Comparison of tolerant and susceptible cultivars revealed the roles of circular RNAs in rice responding to salt stress

Yin, Junliang; Liu, Yike; Lü, Lin; Zhang, Jian; Chen, Shaoyu; Wang, Baotong

doi:10.1007/s10725-021-00772-y

Cited by 12 publications

(4 citation statements)

References 46 publications

(13 reference statements)

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“…Limited evidence is available on ncRNAs associated with the regulation of salt stress in plants [177][178][179][180][181][182][183][184][185][186][187][188][189][190], as listed in Table 1. Nearly 75 conserved miRNAs were identified from the control and NaCl-treated salt-tolerant rice varieties [180].…”

Section: Salt Stressmentioning

confidence: 99%

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

Yadav,

Mathan,

Dubey

et al. 2024

ncRNA

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Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.

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Section: Salt Stressmentioning

confidence: 99%

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

Yadav,

Mathan,

Dubey

et al. 2024

ncRNA

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“…A single gene can produce single or multiple circRNAs, and their occurrence, abundance, and composition can be tissue specific, under developmental control, or respond to biotic or abiotic stress (H. Liu et al, 2020;Philips et al, 2020;Z. Wang et al, 2017;Xia et al, 2023;Yin et al, 2022;P. Zhang et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…CircRNA can originate from exonic, intronic, and intergenic regions. A single gene can produce single or multiple circRNAs, and their occurrence, abundance, and composition can be tissue specific, under developmental control, or respond to biotic or abiotic stress (H. Liu et al., 2020; Philips et al., 2020; Z. Wang et al., 2017; Xia et al., 2023; Yin et al., 2022; P. Zhang et al., 2019). In animal systems, the base‐pairing of reverse complementary sequences in the upstream and downstream regions flanking circularized RNA has been shown to be sufficient for the formation of circRNA (Liang & Wilusz, 2014; X.‐O.…”

Section: Introductionmentioning

confidence: 99%

Long‐ and short‐read sequencing methods discover distinct circular RNA pools in Lotus japonicus

Budnick,

Franklin,

Utley

et al. 2024

The Plant Genome

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Circular RNAs (circRNAs) are covalently closed single‐stranded RNAs, generated through a back‐splicing process that links a downstream 5′ site to an upstream 3′ end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high‐confidence circRNA‐expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.

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“…circRNAs regulate the expression of functional genes by acting as an miRNA sponge or by influencing the splicing of their linear counterparts [ 13 , 16 ]. Previous studies have shown that circRNAs exert important roles in signal transcription, metabolism adaptation, and ion homeostasis under salt and dehydration stresses in cucumbers [ 17 ], rice [ 18 ], wheat [ 19 ], sugar beet [ 20 ], and poplars [ 21 ]. However, there are only a few reports on circRNAs involved in the response to abiotic stresses in maize [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

A Combination of a Genome-Wide Association Study and a Transcriptome Analysis Reveals circRNAs as New Regulators Involved in the Response to Salt Stress in Maize

Liu

Zhu

Líu

et al. 2022

IJMS

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Salinization seriously threatens the normal growth of maize, especially at the seedling stage. Recent studies have demonstrated that circular RNAs (circRNAs) play vital roles in the regulation of plant stress resistance. Here, we performed a genome-wide association study (GWAS) on the survival rate of 300 maize accessions under a salt stress treatment. A total of 5 trait-associated SNPs and 86 candidate genes were obtained by the GWAS. We performed RNA sequencing for 28 transcriptome libraries derived from 2 maize lines with contrasting salt tolerance under normal and salt treatment conditions. A total of 1217 highly expressed circRNAs were identified, of which 371 were responsive to a salt treatment. Using PCR and Sanger sequencing, we verified the reliability of these differentially expressed circRNAs. An integration of the GWAS and RNA-Seq analyses uncovered two differentially expressed hub genes (Zm00001eb013650 and Zm00001eb198930), which were regulated by four circRNAs. Based on these results, we constructed a regulation model of circRNA/miRNA/mRNA that mediated salt stress tolerance in maize. By conducting hub gene-based association analyses, we detected a favorable haplotype in Zm00001eb198930, which was responsible for high salt tolerance. These results help to clarify the regulatory relationship between circRNAs and their target genes as well as to develop salt-tolerant lines for maize breeding.

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Comparison of tolerant and susceptible cultivars revealed the roles of circular RNAs in rice responding to salt stress

Cited by 12 publications

References 46 publications

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

Long‐ and short‐read sequencing methods discover distinct circular RNA pools in Lotus japonicus

A Combination of a Genome-Wide Association Study and a Transcriptome Analysis Reveals circRNAs as New Regulators Involved in the Response to Salt Stress in Maize

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