CK) were collected for high-throughput sequencing analysis. A total of 1197 DEGs, 131 DELs, and 52 DEMs were identified in the GLY samples in relation to CK samples. Genes were significantly enriched for various biological processes involved in detoxification of plant response to stress. A total of 385 known miRNAs from 59 miRNA families and 94 novel miRNAs were identified. Degradome analysis led to the identification of 32 target genes, of which, the squamosa promoter-binding-like protein 12 (SPL12) was identified as a target of osa-miR156a_L+1. The lncRNA-miRNA-mRNA regulatory network consisted of osa-miR156a_L+1, two transcripts of SPL12 (LOC_Os06g49010.3 and LOC_Os06g49010.5), and 13 lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1). Conclusion: Large-scale expression changes in coding and noncoding RNA were observed in rice mainly due to its response to glyphosate. SPL12, osa-miR156, and lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1) could be a novel ceRNA mechanism in response to glyphosate stress in rice.

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Genome-wide lncRNAs identification and meta-analysis for cold-responsive genes at the booting stage in rice (Oryza sativa L)

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