Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.)

Wang, Jinglei; Yang, Qin; Cheng, Feng; Chen, Xiaohua; Zhang, Xiaohui; Wang, Haiping; Song, Jiangping; Duan, Mengmeng; Yang, Haohui; Li, Xixiang

doi:10.1186/s12864-017-4377-z

Cited by 19 publications

(26 citation statements)

References 57 publications

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“…Previous studies have revealed that the circadian clock is tissue-specific (Thain et al , 2002; Endo et al , 2014; Bordage et al , 2016). Differential expression of clock genes has been reported in several tissues including seeds, roots, leaves, stems and flowers at several developmental stages in different plant species such as bamboo (Dutta et al , 2018), radish (Wang et al , 2017) or daisy (Fu et al , 2014). The present study has covered several clock genes, including GI and PRRs paralogs, in petunia leaves and petals and our results are consistent with the existence of organ-specific biological clocks in plants.…”

Section: Discussionmentioning

confidence: 99%

Molecular and transcriptional structure of the petal and leaf circadian clock inPetunia hybrida

Terry

Carrera-Alesina

Weiß

et al. 2019

Preprint

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The plant circadian clock coordinates environmental signals with internal processes. We characterized the genomic and transcriptomic structure of the Petunia hybrida W115 clock in leaves and petals. We found three levels of evolutionary differences. First, PSEUDO-RESPONSE REGULATORS PhPRR5a, PhPRR5b, PhPRR7a, PhPRR7b, and GIGANTEA PhGI1 and PhGI2, differed in gene structure including exon number and deletions including the CCT domain of the PRR family. Second, leaves showed preferential day expression while petals tended to display night expression. Under continuous dark, most genes were delayed in leaves and petals. Importantly, photoperiod sensitivity of gene expression was tissue specific as TIMING OF CAB EXPRESSION PhNTOC1 was affected in leaves but not in petals, and PhPRR5b, PhPRR7b and the ZEITLUPE ortholog CHANEL, PhCHL, were modified in petals but not leaves. Third, we identified a strong transcriptional noise at different times of the day, and high robustness at dawn in leaves and dusk in petals, coinciding with the coordination of photosynthesis and scent emission. Our results indicate multilayered evolution of the Petunia clock including gene structure, number of genes and transcription patterns. The major transcriptional reprogramming of the clock in petals, with night expression may be involved in controlling scent emission in the dark.HighlightThe petunia leaf circadian clock shows maxima during the day while petal clock does it during the night. Reaction to dark is organ specific.

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Section: Discussionmentioning

confidence: 99%

Molecular and transcriptional structure of the petal and leaf circadian clock inPetunia hybrida

Terry

Carrera-Alesina

Weiß

et al. 2019

Preprint

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“…In this study, a total of 1064, 510, and 524 flowering-time genes were identified from B. napus , B. rapa , and B. oleracea , respectively. Compared to other crops or plants, it appears that Brassica crops possess more flowering-time genes [ 22 , 24 , 40 ], due to whole genome triplication (WGT) and a genome merging event during their evolution [ 32 ]. However, no orthologs for some flowering-time genes were found in the Brassica species we studied, suggesting gene loss or genome contraction may have occurred in Brassica after WGT [ 32 , 34 , 41 ].…”

Section: Discussionmentioning

confidence: 99%

“…Understanding the control of flowering time in crops is not only important for improving crop yield, but also provides a theoretical basis for cultivating crops using diverse farming practices. To date, flowering-time genes have been extensively identified and studied in several crops, including cotton ( Gossypium raimondii ), radish ( Raphanus sativus ), wheat ( Triticum aestivum ), and barley ( Hordeum vulgare ) [ 21 , 22 , 23 , 24 , 25 ]. However, this is not the case for crops from the genus Brassica .…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of Flowering-Time Genes in Brassica Species and Reveals a Correlation between Selective Pressure and Expression Patterns of Vernalization-Pathway Genes in Brassica napus

