Comparative transcriptome analysis of nonchilled, chilled, and late-pink bud reveals flowering pathway genes involved in chilling-mediated flowering in blueberry

Song, Guo Qing; Chen, Qiuxia

doi:10.1186/s12870-018-1311-8

Cited by 41 publications

(63 citation statements)

References 51 publications

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“…Studies on transcriptome regulation based on phenotypes is a powerful research method [29,30]. Using this analytical method, DEGs and related regulatory pathways produced by Asiatic lily and tropical lotus during vernalization have been investigated [31,32].…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Vernalization Periods in Brassica rapa

Dai

Zhang

Sun

et al. 2020

Genes

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Brassica rapa is an important Chinese vegetable crop that is beneficial to human health. The primary factor affecting B. rapa yield is low temperature, which promotes bolting and flowering, thereby lowering its commercial value. However, quickened bolting and flowering can be used for rapid breeding. Therefore, studying the underlying molecular mechanism of vernalization in B. rapa is crucial for solving production-related problems. Here, the transcriptome of two B. rapa accessions were comprehensively analyzed during different vernalization periods. During vernalization, a total of 974,584,022 clean reads and 291.28 Gb of clean data were obtained. Compared to the reference genome of B. rapa, 44,799 known genes and 2280 new genes were identified. A self-organizing feature map analysis of 21,035 differentially expressed genes was screened in two B. rapa accessions, ‘Jin Wawa’ and ‘Xiao Baojian’. The analysis indicated that transcripts related to the plant hormone signal transduction, starch and sucrose metabolism, photoperiod and circadian clock, and vernalization pathways changed notably at different vernalization periods. Moreover, different expression patterns of TPS, UGP, CDF, VIN1, and seven hormone pathway genes were observed during vernalization between the two accessions. The transcriptome results of this study provide a new perspective on the changes that occur during B. rapa vernalization, as well as serve as an excellent reference for B. rapa breeding.

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Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Vernalization Periods in Brassica rapa

Dai

Zhang

Sun

et al. 2020

Genes

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“…Previous research has suggested that the openness of flower buds in woody plants was related to dormancy release [13][14][15]. Before the spring flowering of 'Changchun', the long dormancy process of flower buds was released, and the growth amount increased significantly.…”

Section: Flowering Initiation Is An Important Stage During 'Changchunmentioning

confidence: 96%

“…The increased level of PpEBB (EARLY BUD-BREAK) induced high levels of transcription of four PpCYCD3 (D-type CYCLIN) genes, which promoted cell division and resulted in a significant increase in the primordia size of Pyrus pyrifolia 'Kosui' lateral flower buds [14]. The profile of differentially expressed genes (DEGs) suggests that orthologs of FT, FD, TFL1 (TERMINAL FLOWER 1), LFY (LEAFY), and MADS-box genes were the major genes involved in chilling-mediated Vaccinium corymbosum bud-break [15]. Obviously, the identification of genes associated with flowering and dormancy release was due to the comparison of reproductive organs in different seasons.…”

mentioning

confidence: 99%

A New Insight into Flowering Regulation: Molecular Basis of Flowering Initiation in Magnolia × soulangeana ‘Changchun’

Jiang

Sun

Wei

et al. 2019

Genes

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Magnolia × soulangeana 'Changchun' are trees that bloom in spring and summer respectively after flower bud differentiation. Here, we use phenological and morphological observation and RNA-seq technology to study the molecular basis of flowering initiation in 'Changchun'. During the process of flowering initiation in spring and summer, the growth of expanded flower buds increased significantly, and their shape was obviously enlarged, which indicated that flowering was initiated. A total of 168,120 expressed genes were identified in spring and summer dormant and expanded flower buds, of which 11,687 genes showed significantly differential expression between spring and summer dormant and expanded flower buds. These differentially expressed genes (DEGs) were mainly involved in plant hormone signal transduction, metabolic processes, cellular components, binding, and catalytic activity. Analysis of differential gene expression patterns revealed that gibberellin signaling, and some transcription factors were closely involved in the regulation of spring and summer flowering initiation in 'Changchun'. A qRT-PCR (quantitative Real Time Polymerase Chain Reaction) analysis showed that BGISEQ-500 sequencing platform could truly reflect gene expression patterns. It also verified that GID1B (GIBBERELLIN INSENSITIVE DWARF1 B), GID1C, SPL8 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8), and GASA (GIBBERELLIC ACID-STIMULATED ARABIDOPSIS) family genes were expressed at high levels, while the expression of SPY (SPINDLY) was low during spring and summer flowering initiation. Meanwhile, the up-and down-regulated expression of, respectively, AGL6 (AGAMOUS-LIKE 6) and DREB3 (DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 3), AG15, and CDF1 (CYCLIC DOF FACTOR 1) might also be involved in the specific regulation of spring and summer flowering initiation. Obviously, flowering initiation is an important stage of the flowering process in woody plants, involving the specific regulation of relevant genes and transcription factors. This study provides a new perspective for the regulation of the flowering process in perennial woody plants.Genes 2020, 11, 15 2 of 18 Using Solexa/Illumina sequencing platform, researchers have identified almost all transcripts involved in flowering from the vegetative and flower buds in Dimocarpus longan, including putative homologues of DELLA protein, LFY (LEAFY), SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CO1) [2]. Meanwhile, compared to the apical meristem of vegetative growth, gibberellin 3 beta-hydroxylase 2 and LFY were both expressed higher in early flowering, indicated that GA pathway may be related to the early flowering of Angelica sinensis [3]. By comparing the differences in transcript expression levels between flowering and non-flowering Moso bamboo samples at different flowering developmental stages, researchers found that GAMYB, GID1 (GIBBERELLIN INSENSITIVE DWARF1), and GID2 were significantly up-regulated, while DELLA protein was down-regulated, and believed that bamboo flowering was associated with gibbere...

