Role of long non-coding RNAs in rice reproductive development

Babaei, Saeid; Singh, Mohan B.; Bhalla, Prem L.

doi:10.3389/fpls.2022.1040366

Cited by 5 publications

(3 citation statements)

References 82 publications

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“…The plant reproduction stage is highly vulnerable to temperature stress. The stress conditions occurring through the flowering and seed set stage affect the fertility and quality–quantity of the yield [ 92 ]. However, limited studies have focused on applying exogenous melatonin to minimise the adverse effects of abiotic stress during plant reproductive stages.…”

Section: Exogenous Melatonin Application Enhances Abiotic Stress Tole...mentioning

confidence: 99%

Melatonin and Abiotic Stress Tolerance in Crop Plants

Colombage

Singh

Bhalla

2023

IJMS

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Increasing food demand by the growing human population and declining crop productivity due to climate change affect global food security. To meet the challenges, developing improved crops that can tolerate abiotic stresses is a priority. Melatonin in plants, also known as phytomelatonin, is an active component of the various cellular mechanisms that alleviates oxidative damage in plants, hence supporting the plant to survive abiotic stress conditions. Exogenous melatonin strengthens this defence mechanism by enhancing the detoxification of reactive by-products, promoting physiological activities, and upregulating stress-responsive genes to alleviate damage during abiotic stress. In addition to its well-known antioxidant activity, melatonin protects against abiotic stress by regulating plant hormones, activating ER stress-responsive genes, and increasing protein homoeostasis, heat shock transcription factors and heat shock proteins. Under abiotic stress, melatonin enhances the unfolded protein response, endoplasmic reticulum-associated protein degradation, and autophagy, which ultimately protect cells from programmed cell death and promotes cell repair resulting in increased plant survival.

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Section: Exogenous Melatonin Application Enhances Abiotic Stress Tole...mentioning

confidence: 99%

Melatonin and Abiotic Stress Tolerance in Crop Plants

Colombage

Singh

Bhalla

2023

IJMS

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“…LncRNAs, as regulatory molecules, play crucial roles during pollen development and progression; (Xiao-Yan et al, 2004;Ding et al, 2012;Babaei et al, 2022). For example, sufficient expression of lncRNA LONG-DAY-SPECIFIC MALE-FERTILITY-ASSOCIATED RNA or in short, LDMAR is essential for pollen development and fertility in rice; even a single nucleotide mutation alters the secondary structure and expression of LDMAR, which leads to photoperiod-sensitive male sterility (Ding et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

“…LncRNAs show lower inter-species sequence conservation, lower expression, and higher tissue-specificity expression compared to protein-coding RNAs ( Golicz et al., 2018a ). LncRNAs are classified as sense, antisense, intronic, or intergenic based on their genomic location and transcriptional direction ( Babaei et al., 2022 ). In addition, lncRNAs can be identified as “ cis -acting” when they control gene expression at or close to their transcriptional site or “ trans -acting” when they move from their transcriptional sites to act in other locations in the nucleus or cytoplasm ( Gil and Ulitsky, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Identifying long non-coding RNAs involved in heat stress response during wheat pollen development

Babaei,

Bhalla,

Singh

2024

Front. Plant Sci.

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IntroductionWheat is a staple food crop for over one-third of the global population. However, the stability of wheat productivity is threatened by heat waves associated with climate change. Heat stress at the reproductive stage can result in pollen sterility and failure of grain development.MethodsThis study used transcriptome data analysis to explore the specific expression of long non-coding RNAs (lncRNAs) in response to heat stress during pollen development in four wheat cultivars. Results and discussionWe identified 11,054 lncRNA-producing loci, of which 5,482 lncRNAs showed differential expression in response to heat stress. Heat-responsive lncRNAs could target protein-coding genes in cis and trans and in lncRNA-miRNA-mRNA regulatory networks. Gene ontology analysis predicted that target protein-coding genes of lncRNAs regulate various biological processes such as hormonal responses, protein modification and folding, response to stress, and biosynthetic and metabolic processes. We also noted some paired lncRNA/protein-coding gene modules and some lncRNA-miRNA-mRNA regulatory modules shared in two or more wheat cultivars. These modules were related to regulating plant responses to heat stress, such as heat-shock proteins and transcription factors, and protein domains, such as MADS-box, Myc-type, and Alpha crystallin/Hsp20 domain. ConclusionOur results provide the basic knowledge and molecular resources for future functional studies investigating wheat reproductive development under heat stress.

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Genome-wide analysis reveals the crucial role of lncRNAs in regulating the expression of genes controlling pollen development

et al. 2023

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LncRNAs can function in regulating of gene expression, but their roles as essential regulators of developmental processes and organismal phenotypes remain largely unclear. Especially the roles of lncRNAs in plants are largely unexplored. However, it has been proposed that plant lncRNAs act as regulators of protein-coding genes during development and that the similar roles of animal and plant lncRNAs result from convergent evolution. Since pollen development follows an established program with well-defined and characterized stages, we have used it as a model for studying plant lncRNAs and their roles in reproductive development. We investigated of lncRNA expression and function during pollen formation in field mustard (Brassica rapa). Reference-based transcriptome assembly performed to update the existing genome annotation identified novel expressed protein-coding genes and long non-coding RNAs (lncRNAs), including 4,347 long intergenic non-coding RNAs (lincRNAs, 1058 expressed) and 2,045 lncRNAs overlapping protein-coding genes on the opposite strand (lncNATs, 780 expressed). The analysis of expression profiles reveals that lncRNAs are significant and stage-specific contributors to the gene expression profile of developing pollen. Gene co-expression networks accompanied by genome location analysis identified 38 cisacting lincRNA, 31 cis-acting lncNAT, 7 trans-acting lincRNA and 14 trans-acting lncNAT to be substantially co-expressed with target protein-coding genes involved in biological processes regulating pollen development and male lineage specification. These findings provide a foundation for future research aiming at developing strategies to employ lncRNAs as regulatory tools for gene expression control during reproductive development.

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Role of long non-coding RNAs in rice reproductive development

Cited by 5 publications

References 82 publications

Melatonin and Abiotic Stress Tolerance in Crop Plants

Melatonin and Abiotic Stress Tolerance in Crop Plants

Identifying long non-coding RNAs involved in heat stress response during wheat pollen development

Genome-wide analysis reveals the crucial role of lncRNAs in regulating the expression of genes controlling pollen development

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