Fan

et al. 2018

IJMS

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Flowering time is a key agronomic trait, directly influencing crop yield and quality. Many flowering-time genes have been identified and characterized in the model plant Arabidopsis thaliana; however, these genes remain uncharacterized in many agronomically important Brassica crops. In this study, we identified 1064, 510, and 524 putative orthologs of A. thaliana flowering-time genes from Brassica napus, Brassica rapa, and Brassica oleracea, respectively, and found that genes involved in the aging and ambient temperature pathways were fewer than those in other flowering pathways. Flowering-time genes were distributed mostly on chromosome C03 in B. napus and B. oleracea, and on chromosome A09 in B. rapa. Calculation of non-synonymous (Ka)/synonymous substitution (Ks) ratios suggested that flowering-time genes in vernalization pathways experienced higher selection pressure than those in other pathways. Expression analysis showed that most vernalization-pathway genes were expressed in flowering organs. Approximately 40% of these genes were highly expressed in the anther, whereas flowering-time integrator genes were expressed in a highly organ-specific manner. Evolutionary selection pressures were negatively correlated with the breadth and expression levels of vernalization-pathway genes. These findings provide an integrated framework of flowering-time genes in these three Brassica crops and provide a foundation for deciphering the relationship between gene expression patterns and their evolutionary selection pressures in Brassica napus.

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“…Genes involved in flowering pathways in B. rapa have been identified (Wang et al, 2017), and 89 genes mainly involved in vernalization and autonomous pathways were selected in this study (Table S4). In our RNA-seq data, 29 out of 89 genes showed differential expression in vernalized samples compared with nonvernalized samples for at least one cold treatment condition ( Fig.…”

Section: Transcriptional Changes In Flowering Pathway Genes Followingmentioning

confidence: 99%

Gene Expression Analysis in Response to Vernalization in Chinese Cabbage (<i>Brassica rapa</i> L.)

et al. 2020

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Chinese cabbage (Brassica rapa L. var. pekinensis) is an economically and agriculturally significant leafy vegetable that is extensively cultivated throughout the world. Vernalization is exposure to prolonged cold that alters gene expression and accelerates a transition from the vegetative to reproductive phase. Premature bolting caused by exposure to cold inhibits head production and reduces the yield of Chinese cabbage, and developing a late bolting line is important for breeding. Therefore, it is critical to identify the genes showing differential expression patterns during cold treatment in Chinese cabbage. However, there are few studies on the transcriptome profiling of different durations of cold treatments in Chinese cabbage. Here, we analyzed the gene expression profiles in a Chinese cabbage inbred line, RJKB-T24, given different durations of cold treatments using RNA sequencing. Differentially expressed genes (DEGs) between non-vernalized and vernalized samples tended to be downregulated, and some genes involved in the flowering pathway (including BrFLC and BrMAF genes) were downregulated following cold treatment. Functional enrichment analysis indicated that some DEGs were involved in the stress response and hormone signaling pathways. For genes involved in the FRI-containing complex, a known activator of FLC in Arabidopsis thaliana, only BrFRL1 showed changes in expression. In contrast to A. thaliana, BrVIP and BrVRN genes showed different expression patterns between paralogs during cold treatment, suggesting that Chinese cabbage's flowering pathway is somehow different and more complex than in A. thaliana. These outcomes provide significant insights into the genetic control of bolting and flowering that occur during the vernalization of Chinese cabbage.

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Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.)

Cited by 19 publications

References 57 publications

Molecular and transcriptional structure of the petal and leaf circadian clock inPetunia hybrida

Molecular and transcriptional structure of the petal and leaf circadian clock inPetunia hybrida

Genome-Wide Identification of Flowering-Time Genes in Brassica Species and Reveals a Correlation between Selective Pressure and Expression Patterns of Vernalization-Pathway Genes in Brassica napus

Gene Expression Analysis in Response to Vernalization in Chinese Cabbage (<i>Brassica rapa</i> L.)

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