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“…Working in an antagonistic manner to VRN1 and VIN3, which downregulate repressors of endodormancy release, are FRIGIDA 4 and CONSTANS-like genes. Increased expression and activity of FRIGIDA 4 results in increased activity of repressors of endodormancy release, such as Flowering Locus C (FLC), in Arabidopsis [64] and blueberry [65]. FRIGIDA 4 decreased significantly in expression throughout conditioning in 'Bartlett', suggesting that its downregulation may correspond to decreased activation of ripening repressors in a role homologous to regulation of flowering time (Figure 4).…”

Section: Cold and Temperature Stress-induced Processesmentioning

confidence: 99%

Evidence for the Involvement of Vernalization-related Genes in the Regulation of Cold-induced Ripening in ‘D’Anjou’ and ‘Bartlett’ Pear Fruit

Hewitt

Hendrickson

Dhingra

2019

Preprint

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European pear (Pyrus communis L.) cultivars require a genetically pre-determined duration of cold-temperature exposure to induce autocatalytic system 2 ethylene biosynthesis and subsequent fruit ripening. The physiological responses of pear to cold-temperature-induced ripening have been well characterized, but the molecular mechanisms underlying this phenomenon continue to be elucidated. This study employed established cold temperature conditioning treatments for ripening of two pear cultivars, 'D'Anjou' and 'Bartlett'. Using a time-course transcriptomics approach, global gene expression responses of each cultivar were assessed at four different developmental stages during the cold conditioning process. Differential expression, functional annotation, and gene ontology enrichment analyses were performed. Interestingly, evidence for the involvement of cold-induced, vernalization-related genes and repressors of endodormancy release was found. These genes have not previously been described to play a role in fruit during the ripening transition. The resulting data provide insight into cultivar-specific mechanisms of cold-induced transcriptional regulation of ripening in European pear, as well as a unique comparative analysis of the two cultivars with very different cold conditioning requirements.For both cultivars, fruit softening accelerated once the fruit was transferred to 20°C. The rate of softening was more rapid for 'Bartlett' than 'D'Anjou'. RNAseq Assembly AnalysisRNAseq assembly generated 140077 contigs (Supplementary File 1). In the OmicsBox suite, the maSigPro R package was used to conduct time course differential expression analyses for both cultivars. 17,711 differentially expressed contigs (p<0.05) were identified for 'D'Anjou', with 7,174 of these contigs exhibiting significant linear or quadratic trends over time (R>0.8). In 'Bartlett' 31,481 contigs were identified as being differentially expressed, with 7,174 contigs exhibiting significant quadratic or linear trends over time (R>0.8) (Supplementary File 2). Similarities and differences in expression trends of contigs of interest between 'D'Anjou' and 'Bartlett', as well as expression patterns of differentially expressed contigs (DECs) associated with ethylene and phytohormone metabolism, abscisic acid metabolism, TCA cycle, respiration, were assessed. Additionally, in order to better understand the mechanisms underlying the chilling requirement for ripening in Pyrus, the expression of genes associated with: vernalization, flowering, dormancy, and other processes directly induced by cold/chilling were observed. Preclimacteric expression of AOX1 peaked during conditioning prior to onset of ripening (Figure 1), supporting the hypothesis. Additional key genes, including those that mediate vernalization and endodormancy release were also observed to be differentially expressed. Detailed analysis of RNAseq results and enriched gene ontologies related to phytohormone metabolism and coldresponse pathways are discussed in detail in the following sections.

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Comparative transcriptome analysis of nonchilled, chilled, and late-pink bud reveals flowering pathway genes involved in chilling-mediated flowering in blueberry

Cited by 41 publications

References 51 publications

Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Vernalization Periods in Brassica rapa

Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Vernalization Periods in Brassica rapa

A New Insight into Flowering Regulation: Molecular Basis of Flowering Initiation in Magnolia × soulangeana ‘Changchun’

Evidence for the Involvement of Vernalization-related Genes in the Regulation of Cold-induced Ripening in ‘D’Anjou’ and ‘Bartlett’ Pear Fruit

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