MicroRNA Profiling of Root Meristematic Zone in Contrasting Genotypes Reveals Novel Insight into in Rice Response to Water Deficiency

Ghorbanzadeh, Zahra; Hamid, Rasmieh; Jacob, Feba; Mirzaei, Mehdi; Zeinalabedini, Mehrshad; Abdirad, Somayeh; Atwells, Brian J; Haynes, Paul A.; Ghaffari, Mohammad Reza; Salekdeh, Ghasem Hosseini

doi:10.1007/s00344-022-10842-8

Cited by 5 publications

(3 citation statements)

References 74 publications

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“…For instance, miR529 and miR156 family members were upregulated under drought stress (D1 and D3, Table S4), similar to their counterparts in rice [63] and maize [64], respectively. Conversely, miR159, miR166, miR168 and miR398 members were downregulated under drought stress (D1 and D3, Figure 4A, Table S4), consistent with findings in alfalfa [65], rice [66], Ammopiptanthus mongolicus [67], and pea [68], respectively. Interestingly, the miR397 and miR535 families showed contrasting expression patterns at different stages of drought stress (D1 and D3, Table S4), indicating their distinct regulatory roles.…”

Section: Stress Responsive Mirnas Families In P Massoniana Rootsupporting

confidence: 85%

The miRNA-mRNA Regulatory Modules of Pinus massoniana Lamb. in Response to Drought Stress

Chen,

Shen

et al. 2023

IJMS

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Masson pine (Pinus massoniana Lamb.) is a major fast-growing woody tree species and pioneer species for afforestation in barren sites in southern China. However, the regulatory mechanism of gene expression in P. massoniana under drought remains unclear. To uncover candidate microRNAs, their expression profiles, and microRNA-mRNA interactions, small RNA-seq was used to investigate the transcriptome from seedling roots under drought and rewatering in P. massoniana. A total of 421 plant microRNAs were identified. Pairwise differential expression analysis between treatment and control groups unveiled 134, 156, and 96 differential expressed microRNAs at three stages. These constitute 248 unique microRNAs, which were subsequently categorized into six clusters based on their expression profiles. Degradome sequencing revealed that these 248 differentially expressed microRNAs targeted 2069 genes. Gene Ontology enrichment analysis suggested that these target genes were related to translational and posttranslational regulation, cell wall modification, and reactive oxygen species scavenging. miRNAs such as miR482, miR398, miR11571, miR396, miR166, miRN88, and miRN74, along with their target genes annotated as F-box/kelch-repeat protein, 60S ribosomal protein, copper-zinc superoxide dismutase, luminal-binding protein, S-adenosylmethionine synthase, and Early Responsive to Dehydration Stress may play critical roles in drought response. This study provides insights into microRNA responsive to drought and rewatering in Masson pine and advances the understanding of drought tolerance mechanisms in Pinus.

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Section: Stress Responsive Mirnas Families In P Massoniana Rootsupporting

confidence: 85%

The miRNA-mRNA Regulatory Modules of Pinus massoniana Lamb. in Response to Drought Stress

Chen,

Shen

et al. 2023

IJMS

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“…Recently, several miRNAs involved in various metabolic processes, development and environmental stresses have been identified in multiple plants [ 33 , 73 , 74 ], in Arabidopsis, miRNAs such as trans-acting small interfering RNA (tasiRNA) were shown to be involved in CER3 silencing during stem wax synthesis [ 75 ]. likewise, Liu et al (2019) suggested that Brassica miRNA ( bna-miR165a-5p ) may be involved in wax formation by modulating the expression of the gene BnaA06g40560D [ 76 ].…”

Section: Discussionmentioning

confidence: 99%

“…This experiment comprised twenty replicates for both drought and well-watered conditions. Subsequent to harvesting leaves from the plants with silencing and the negative control, the levels of malondialdehyde (MDA), water loss rate, and proline levels were assessed, as outlined in previous reports [ 73 ]. According to RNA-Seq, most genes showed a sustained increase in response to PEG treatment within 12 h. Therefore, we treated the plant for 12 h, and the real-time and physobiochemical studies were performed on plants treated with 20% PEG6000 for 12 h.…”

Section: Methodsmentioning

confidence: 99%

Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation

Hamid,

Ghorbanzadeh,

Jacob

et al. 2024

BMC Plant Biol

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Background The cuticular wax serves as a primary barrier that protects plants from environmental stresses. The Eceriferum (CER) gene family is associated with wax production and stress resistance. Results In a genome-wide identification study, a total of 52 members of the CER family were discovered in four Gossypium species: G. arboreum, G. barbadense, G. raimondii, and G. hirsutum. There were variations in the physicochemical characteristics of the Gossypium CER (GCER) proteins. Evolutionary analysis classified the identified GCERs into five groups, with purifying selection emerging as the primary evolutionary force. Gene structure analysis revealed that the number of conserved motifs ranged from 1 to 15, and the number of exons varied from 3 to 13. Closely related GCERs exhibited similar conserved motifs and gene structures. Analyses of chromosomal positions, selection pressure, and collinearity revealed numerous fragment duplications in the GCER genes. Additionally, nine putative ghr-miRNAs targeting seven G. hirsutum CER (GhCER) genes were identified. Among them, three miRNAs, including ghr-miR394, ghr-miR414d, and ghr-miR414f, targeted GhCER09A, representing the most targeted gene. The prediction of transcription factors (TFs) and the visualization of the regulatory TF network revealed interactions with GhCER genes involving ERF, MYB, Dof, bHLH, and bZIP. Analysis of cis-regulatory elements suggests potential associations between the CER gene family of cotton and responses to abiotic stress, light, and other biological processes. Enrichment analysis demonstrated a robust correlation between GhCER genes and pathways associated with cutin biosynthesis, fatty acid biosynthesis, wax production, and stress response. Localization analysis showed that most GCER proteins are localized in the plasma membrane. Transcriptome and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) expression assessments demonstrated that several GhCER genes, including GhCER15D, GhCER04A, GhCER06A, and GhCER12D, exhibited elevated expression levels in response to water deficiency stress compared to control conditions. The functional identification through virus-induced gene silencing (VIGS) highlighted the pivotal role of the GhCER04A gene in enhancing drought resistance by promoting increased tissue water retention. Conclusions This investigation not only provides valuable evidence but also offers novel insights that contribute to a deeper understanding of the roles of GhCER genes in cotton, their role in adaptation to drought and other abiotic stress and their potential applications for cotton improvement.

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Characterization of Two-Component System gene (TCS) in melatonin-treated common bean under salt and drought stress

Kasapoglu,

Ilhan,

Aydin

et al. 2023

Physiol Mol Biol Plants

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MicroRNA Profiling of Root Meristematic Zone in Contrasting Genotypes Reveals Novel Insight into in Rice Response to Water Deficiency

Cited by 5 publications

References 74 publications

The miRNA-mRNA Regulatory Modules of Pinus massoniana Lamb. in Response to Drought Stress

The miRNA-mRNA Regulatory Modules of Pinus massoniana Lamb. in Response to Drought Stress

Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation

Characterization of Two-Component System gene (TCS) in melatonin-treated common bean under salt and drought stress

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