Dataset Information

Deciphering the non-coding RNA-level response to arsenic stress in rice (Oryza sativa).

ABSTRACT: Arsenic (As) contamination in subsoil and groundwater is a big problem, especially in many South-East Asian countries. As a staple crop growing under flooded condition in these areas, rice (Oryza sativa L.) becomes a big threat to human health through the food chain since As is highly accumulated in grains. Thus, reducing As accumulation in rice through molecular breeding and identification of rice varieties with low As content are the pressing issues. However, the current understanding on the molecular mechanism of As stress response is still limited for rice. In this study, we performed a comprehensive search for the As-responsive small RNAs (sRNAs) of rice. Briefly, 4,762 and 18,152 sRNAs were identified to be highly activated under As stress in roots and shoots respectively, while 14,603 and 8,308 sRNAs were intensively repressed by As treatment in roots and shoots, respectively. A number of the As-responsive sRNAs found their loci on tRNAs, rRNAs or long non-coding RNAs (lncRNAs). Interestingly, these loci preferentially distributed on the 5' halves of the tRNA, rRNA or lncRNA precursors. Among the above-identified As-responsive sRNAs, 252 Argonaute 1 (AGO1)-enriched sRNAs were extracted for target identification, resulting in 200 pairs of sRNA-protein-coding target interactions. Many targets are functionally involved in the development, stress response, reproduction, or lipid metabolism. Additionally, 56 lncRNAs were discovered to be targeted by nine AGO1-enriched sRNAs, indicating the potential involvement of these lncRNAs in As signaling. Taken together, our results could expand the understanding on the non-coding RNA-mediated As stress response in rice.

SUBMITTER: Tang Z

PROVIDER: S-EPMC6768179 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Deciphering the non-coding RNA-level response to arsenic stress in rice (<i>Oryza sativa</i>).

Tang Zhonghai Z Xu Min M Ito Hidetaka H Cai Jiahui J Ma Xiaoxia X Qin Jingping J Yu Dongliang D Meng Yijun Y

Plant signaling & behavior 20190612 9

Arsenic (As) contamination in subsoil and groundwater is a big problem, especially in many South-East Asian countries. As a staple crop growing under flooded condition in these areas, rice (<i>Oryza sativa</i> L.) becomes a big threat to human health through the food chain since As is highly accumulated in grains. Thus, reducing As accumulation in rice through molecular breeding and identification of rice varieties with low As content are the pressing issues. However, the current understanding o ...[more]

PMID: 31187662

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Project description:BackgroundArsenic (As) is an unwanted toxic mineral that threatens the major rice-growing regions in the world, especially in South Asia. Rice production in Bangladesh and India depends on As-contaminated groundwater sources for irrigating paddy fields, resulting in elevated amounts of As in the topsoil. Arsenic accumulating in rice plants has a significant negative effect on human and animal health. Here, we present a quantitative trait locus (QTL) mapping study to identify candidate genes conferring As toxicity tolerance and accumulation in rice (Oryza sativa L.) seedlings. An early backcross breeding population consisting of 194 lines derived from a cross between WTR1 (indica) and Hao-an-nong (japonica) was grown in hydroponics for 25 days, from the seventh day exposed to an environmentally relevant concentration of 10 ppm As.ResultsArsenic toxicity leads to significantly negative plant responses, including reduced biomass, stunted plant growth, reduced leaf chlorophyll content, and increased shoot As concentration ranging from 9 to 20 mg kg- 1. Marker-trait association was determined for seven As-related traits using 704 single nucleotide polymorphism (SNP) markers generated from a 6 K SNP-array. One QTL was mapped on chromosome 1 for relative chlorophyll content, two QTLs for As content in roots were mapped on chromosome 8, and six QTLs for As content in shoots were mapped on chromosomes 2, 5, 6, and 9. Using the whole-genome sequence of the parents, we narrowed down the number of candidate genes associated with the QTL intervals based on the existence of a non-synonymous mutation in genes between the parental lines. Also, by using publicly available gene expression profiles for As stress, we further narrowed down the number of candidate genes in the QTL intervals by comparing the expression profiles of genes under As stress and control conditions. Twenty-five genes showing transcription regulation were considered as candidate gene nominees for As toxicity-related traits.ConclusionsOur study provides insight into the genetic basis of As tolerance and uptake in the early seedling stage of rice. Comparing our findings with the previously reported QTLs for As toxicity stress in rice, we identified some novel and co-localized QTLs associated with As stress. Also, the mapped QTLs harbor gene models of known function associated with stress responses, metal homeostasis, and transporter activity in rice. Overall, our findings will assist breeders with initial marker information to develop suitable varieties for As-contaminated ecosystems.

