Identification of bolting-related microRNAs and their targets reveals complex miRNA-mediated flowering-time regulatory networks in radish (Raphanus sativus L.)

Nie, Shaoping; Xu, Liang; Wang, Yan; Huang, Danqiong; Muleke, Everlyne M.; Sun, Xiaochuan; Wang, Ronghua; Xie, Yang; Gong, Yiqin; Liu, Liwang

doi:10.1038/srep14034

Cited by 46 publications

(43 citation statements)

References 60 publications

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“…At present, we cannot exclude the possibility that this gene acts like Arabidopsis FRI, but it is also possible that yet another gene serves this function in radish. Recently, Nie et al reported genes associated with bolting in radish based on de novo transcriptome analysis (Nie et al, 2015). They found one FRI gene in radish, but it is not clear whether its sequence is also present in the current version of the radish genome.…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, there may be some errors in gene prediction. Recently, Nie et al reported three radish LFY genes (Nie et al, 2015). cDNA cloning and detailed analysis may help resolve the apparent discrepancy between our studies.…”

Section: Discussionmentioning

confidence: 99%

“…Although flowering is the most important agricultural trait in cultivation, Ft genes and their associated mechanisms have not been extensively analyzed at a whole-genome scale in radish. Recently, bolting-related miRNAs and their targets were identified in radish using small RNA libraries from leaves at vegetative and reproductive stages (Nie et al, 2015). In addition, differentially expressed genes (DEGs) involved in the transition from vegetative growth to flowering, as well as flowering itself, were identified in radish by RNA-Seq (Nie et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Identification of Flowering-Related Genes Responsible for Differences in Bolting Time between Two Radish Inbred Lines

et al. 2016

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Late bolting after cold exposure is an economically important characteristic of radish (Raphanus sativus L.), an important Brassicaceae root vegetable crop. However, little information is available regarding the genes and pathways that govern flowering time in this species. We performed high-throughput RNA sequencing analysis to elucidate the molecular mechanisms that determine the differences in flowering times between two radish lines, NH-JS1 (late bolting) and NH-JS2 (early bolting). In total, 71,188 unigenes were identified by reference-guided assembly, of which 309, 788, and 980 genes were differentially expressed between the two inbred lines after 0, 15, and 35 days of vernalization, respectively. Among these genes, 218 homologs of Arabidopsis flowering-time (Ft) genes were identified in the radish, and 49 of these genes were differentially expressed between the two radish lines in the presence or absence of vernalization treatment. Most of the Ft genes up-regulated in NH-JS1 vs. NH-JS2 were repressors of flowering, such as RsFLC, consistent with the late-bolting phenotype of NH-JS1. Although, the functions of genes down-regulated in NH-JS1 were less consistent with late-bolting characteristics than the up-regulated Ft genes, several Ft enhancer genes, including RsSOC1, a key floral integrator, showed an appropriate expression to the late-bolting phenotype. In addition, the patterns of gene expression related to the vernalization pathway closely corresponded with the different bolting times of the two inbred lines. These results suggest that the vernalization pathway is conserved between radish and Arabidopsis.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification of Flowering-Related Genes Responsible for Differences in Bolting Time between Two Radish Inbred Lines

et al. 2016

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“…In the complete life cycle of radish, bolting and flowering are some of the critical factors which affect the yield and quality. Premature bolting seriously decreases the production of vegetable crops which ultimately lead to the reduction of economic benefits ( Nie et al, 2015 ). Consequently, it is extremely essential to explore the MADS-box gene family whose primary function is to regulate flowering time and floral organ development.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Characterization of the MADS-Box Gene Family in Radish (Raphanus sativus L.) and Assessment of Its Roles in Flowering and Floral Organogenesis

Wang

et al. 2016

Front. Plant Sci.

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The MADS-box gene family is an important transcription factor (TF) family that is involved in various aspects of plant growth and development, especially flowering time and floral organogenesis. Although it has been reported in many plant species, the systematic identification and characterization of MADS-box TF family is still limited in radish (Raphanus sativus L.). In the present study, a comprehensive analysis of MADS-box genes was performed, and a total of 144 MADS-box family members were identified from the whole radish genome. Meanwhile, a detailed list of MADS-box genes from other 28 plant species was also investigated. Through the phylogenetic analysis between radish and Arabidopsis thaliana, all the RsMADS genes were classified into two groups including 68 type I (31 Mα, 12 Mβ and 25Mγ) and 76 type II (70 MIKCC and 6 MIKC∗). Among them, 41 (28.47%) RsMADS genes were located in nine linkage groups of radish from R1 to R9. Moreover, the homologous MADS-box gene pairs were identified among radish, A. thaliana, Chinese cabbage and rice. Additionally, the expression profiles of RsMADS genes were systematically investigated in different tissues and growth stages. Furthermore, quantitative real-time PCR analysis was employed to validate expression patterns of some crucial RsMADS genes. These results could provide a valuable resource to explore the potential functions of RsMADS genes in radish, and facilitate dissecting MADS-box gene-mediated molecular mechanisms underlying flowering and floral organogenesis in root vegetable crops.

