Genome‐wide analysis of coding and non‐coding RNA reveals a conserved miR164‐<i>NAC</i> regulatory pathway for fruit ripening

Wang, Wen-Qiu; Wang, Jian; Wu, Ying‐Ying; Li, Dawei; Allan, Andrew C.; Yin, Xin

doi:10.1111/nph.16233

Cited by 100 publications

(84 citation statements)

References 72 publications

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“…Indeed, a NAC-domain-containing protein (Ga12G1047) was found up-regu-lated in 15 to 20 DPA ovules, correlated with ovule ripening and a declination of gar-miR164 content (Figure S1 in Supporting Information). This gar-miR164-NAC-mediated regulatory process for fruit ripening is reported previously in kiwifruit (Wang W.Q. et al, 2019).…”

Section: Overview Of Newly Identified Mirnas In G Arboreum By Small supporting

confidence: 78%

A Malvaceae-specific miRNA targeting the newly duplicated GaZIP1L to regulate Zn2+ ion transporter capacity in cotton ovules

Wen

Huang

et al. 2021

Sci. China Life Sci.

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MicroRNAs (miRNAs) play critical roles in regulating gene expression in plants, yet their functions underlying cultivated diploid Gossypium arboreum cotton ovule development are largely unknown. Here, we acquired small RNA profiles from G. arboreum ovules and fibers collected at different growth stages, and identified 46 novel miRNAs that accounted for 23.7% of all miRNAs in G. arboreum reported in the latest plant sRNA database. Through analysis of 84 (including 38 conserved) differentially expressed G. arboreum miRNAs, we detected 215 putative protein-coding genes in 26 biological processes as their potential targets. A Malvaceae-specific novel miRNA named gar-miRN44 was found to likely regulate cotton ovule growth by targeting to a newly duplicated Zn 2+ ion transporter gene GaZIP1L. During cotton ovule development, gar-miRN44 transcript level decreased sharply after 10 to 15 days post-anthesis (DPA), while that of the GaZIP1L increased significantly, with a concomitant increase of Zn 2+ ion concentration in late ovule developmental stages. Molecular dynamics simulation and ion absorption analysis showed that GaZIP1L has stronger Zn 2+ ion binding ability than the original GaZIP1, indicating that the newly evolved GaZIP1L may be more suitable for maintaining high Zn 2+ ion transport capacity that is likely required for cotton ovule growth via enhanced cellulose synthase activities. Our systematic miRNA profiling in G. arboreum and characterization of gar-miRN44 not only contribute to the understanding of miRNA function in cotton, but also provide potential targets for plant breeding.gar-miRN44, Malvaceae, GaZIP1L, Zn 2+ ion transport, cotton ovule development

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Section: Overview Of Newly Identified Mirnas In G Arboreum By Small supporting

confidence: 78%

A Malvaceae-specific miRNA targeting the newly duplicated GaZIP1L to regulate Zn2+ ion transporter capacity in cotton ovules

Wen

Huang

et al. 2021

Sci. China Life Sci.

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“…Although tomato has been an important ripening model [ 3 , 8 , 9 , 10 , 11 , 12 ], the fact that ripening has arisen several times during the course of evolution, and the differences between climacteric and non-climacteric fruits, caution against a “one type fits all” model [ 13 ]. Furthermore, initial conclusions about the function of key tomato ripening “master regulator” TFs (NAC-NOR, MADS-RIN, SPL-CNR), which strongly influenced ripening models, have turned out to be misleading and their roles in ripening have been revised [ 14 , 15 , 16 , 17 , 18 , 19 , 20 ]. In this article, we shall focus on the recent, very significant changes in understanding of the mechanisms underlying the control of fleshy fruit ripening and quality.…”

Section: Introductionmentioning

confidence: 99%

Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening

Chen

Grierson

2021

Cells

116

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This article focuses on the molecular and hormonal mechanisms underlying the control of fleshy fruit ripening and quality. Recent research on tomato shows that ethylene, acting through transcription factors, is responsible for the initiation of tomato ripening. Several other hormones, including abscisic acid (ABA), jasmonic acid (JA) and brassinosteroids (BR), promote ripening by upregulating ethylene biosynthesis genes in different fruits. Changes to histone marks and DNA methylation are associated with the activation of ripening genes and are necessary for ripening initiation. Light, detected by different photoreceptors and operating through ELONGATED HYPOCOTYL 5(HY5), also modulates ripening. Re-evaluation of the roles of ‘master regulators’ indicates that MADS-RIN, NAC-NOR, Nor-like1 and other MADS and NAC genes, together with ethylene, promote the full expression of genes required for further ethylene synthesis and change in colour, flavour, texture and progression of ripening. Several different types of non-coding RNAs are involved in regulating expression of ripening genes, but further clarification of their diverse mechanisms of action is required. We discuss a model that integrates the main hormonal and genetic regulatory interactions governing the ripening of tomato fruit and consider variations in ripening regulatory circuits that operate in other fruits.

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“…The functions of the CUC genes are likely to be conserved widely across eudicots (Aida et al ., 1997; Weir et al ., 2004; Cheng et al ., 2012; Wang et al ., 2019; Zheng et al ., 2019); however, there have been no functional studies on these genes in monocots.…”

Section: Discussionmentioning

confidence: 99%

OsmiR164‐targeted OsNAM, a boundary gene, plays important roles in rice leaf and panicle development

Chang

Xun

et al. 2021

The Plant Journal

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SUMMARY The CUP‐SHAPED COTYLEDON (CUC) genes (CUC1, CUC2 and CUC3) regulate organ boundary formation in Arabidopsis. However, the functions of their homologous genes in rice (Oryza sativa) are still unknown. Here, we have identified an orthologous gene of CUC1 and CUC2 in rice, named OsNAM. Subcellular localization and yeast two‐hybrid assay results have suggested that OsNAM encodes a conserved nuclear NAC (NAM/ATAF1/CUC2) protein with a transcriptional activator. The null mutant osnam‐1 presented a fused leaf structure, small panicles, reduced branches and aberrant floral organ identities when compared with those of the wild type. Beta‐glucuronidase staining and GFP reporter lines indicated that OsNAM was expressed in young tissues and that its boundary enrichment expression was regulated by OsmiR164. Loss‐of‐function mutants for OsCUC3 resulted in no obvious defects throughout rice development. The osnam oscuc3 double mutant, however, resulted in severe leaf fusion of the first two leaves, while the osnam single mutant showed a similar phenotype from the seventh leaf. These results indicated that OsNAM and OsCUC3 act redundantly for boundary specification during post‐embryonic development. Overall, we describe the biological functions of OsNAM and OsCUC3 in rice development and the expression characteristics of OsNAM. This work reveals the important role of CUC genes in rice.

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Genome‐wide analysis of coding and non‐coding RNA reveals a conserved miR164‐NAC regulatory pathway for fruit ripening

Cited by 100 publications

References 72 publications

A Malvaceae-specific miRNA targeting the newly duplicated GaZIP1L to regulate Zn2+ ion transporter capacity in cotton ovules

A Malvaceae-specific miRNA targeting the newly duplicated GaZIP1L to regulate Zn2+ ion transporter capacity in cotton ovules

Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening

OsmiR164‐targeted OsNAM, a boundary gene, plays important roles in rice leaf and panicle development

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