Overexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in rice

Wang, Ying; Luo, Xin; Sun, Fan; Hu, Jianhua; Zha, Xiaojun; Su, Wei; Yang, Jinshui

doi:10.1038/s41467-018-05829-7

Cited by 163 publications

(134 citation statements)

References 54 publications

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“…Despite the tremendous progress in the identification of lncRNAs, few of them are functionally characterized thus far. In rice, a lncRNA LAIR was identified and found to be regulated in grain yield by changing its expression level [31]. Plants overexpressing LAIR exhibited larger primary panicles and more panicles per plant while silencing LAIR decreased grain yield [31].…”

Section: Discussionmentioning

confidence: 99%

“…In rice, a lncRNA LAIR was identified and found to be regulated in grain yield by changing its expression level [31]. Plants overexpressing LAIR exhibited larger primary panicles and more panicles per plant while silencing LAIR decreased grain yield [31]. Zhanget al [12] performed RNA sequencing and identified lncRNAs that are involved in the reproduction of rice, and studied the function of one lncRNA XLOC_057324 by Tos17 insertion.…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Identification of lncRNAs During Rice Seed Development

Zhao

Ajadi

Wang

et al. 2020

Genes

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Rice seed is a pivotal reproductive organ that directly determines yield and quality. Long non-coding RNAs (lncRNAs) have been recognized as key regulators in plant development, but the roles of lncRNAs in rice seed development remain unclear. In this study, we performed a paired-end RNA sequencing in samples of rice pistils and seeds at three and seven days after pollination (DAP) respectively. A total of 540 lncRNAs were obtained, among which 482 lncRNAs had significantly different expression patterns during seed development. Results from semi-qPCR conducted on 15 randomly selected differentially expressed lncRNAs suggested high reliability of the transcriptomic data. RNA interference of TCONS_00023703, which is predominantly transcribed in developing seeds, significantly reduced grain length and thousand-grain weight. These results expanded the dataset of lncRNA in rice and enhanced our understanding of the biological functions of lncRNAs in rice seed development

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of lncRNAs During Rice Seed Development

Zhao

Ajadi

Wang

et al. 2020

Genes

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“…The lncRNAs of COLDAIR and COOLAIR negatively modulate FLC by different models [14][15][16]. A large number of lncRNAs involved in the regulation of plant responses to abiotic stresses has been characterized in recent years [17][18][19].…”

Section: Introductionmentioning

confidence: 99%

Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

et al. 2020

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Background: Long non-coding RNAs (lncRNAs) play important roles in the regulation of plant responses to environmental stress by acting as essential regulators of gene expression. However, whether and how lncRNAs are involved in cold acclimation-dependent freezing tolerance in plants remains largely unknown. Medicago truncatula is a prominent model for studies of legume genomics, and distinguished by its cold-acclimation characteristics. To determine the roles of lncRNAs in plant cold stress response, we conducted genome-wide high-throughput sequencing in the legume model plant M. truncatula. Results: RNA-seq data were generated from twelve samples for the four treatments, i.e., non-cold treated leaves and roots, cold-treated leaves and roots of M. truncatula Jemalong A17 seedlings. A total of 1204 million raw reads were generated. Of them, 1150 million filtered reads after quality control (QC) were subjected to downstream analysis. A large number of 24,368 unique lncRNAs were identified from the twelve samples. Among these lncRNAs, 983 and 1288 were responsive to cold treatment in the leaves and roots, respectively. We further found that the intronic-lncRNAs were most sensitive to the cold treatment. The cold-responsive lncRNAs were unevenly distributed across the eight chromosomes in M. truncatula seedlings with obvious preferences for locations. Further analyses revealed that the cold-responsive lncRNAs differed between leaves and roots. The putative target genes of the lncRNAs were predicted to mainly involve the processes of protein translation, transport, metabolism and nucleic acid transcription. Furthermore, the networks of a tandem array of CBF/DREB1 genes that were reported to be located in a major freezing tolerance QTL region on chromosome 6 and their related lncRNAs were dissected based on their gene expression and chromosome location. Conclusions:We identified a comprehensive set of lncRNAs that were responsive to cold treatment in M. truncatula seedlings, and discovered tissue-specific cold-responsive lncRNAs in leaves and roots. We further dissected potential regulatory networks of CBF Intergenic RNA (MtCIR1) and MtCBFs that play critical roles in response and adaptation of M. truncatula to cold stress.

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“…tomato DC3000, directly interacts with FIB2 and mediator subunit 19a (FIB2/MED19a) and affects the enrichment of MED19a on the PR1 promoter [41,72]. Overexpressing lncRNA LAIR was proven to increase grain yield and regulate the neighboring gene cluster's expression in rice [14]. Although most of the experiments focused on plant development, it is no doubt that these works give confidence to the researcher in finding functional lncRNAs in plants responding to pathogen stress.…”

Section: Prospect Of Plant Lncrnas Related To Resistancementioning

confidence: 99%

“…Some lncRNAs bind miRNAs and competitively inhibit the interaction between miRNAs and target mRNAs to modulate gene expression [10][11][12]. LincRNA transcription appears to positively or negatively affect the expression of nearby genes, although not all are active [13,14]. Thus, lncRNAs in plants can be considered as essential elements of gene regulation and as a potential resistant gene resource.…”

Section: Introductionmentioning

confidence: 99%

The Emerging Role of Long Non-Coding RNAs in Plant Defense Against Fungal Stress

Zhang

Guo

et al. 2020

IJMS

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Growing interest and recent evidence have identified long non-coding RNA (lncRNA) as the potential regulatory elements for eukaryotes. LncRNAs can activate various transcriptional and post-transcriptional events that impact cellular functions though multiple regulatory functions. Recently, a large number of lncRNAs have also been identified in higher plants, and an understanding of their functional role in plant resistance to infection is just emerging. Here, we focus on their identification in crop plant, and discuss their potential regulatory functions and lncRNA-miRNA-mRNA network in plant pathogen stress responses, referring to possible examples in a model plant. The knowledge gained from a deeper understanding of this colossal special group of plant lncRNAs will help in the biotechnological improvement of crops.

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Overexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in rice

Cited by 163 publications

References 54 publications

Genome-Wide Identification of lncRNAs During Rice Seed Development

Genome-Wide Identification of lncRNAs During Rice Seed Development

Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

The Emerging Role of Long Non-Coding RNAs in Plant Defense Against Fungal Stress

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