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“…MicroRNAs (miRNAs) are a class of non-coding endogenous ~21 nt small RNAs (Bartel et al 2004) that play vital regulatory roles in plant growth and development, such as flowering-time regulation (Nie et al 2015), heat tolerance (Liu et al 2017a), accumulation of anthocyanins (Liu et al 2017b), response to the phytohormone abscisic acid (Duan et al 2016), cotton fiber elongation (Wang et al 2016b), pollen or flower bud development (Shen et al 2011; Yang et al 2013; Jiang et al 2014; Ding et al 2016; Zhang et al 2016), and so on. Among all of the miRNA families, MIR156 is one of the most conserved families in plants (Wang et al 2016c) and regulates the vegetative phase change floral transition, integrated into flowering pathways by target squamosa promoter binding protein-like (SPL) transcription factors (Spanudakis et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Exploration of miRNA-mediated fertility regulation network of cytoplasmic male sterility during flower bud development in soybean

Ding

Zhang

Ruan

et al. 2018

Preprint

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34Cytoplasmic male sterility (CMS) plays an important role in the production of soybean hybrid 35 seeds. MicroRNAs (miRNAs) are a class of non-coding endogenous ~21 nt small RNAs that 36 play crucial roles in flower and pollen development by targeting genes in plants. Here, two 37 small RNA libraries and two degradome libraries were constructed from the flower buds of 38 the soybean CMS line NJCMS1A and its restorer (Rf) line NJCMS1C. Following 39 high-throughput sequencing, 558 known miRNAs, 103 novel miRNAs on the other arm of 40 known pre-miRNAs, 10 novel miRNAs, and a number of base-edited miRNAs were 41 identified. Among the identified miRNAs, 76 differentially expressed miRNAs were 42 discovered with greater than two-fold changes between NJCMS1A and NJCMS1C. By 43 degradome analysis, a total of 466 distinct transcripts targeted by 200 miRNAs and 122 44 distinct transcripts targeted by 307 base-edited miRNAs were detected. Further integrated 45 analysis of transcriptome and small RNA found some miRNAs and their targets' expression 46 patterns showing a negative correlation, such as miR156b-GmSPL and miR4413b-GmPPR. 47 Previous reports showed that these targets might be related to flower bud development, 48 suggesting that miRNAs might act as regulators of soybean CMS fertility. These findings may 49 provide a better understanding of the miRNA-mediated regulatory networks in CMS 50 mechanisms of soybean.51 52 KEYWORDS: Soybean (Glycine max (L.) Merr.), Cytoplasmic male sterility, Flower bud, 53 miRNA, Target gene 54 55 56Soybean is one of the most important oil crops in the world. However, soybean yields are 57 relatively low and the utilization of heterosis is one of the effective ways to improve them. 58Cytoplasmic male sterility (CMS) is a simple and efficient pollination control system that 59 plays an important role in the production of hybrid seed. CMS is caused by mitochondrial 60 genes with coupled nuclear genes, and CMS-based hybrid seed technology uses a three-line 61 system: the CMS line, the maintainer line, and the restorer of fertility (Rf) line (Chen et al. 62 2014). The CMS line is propagated by crossing with the maintainer line and by crossing the 63 CMS line with the Rf line, the male fertility of the F 1 plants can be restored by the Rf gene(s) 64 that come from the nuclear genome of the Rf line. Whether it is the production of CMS or F 1 65fertility restoration, a series of changes will occur at both the molecular and physiological 66 levels. In this process, the interaction between genes is very obvious. Therefore, the molecular 67 3 mechanism of CMS is a hot research topic and there may be a high degree of epigenetic 68 regulation involvement. 69 MicroRNAs (miRNAs) are a class of non-coding endogenous ~21 nt small RNAs (Bartel et 70 al. 2004) that play vital regulatory roles in plant growth and development, such as 71 flowering-time regulation (Nie et al. 2015), heat tolerance (Liu et al. 2017a), accumulation of 72 anthocyanins (Liu et al. 2017b), response to the phytohormone abs...

show abstract

Identification of bolting-related microRNAs and their targets reveals complex miRNA-mediated flowering-time regulatory networks in radish (Raphanus sativus L.)

Cited by 46 publications

References 60 publications

Identification of Flowering-Related Genes Responsible for Differences in Bolting Time between Two Radish Inbred Lines

Identification of Flowering-Related Genes Responsible for Differences in Bolting Time between Two Radish Inbred Lines

Genome-Wide Characterization of the MADS-Box Gene Family in Radish (Raphanus sativus L.) and Assessment of Its Roles in Flowering and Floral Organogenesis

Exploration of miRNA-mediated fertility regulation network of cytoplasmic male sterility during flower bud development in soybean

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