Stages identifying and transcriptome profiling of the floral transition in Juglans regia

Quan, Shaowen; Niu, Jianxin; Zhou, Li; Xu, Hang; Ma, Lan; Yang, Qin

doi:10.1038/s41598-019-43582-z

Cited by 16 publications

(17 citation statements)

References 54 publications

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“…In our data, the PIF3, COL, CHS, and FT genes, which are related to the photoperiod (circadian rhythm), increased from BS to FS, while CDF1, which inhibits the expression of CO, was downregulated (Appendix S2), indicating that the photoperiod positively mediates the saffron flowering transition. Similar observations have been reported in A. sinensis 40 and Juglans regia 49 .…”

Section: Discussionsupporting

confidence: 90%

Transcriptome profiling of the flowering transition in saffron (Crocus sativus L.)

Liu

Tang

et al. 2020

Sci Rep

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Saffron, derived from the stigma of Crocus sativus, is not only a valuable traditional Chinese medicine but also the expensive spice and dye. Its yield and quality are seriously influenced by its flowering transition. However, the molecular regulatory mechanism of the flowering transition in C. sativus is still unknown. In this study, we performed morphological, physiological and transcriptomic analyses using apical bud samples from C. sativus during the floral transition process. Morphological results indicated that the flowering transition process could be divided into three stages: an undifferentiated period, the early flower bud differentiation period, and the late flower bud differentiation period. Sugar, gibberellin (GA 3), auxin (IAA) and zeatin (ZT) levels were steadily upregulated, while starch and abscisic acid (ABA) levels were gradually downregulated. Transcriptomic analysis showed that a total of 60 203 unigenes were identified, among which 19 490 were significantly differentially expressed. Of these, 165 unigenes were involved in flowering and were significantly enriched in the sugar metabolism, hormone signal transduction, cell cycle regulatory, photoperiod and autonomous pathways. Based on the above analysis, a hypothetical model for the regulatory networks of the saffron flowering transition was proposed. This study lays a theoretical basis for the genetic regulation of flowering in C. sativus. Crocus sativus L., commonly called saffron, is a perennial stemless herb belonging to the family Iridaceae (monocots), which is widely distributed in Iran, Spain, Greece, Italy and Nepal 1. Due to the triploidy of its chromosomes, this plant produces sterile flowers and reproduces asexually by corm nutrition. Saffron was introduced to China from abroad, passing through Tibet, and has been successfully cultivated in many of its provinces, such as Shanghai, Zhejiang, Sichuan and Anhui, since the 1970s. The flower, the most valuable part of saffron, consists of six tepals, three stamens and three stigmas. Among these, the stigma is widely used as a spice or coloring and flavoring agent in both the agro-food and cosmetic industries 2. The stigma is also used as a medicine due to its important pharmacological efficiency 3. Thus, saffron is greatly required worldwide due to its wide use. However, in recent years, the saffron flower has experienced increased incidences of withering, rotting, and delayed flowering, which has severely affected the quality and quantity of its stigmas and restricted the sustainable development of the saffron industry. Therefore, this study on the molecular regulatory mechanisms of the saffron flowering transition is particularly urgent and important for understanding and solving the problems related to saffron flowering. The complex process of the flowering transition is coregulated by both the external environment and the internal factors in plants to ensure flowering at an appropriate time 4. In the model plant Arabidopsis thaliana, the flowering transition was found to mainly invo...

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Section: Discussionsupporting

confidence: 90%

Transcriptome profiling of the flowering transition in saffron (Crocus sativus L.)

Liu

Tang

et al. 2020

Sci Rep

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“…Expression analysis of critical genes helped to dissect the genetic basis of important traits, such as floral in hickory [ 46 ] and Persian walnut [ 47 ]. Based on our analysis, the pathway of circadian rhythm-plant was enriched during the development of flower buds of walnut, which is also observed by Quan [ 15 ]. A total of 14 DEGs involved to the circadian rhythm were identified during the study.…”