Project description:BACKGROUND:Nitrogen (N) is a key macronutrient essential for plant growth, and its availability has a strong influence on crop development. The application of synthetic N fertilizers on crops has increased substantially in recent decades; however, the applied N is not fully utilized due to the low N use efficiency of crops. To overcome this limitation, it is important to understand the genome-wide responses and functions of key genes and potential regulatory factors in N metabolism. RESULTS:Here, we characterized changes in the rice (Oryza sativa) transcriptome, including genes, newly identified putative long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) and their target mRNAs in response to N starvation using four different transcriptome approaches. Analysis of rice genes involved in N metabolism and/or transport using strand-specific RNA-Seq identified 2588 novel putative lncRNA encoding loci. Analysis of previously published RNA-Seq datasets revealed a group of N starvation-responsive lncRNAs showing differential expression under other abiotic stress conditions. Poly A-primed sequencing (2P-Seq) revealed alternatively polyadenylated isoforms of N starvation-responsive lncRNAs and provided precise 3' end information on the transcript models of these lncRNAs. Analysis of small RNA-Seq data identified N starvation-responsive miRNAs and down-regulation of miR169 family members, causing de-repression of NF-YA, as confirmed by strand-specific RNA-Seq and qRT-PCR. Moreover, we profiled the N starvation-responsive down-regulation of root-specific miRNA, osa-miR444a.4-3p, and Degradome sequencing confirmed MADS25 as a novel target gene. CONCLUSIONS:In this study, we used a combination of multiple RNA-Seq analyses to extensively profile the expression of genes, newly identified lncRNAs, and microRNAs in N-starved rice roots and shoots. Data generated in this study provide an in-depth understanding of the regulatory pathways modulated by N starvation-responsive miRNAs. The results of comprehensive, large-scale data analysis provide valuable information on multiple aspects of the rice transcriptome, which may be useful in understanding the responses of rice plants to changes in the N supply status of soil.

Project description:The present study investigated the role of graphitic carbon nitride (C3N4) in alleviating cadmium (Cd)- and arsenic (As)-induced phytotoxicity to rice (Oryza sativa L.). A high-temperature pyrolysis was used to synthesize the C3N4, which was characterized by transmission electron microscopy, Fourier-transform infrared spectroscopy, and dynamic light scattering. Rice seedlings were exposed to C3N4 at 50 and 250 mg/L in half-strength Hoagland's solution amended with or without 10 mg/L Cd or As for 14 days. Both Cd and As alone resulted in 26-38% and 49-56% decreases in rice root and shoot biomass, respectively. Exposure to 250 mg/L C3N4 alone increased the root and shoot fresh biomass by 17.5% and 25.9%, respectively. Upon coexposure, Cd + C3N4 and As + C3N4 alleviated the heavy metal-induced phytotoxicity and increased the fresh weight by 26-38% and 49-56%, respectively. Further, the addition of C3N4 decreased Cd and As accumulation in the roots by 32% and 25%, respectively, whereas the metal contents in the shoots were 30% lower in the presence of C3N4. Both As and Cd also significantly altered the macronutrient (K, P, Ca, S, and Mg) and micronutrient (Cu, Fe, Zn, and Mn) contents in rice, but these alterations were not evident in plants coexposed to C3N4. Random amplified polymorphic DNA analysis suggests that Cd significantly altered the genomic DNA of rice roots, while no difference was found in shoots. The presence of C3N4 controlled Cd and As uptake in rice by regulating transport-related genes. For example, the relative expression of the Cd transporter OsIRT1 in roots was upregulated by approximately threefold with metal exposure, but C3N4 coamendment lowered the expression. Similar results were evident in the expression of the As transporter OsNIP1;1 in roots. Overall, these findings facilitate the understanding of the underlying mechanisms by which carbon-based nanomaterials alleviate contaminant-induced phyto- and genotoxicity and may provide a new strategy for the reduction of heavy metal contamination in agriculture.

Dataset Information

Deciphering the non-coding RNA-level response to arsenic stress in rice (Oryza sativa).

Publications

Deciphering the non-coding RNA-level response to arsenic stress in rice (<i>Oryza sativa</i>).

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