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An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [transcriptome]

ABSTRACT: Cadmium (Cd) influence in rice is a growing global environmental concern. Although many miRNAs and target genes have been identified in rice exposure to Cd stress, no comprehensive study has been done comprising integrative analysis of small RNAs, degradome and trascriptome sequencing to identify Cd-regulated miRNAs and their targets under Cd stress. In this study, 40 miRNAs including 38 known miRNAs representing 22 miRNA families and 2 novel miRNAs were substantially altered in response to Cd exposure. 18 differentially altered target genes were inversely correlated with 18 Cd responsive miRNAs. Majority of these targeted genes are transcript factors such as Auxin response factor 13 (ARF13), Scarecrow-like protein 6 (SCL6), Squamosa promoter-binding-like proteins (SPLs), Nuclear transcription factor Y subunit A-6 (NFYA6), Gibberellin-dependent avian myeloblastosis virus oncogene (GAMYB) and No apical meristem protein domain containing proteins (NACs), most of which were involved in signal transduction such as abscisic acid (ABA), Auxin, Gibberellin acid (GA) and MAPK (Mitogen-activated protein kinase). Functional analysis revealed that genes involved in photosynthesis pathway (osa00196, osa00195 and osa00710) and protein degradation pathway (osa04612) were identified to be participated in response to Cd in rice, including osa-miR156I-5p_R-1/SPLs, osa-miR171a_1ss12CT/DEGP10 and osa-miR169r-5p_R/NFYA6 circuits, respectively. We conclude that a combination of transcriptome, sRNAs and the degradome would confer a useful approach to investigate miRNA-mediated molecular mechanisms underlying plant response to Cd stress.

ORGANISM(S): Oryza sativa

PROVIDER: GSE116214 | GEO | 2021/06/24

REPOSITORIES: GEO

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Project description:Enhancing grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human being. One approach to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. microRNAs (miRNAs) are key regulators for aging and cellular senescence in eukayotes. However, miRNAs and their roles in rice leaf senescence remain unexplored. Here, we report identification of miRNAs and their putative target genes by deep sequencing of six small RNA libraries, six RNA-seq libraries and two degradome libraries from the leaves of two super hybrid rice, Nei-2-You 6 (N2Y6, age-resistant rice) and Liang-You-Pei 9 (LYP9, age-sensitive rice). Totally 372 known miRNAs and 162 miRNA candidates were identified, and 1145 targets were identified. Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), Auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding. [miRNA] sample 1:The flag leaves at early stage of grain-filling of N2Y6 rice; sample 2: The flag leaves at middle stage of grain-filling of N2Y6 rice;sample 3:The flag leaves at late stage of grain-filling of N2Y6 rice; sample 4:The flag leaves at early stage of grain-filling of LYP9 rice; sample 5: The flag leaves at middle stage of grain-filling of LYP9 rice;sample 6:The flag leaves at late stage of grain-filling of LYP9 rice. [DGE]: samples 7-12 [degradome (targets)]: samples 13:The flag leaves at mixed stages of grain-filling of N2Y6 rice; sample 14:The flag leaves at mixed stages of grain-filling of LYP9 rice

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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An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [transcriptome]

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