Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field

Li, Yongfang; Wei, Kangning; Wang, Menglei; Wang, Li; Cui, Junxia; Zhang, Daijing; Guo, Junqiang; Zhao, Miao; Zheng, Yun

doi:10.3389/fgene.2019.00779

Cited by 12 publications

(30 citation statements)

References 91 publications

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“…The size distributions of the four sRNA libraries showed similar patterns ( Figure 2 ). The 24-nt reads were the most abundant class (about 50%), followed by 21-nt reads (17%) ( Figure 2 ), in agreement with previous reports on cotton and other plant species ( An et al, 2015 ; Li et al, 2019 ; Zhao et al, 2020 ). On the average, 84.18% of the reads were successfully aligned to the AD genome of G .…”

Section: Resultssupporting

confidence: 92%

Profiling of MicroRNAs Involved in Mepiquat Chloride-Mediated Inhibition of Internode Elongation in Cotton (Gossypium hirsutum L.) Seedlings

et al. 2021

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Mepiquat chloride (MC) is the most important plant growth retardant that is widely used in cotton (Gossypium hirsutum L.) production to suppress excessive vegetative growth and improve plant architecture. MicroRNAs (miRNAs) are important gene expression regulators that control plant growth and development. However, miRNA-mediated post-transcriptional regulation in MC-induced growth inhibition remains unclear. In this study, the dynamic expression profiles of miRNAs responsive to MC in cotton internodes were investigated. A total of 508 known miRNAs belonging to 197 families and five novel miRNAs were identified. Among them, 104 miRNAs were differentially expressed at 48, 72, or 96 h post MC treatment compared with the control (0 h); majority of them were highly conserved miRNAs. The number of differentially expressed miRNAs increased with time after treatment. The expression of 14 known miRNAs was continuously suppressed, whereas 12 known miRNAs and one novel miRNA were continuously induced by MC. The expression patterns of the nine differentially expressed miRNAs were verified using qRT-PCR. The targets of the known and novel miRNAs were predicted. Four conserved and six novel targets were validated using the RLM-5′ RACE assay. This study revealed that miRNAs play crucial regulatory roles in the MC-induced inhibition of internode elongation. It can improve our understanding of post-transcriptional gene regulation in MC-mediated growth inhibition and could potentially facilitate the breeding of dwarf cotton.

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Section: Resultssupporting

confidence: 92%

Profiling of MicroRNAs Involved in Mepiquat Chloride-Mediated Inhibition of Internode Elongation in Cotton (Gossypium hirsutum L.) Seedlings

et al. 2021

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“…Approximately, 24 to 26 million raw reads of 18–30 nt in length were obtained for each library. The size distribution of sRNAs in crowns were similar to that in wheat leaves and other studies [ 43 ], with fragment sizes mainly at 21 nt and 24 nt (Fig. 1 ).…”

Section: Resultssupporting

confidence: 85%

“…Comparison of miRNA expression between different growth stages could provide insights into the post-transcriptional mechanism mediated by miRNAs during winter wheat cold acclimation and flowering initiation. In total, 92 miRNAs were significantly regulated in wheat crown tissues from the three-leaf stage to the jointing stage (Additional file 5 ), including 19 miRNAs that were first reported in wheat leaves [ 43 ]. Based on the expression patterns, these DEMs were grouped into five clusters.…”

Section: Resultsmentioning

confidence: 99%

“…Further study revealed that the suppression of TOC1s by miR408 could activate the expression of VRN3 and stimulate wheat phase transition [ 42 ]. We previously studied the miRNA profiles in the leaves of winter wheat grown under field conditions that consisted of various environmental factors [ 43 ]. However, less information is available on miRNA mediated post-transcriptional regulation in crown tissues during the process of cold acclimation and floral initiation.…”

