Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development

Jha, Uday Chand; Nayyar, Harsh; Mantri, Nitin; Siddique, Kadambot H. M.

doi:10.3390/cells10071674

Cited by 35 publications

(23 citation statements)

References 191 publications

(306 reference statements)

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“…The molecular mechanism of heterosis is still unclear through extensive studies on genome, transcriptome and epigenetics ( Larièpe et al, 2012 ; Shen et al, 2014 ; Shao et al, 2019 ; Wang and Wang, 2022 ; Zhang, 2022 ). In recent years, several ncRNAs and their corresponding regulatory networks have been proved to play important roles in plant growth and development ( Ohtani, 2017 ; Yuan et al, 2018 ; Luan et al, 2019 ; Wang et al, 2020 ; Zhai et al, 2020 ; Chand Jha et al, 2021 ; Qiao et al, 2021 ). However, there are few studies on the role of ncRNA in plant heterosis so far, which have been conducted in maize and cabbage ( Crisp et al, 2020 ; Hou et al, 2020 ; Li et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, studies on plant ncRNAs have mainly focused on lncRNAs, circRNAs and miRNAs ( Dou et al, 2017 ; Wang et al, 2018 , 2021c ; Li et al, 2020 ; You et al, 2021 ; Zhou et al, 2021 ). Due to the differences in the sources and functions of these three types of ncRNAs, they play a role in various plant growth and development processes ( Voinnet, 2009 ; Tang and Chu, 2017 ; Zhai et al, 2020 ; Chand Jha et al, 2021 ). A total of 3,278 lncRNAs, 2,521 circRNAs and 867 miRNAs (including 345 newly predicted miRNAs) were identified in this study.…”

Section: Discussionmentioning

confidence: 99%

“…With the rapid rise of modern genomics techniques, noncoding RNA or nonprotein-coding RNAs (ncRNA or npcRNA), once called genomic “dark matter,” has been discovered ( Morris and Mattick, 2014 ; Yu et al, 2019 ). By targeting to corresponding DNA, RNA and proteins, ncRNAs participate in a variety of biological processes and molecular mechanisms in plants ( Ohtani, 2017 ; Chand Jha et al, 2021 ). In rice, many experimental reports have indicated the importance of ncRNAs in growth, development, environmental response ( Yuan et al, 2018 ; Luan et al, 2019 ; Wang et al, 2020 ; Zhai et al, 2020 ; Qiao et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice

Wang

2022

Front. Plant Sci.

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Heterosis has been used widespread in agriculture, but its molecular mechanism is inadequately understood. Plants have a large number of non-coding RNAs (ncRNAs), among them, functional ncRNAs that have been studied widely containing long non-coding RNA (lncRNA) and circular RNA (circRNA) that play a role in varied biological processes, as well as microRNA (miRNA), which can not only regulate the post-transcriptional expression of target genes, but also target lncRNA and circRNA then participate the competing endogenous RNA (ceRNA) regulatory network. However, the influence of these three ncRNAs and their regulatory relationships on heterosis is unknown in rice. In this study, the expression profile of ncRNAs and the ncRNA regulatory network related to heterosis were comprehensively analyzed in inter-subspecific hybrid rice. A total of 867 miRNAs, 3,278 lncRNAs and 2,521 circRNAs were identified in the hybrid and its parents. Analysis of the global profiles of these three types of ncRNAs indicated that significant differences existed in the distribution and sequence characteristics of the corresponding genes. The numbers of miRNA and lncRNA in hybrid were higher than those in its parents. A total of 784 ncRNAs (169 miRNAs, 573 lncRNAs and 42 circRNAs) showed differentially expressed in the hybrid, and their target/host genes were vital in stress tolerance, growth and development in rice. These discoveries suggested that the expression plasticity of ncRNA has an important role of inter-subspecific hybrid rice heterosis. It is worth mentioning that miRNAs exhibited substantially more variations between hybrid and parents compared with observed variation for lncRNA and circRNA. Non-additive expression ncRNAs and allele-specific expression genes-related ncRNAs in hybrid were provided in this study, and multiple sets of ncRNA regulatory networks closely related to heterosis were obtained. Meanwhile, heterosis-related regulatory networks of ceRNA (lncRNA and circRNA) and miRNA were also demonstrated.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice

Wang

2022

Front. Plant Sci.

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“…With the advances in sequencing methods, more and more research has been carried out to identify ncRNAs governing nodulation and nitrogen fixation. Up to now, miRNAs, siRNAs, lncRNAs and circRNAs have been identified in a number of legume species, especially in soybean, Medicago truncatula , common bean ( Phaseolus vulgaris ) and Lotus japonicus ( Wang et al., 2020 ; Chand Jha et al., 2021 ).…”

Section: Identification Of Non-coding Rnas Governing Nodulation and N...mentioning

confidence: 99%

“…Various ncRNAs are reported to play roles in plant development, plant immunity and responses to abiotic and biotic stress ( Wang T. et al., 2017 ; Chand Jha et al., 2021 ), indicating the importance of ncRNAs in plants. There are also many studies illustrating that ncRNAs are critical regulators in the nodulation process.…”

Section: Introductionmentioning

confidence: 99%

Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation

Fan

Sze²,

Li³

et al. 2022

Front. Plant Sci.

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Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.

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Changes in epigenetic features in legumes under abiotic stresses

Yung

Huang

et al. 2022

The Plant Genome

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Legume crops are rich in nutritional value for human and livestock consumption. With global climate change, developing stress‐resilient crops is crucial for ensuring global food security. Because of their nitrogen‐fixing ability, legumes are also important for sustainable agriculture. Various abiotic stresses, such as salt, drought, and elevated temperatures, are known to adversely affect legume production. The responses of plants to abiotic stresses involve complicated cellular processes including stress hormone signaling, metabolic adjustments, and transcriptional regulations. Epigenetic mechanisms play a key role in regulating gene expressions at both transcriptional and posttranscriptional levels. Increasing evidence suggests the importance of epigenetic regulations of abiotic stress responses in legumes, and recent investigations have extended the scope to the epigenomic level using next‐generation sequencing technologies. In this review, the current knowledge on the involvement of epigenetic features, including DNA methylation, histone modification, and noncoding RNAs, in abiotic stress responses in legumes is summarized and discussed. Since most of the available information focuses on a single aspect of these epigenetic features, integrative analyses involving omics data in multiple layers are needed for a better understanding of the dynamic chromatin statuses and their roles in transcriptional regulation. The inheritability of epigenetic modifications should also be assessed in future studies for their applications in improving stress tolerance in legumes through the stable epigenetic optimization of gene expressions.

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Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development

Cited by 35 publications

References 191 publications

Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice

Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice

Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation

Changes in epigenetic features in legumes under abiotic stresses

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