Section: Discussionsupporting

confidence: 75%

“…GI is nuclear protein physically interacted with diverse proteins acted under short period [ 49 ]. The interaction of JrGI and JrCOP1 was previously found during the floral transition in walnut [ 15 ]. In this context, JrGI was up-regulated, while JrCOP1-like ( WALNUT_00024934-RA ) was down-regulated from P04 to P05, indicating their opposite regulation pattern.…”

Section: Discussionmentioning

confidence: 96%

“…MicroRNAs sequencing revealed that the differentially expressed miRNAs mainly enriched to ubiquitin mediated proteolysis, RNA degradation and various carbohydrate metabolism pathways were related to the female flower induction [ 14 ]. Transcriptome profiling identified 374 genes, which differentially expressed to regulate the transition between female buds and leaf buds [ 15 ]. To date, however, none of the reported miRNAs or genes can completely explain the genetic basis of flower bud development in walnut.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome profiling based on Illumina- and SMRT-based RNA-seq reveals circadian regulation of key pathways in flower bud development in walnut

Luo

Han

et al. 2021

PLoS ONE

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Flower bud development is a defining feature of walnut, which contributes to the kernel yield, yield stability, fruit quality and commodity value. However, little is known about the mechanism of the flower bud development in walnut. Here, the stages of walnut female flower bud development were divided into five period (P01-05) by using histological observation. They were further studied through PacBio Iso-Seq and RNA-seq analysis. Accordingly, we obtained 52,875 full-length transcripts, where 4,579 were new transcripts, 3,065 were novel genes, 1,437 were consensus lncRNAs and 20,813 were alternatively spliced isoforms. These transcripts greatly improved the current genome annotation and enhanced our understanding of the walnut transcriptome. Next, RNA sequencing of female flower buds at five periods revealed that circadian rhythm-plant was commonly enriched along with the flower bud developmental gradient. A total of 14 differentially expressed genes (DEGs) were identified, and six of them were confirmed by real-time quantitative analysis. Additionally, six and two differentially expressed clock genes were detected to be regulated by AS events and lncRNAs, respectively. All these detected plant circadian genes form a complex interconnected network to regulate the flower bud development. Thus, investigation of key genes associated with the circadian clock could clarify the process of flower bud development in walnut.

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“…Transcriptome sequencing and library construction were reported in our previous study 57 . Expression analysis of walnut GRAS members was evaluated using the walnut RNA-sequence data among different tissues (leaf bud and female flower bud), development stages (F_1, F_2, F_3).…”

Section: Methodsmentioning

confidence: 99%

Genome-wide Identification, Classification, Expression and Duplication Analysis of GRAS Family Genes in Juglans regia L.

Quan

Niu

Zhou

et al. 2019

Sci Rep

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Fifty-two GRAS genes are identified in walnut genome. Based on the evolutionary relationship and motif analysis, the walnut GRAS gene family was divided into eight subfamilies, and the sequence features analysis of Jr GRAS proteins showed that the Jr GRAS protein sequences were both conserved and altered during the evolutionary process. Gene duplication analysis indicated that seven GRAS genes in walnut have orthologous genes in other species, and five of them occurred duplicated events in walnut genome. Expression pattern analysis of the GRAS family genes in walnut showed that two Jr GRAS genes ( JrCIGRa-b and JrSCL28a ) were differentially expressed between flower bud and leaf bud (p < 0.01), and two JrGRAS genes ( JrCIGRa - b and JrSCL1 3 b - d ) were differentially expressed between the different development stages of flower buds transition (p < 0.01), besides, three hub genes ( JrGAIa , JrSCL3f and JrSHRc ) were identified by co-expression analysis, which suggested these GRAS genes may play an important role in regulating the development of apical meristem in walnut. This study laid a foundation for further understanding of the function of GRAS family genes in walnut.

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Stages identifying and transcriptome profiling of the floral transition in Juglans regia

Cited by 16 publications

References 54 publications

Transcriptome profiling of the flowering transition in saffron (Crocus sativus L.)

Transcriptome profiling of the flowering transition in saffron (Crocus sativus L.)

Transcriptome profiling based on Illumina- and SMRT-based RNA-seq reveals circadian regulation of key pathways in flower bud development in walnut

Genome-wide Identification, Classification, Expression and Duplication Analysis of GRAS Family Genes in Juglans regia L.

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