Section: Introductionmentioning

confidence: 99%

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Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions

et al. 2021

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Background Winter wheat requires prolonged exposure to low temperature to initiate flowering (vernalization). Shoot apical meristem of the crown is the site of cold perception, which produces leaf primordia during vegetative growth before developing into floral primordia at the initiation of the reproductive phase. Although many essential genes for winter wheat cold acclimation and floral initiation have been revealed, the importance of microRNA (miRNA) meditated post-transcriptional regulation in crowns is not well understood. To understand the potential roles of miRNAs in crown tissues, we performed a temporal expression study of miRNAs in crown tissues at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage of winter wheat grown under natural growth conditions. Results In total, 348 miRNAs belonging to 298 miRNA families, were identified in wheat crown tissues. Among them, 92 differentially expressed miRNAs (DEMs) were found to be significantly regulated from the three-leaf stage to the jointing stage. Most of these DEMs were highly expressed at the three-leaf stage and winter dormancy stage, and then declined in later stages. Six DEMs, including miR156a-5p were markedly induced during the winter dormancy stage. Eleven DEMs, including miR159a.1, miR390a-5p, miR393-5p, miR160a-5p, and miR1436, were highly expressed at the green-up stage. Twelve DEMs, such as miR172a-5p, miR394a, miR319b-3p, and miR9676-5p were highly induced at the jointing stage. Moreover, 14 novel target genes of nine wheat or Pooideae-specific miRNAs were verified using RLM-5′ RACE assay. Notably, six mTERFs and two Rf1 genes, which are associated with mitochondrial gene expression, were confirmed as targets of three wheat-specific miRNAs. Conclusions The present study not only confirmed the known miRNAs associated with phase transition and floral development, but also identified a number of wheat or Pooideae-specific miRNAs critical for winter wheat cold acclimation and floral development. Most importantly, this study provided experimental evidence that miRNA could regulate mitochondrial gene expression by targeting mTERF and Rf1 genes. Our study provides valuable information for further exploration of the mechanism of miRNA mediated post-transcriptional regulation during winter wheat vernalization and inflorescent initiation.

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“…Many of these identi ed miRNA-target pairs were previously reported. The miRNAs belonging to miR9662 family targeted mitochondrial transcription termination factor, mTERF15 in bread wheat [66]. They also speculate that miR9662a-3p might be a vital modulator of wheat growth and development since their expression is damped with the plant's growth.…”

Section: Discussionmentioning

confidence: 99%

Wheat sRNA transcriptome reveals R-gene associated distinct temporal miRNA profiles in response to stem rust and leaf rust diseases

Nair

Kumar

Jyothsna

et al. 2021

Preprint

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Wheat rusts, the dreadful fungal diseases caused by members of the Puccinia genus remain as a major threat to global wheat production and food security. The R-gene mediated resistance has been employed as an efficient approach to develop rust resistant varieties. However, evolution of new fungal races and infection strategies put forward the urgency of unravelling novel genomics assisted molecular players, including non-coding RNAs for rust disease management. MicroRNAs are crucial regulators of genes associated with plant growth, development, abiotic and biotic stress responses. In this study, high throughput small RNA sequencing was performed on susceptible and resistant wheat near-isogenic lines inoculated with stem rust and leaf rust, together with mock inoculated controls. While miRNA mining in stem rust inoculated libraries revealed a total of twenty-six known and seven novel miRNAs, the search in leaf rust libraries culminated with twenty-two known and four novel miRNAs. The identified candidate miRNAs constituted both guide and passenger miRNA strands along with their isomiRs. Temporal expression pattern of differentially expressed miRNAs pinpoints their possible role during the progress of infection. Comparative analysis provides a better understanding of altered miRNA profiles associated with Sr36 and Lr45 disease resistance genes in response to stem rust and leaf rust, respectively. Also, the disclosure of guide strand, passenger strand and a variant of novel-Tae-miR02 with various sub-genomal origins might serve as an important common link between stem rust and leaf rust defense mechanisms downstream to the respective R-genes. Further, cis-regulatory elements that modulate MIR genes, targets of identified miRNAs related to various signal transduction pathways, and miR-SSRs which might be useful for rust disease control, are the emphasized attributes of our results. The outcome from this simultaneous study of miRNA profiles among two rust diseases and further characterization of the identified miRNAs can contribute to the expanding rust disease management programs.

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Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field

Cited by 12 publications

References 91 publications

Profiling of MicroRNAs Involved in Mepiquat Chloride-Mediated Inhibition of Internode Elongation in Cotton (Gossypium hirsutum L.) Seedlings

Profiling of MicroRNAs Involved in Mepiquat Chloride-Mediated Inhibition of Internode Elongation in Cotton (Gossypium hirsutum L.) Seedlings

Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions

Wheat sRNA transcriptome reveals R-gene associated distinct temporal miRNA profiles in response to stem rust and leaf rust diseases

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