De novo transcriptome analysis reveals insights into dynamic homeostasis regulation of somatic embryogenesis in upland cotton (G. hirsutum L.)

Wei, Cheng; Zhu, Huayu; Tian, Wengang; Zhu, Shanfeng; Xiong, Xingjiang; Sun, Yuqiang; Zhu, Qian‐Hao; Sun, Jie

doi:10.1007/s11103-016-0511-6

Cited by 31 publications

(41 citation statements)

References 53 publications

(71 reference statements)

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“…Our callus differentiation rate statistics for exogenously applied auxin and cytokinin were consistent with previous studies, i.e., the induction of EC and SEs, and the concentration of 2, 4-D in the medium was replaced by a combination of IBA and KT [24,37]. In this experiment, the role of auxin and cytokinin was not achieved alone, but by interacting with other pathways and components involved in the differentiation and development of SEs, such as their upstream TF regulators and hormone signaling pathways [38]. Wang et al [39] found that, in cotton tissue cultures, the effect of IBA is stronger than that of the other auxins or auxin analogues.…”

Section: Iba Embryogenic Inductive Effect and Dose Effect During Diffsupporting

confidence: 86%

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Dose IBA-Induced Embryogenic Redifferentiation in Cotton

Fan

Guo

et al. 2020

IJMS

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The somatic embryogenesis (SE) process of plants is regulated by exogenous hormones. During the SE, different genes sensitively respond to hormone signals through complex regulatory networks to exhibit plant totipotency. When cultured in indole-3-butyric acid (IBA) concentration gradient medium supplemented with 0 mg dm −3 , 0.025 mg dm −3 , and 0.05 mg dm −3 IBA, the callus differentiation rate first increased then decreased in cotton. To characterize the molecular basis of IBA-induced regulating SE, transcriptome analysis was conducted on embryogenic redifferentiation. Upon the examination of the IBA's embryogenic inductive effect, it was revealed that pathways related to plant hormone signal transduction and alcohol degradation were significantly enriched in the embryogenic responsive stage (5 days). The photosynthesis, alcohol metabolism and cell cycle pathways were specifically regulated in the pre-embryonic initial period (20 days). Upon the effect of the IBA dose, in the embryogenic responsive stage (5 days), the metabolism of xenobiotics by the cytochrome P450 pathway and secondary metabolism pathways of steroid, flavonoid, and anthocyanin biosynthesis were significantly enriched. The phenylpropanoid, brassinosteroid, and anthocyanin biosynthesis pathways were specifically associated in the pre-embryonic initial period (20 days). At different developmental stages of embryogenic induction, photosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, mitogen-activated protein kinase (MAPK) signaling, xenobiotics metabolism by cytochrome P450, and brassinosteroid biosynthesis pathways were enriched at low a IBA concentration. Meanwhile, at high IBA concentration, the carbon metabolism, alcohol degradation, circadian rhythm and biosynthesis of amino acids pathways were significantly enriched. The results reveal that complex regulating pathways participate in the process of IBA-induced redifferentiation in cotton somatic embryogenesis. In addition, collections of potential essential signaling and regulatory genes responsible for dose IBA-induced efficient embryogenic redifferentiation were identified. Quantitative real-time PCR (qRT-PCR) was performed on the candidate genes with different expression patterns, and the results are basically consistent with the RNA-seq data. The results suggest that the complicated and concerted IBA-induced mechanisms involving multiple cellular pathways are responsible for dose-dependent plant growth regulator-induced SE. This report represents a systematic study and provides new insight into molecular signaling and regulatory basis underlying the process of dose IBA-induced embryogenic redifferentiation during SE.

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Section: Iba Embryogenic Inductive Effect and Dose Effect During Diffsupporting

confidence: 86%

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Dose IBA-Induced Embryogenic Redifferentiation in Cotton

Fan

Guo

et al. 2020

IJMS

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“…It seems that not the initial level of IAA in explant tissue but rather a dynamic increase of the endogenous auxin content in response to the SE-induction factors might provide an indispensable signal for the embryogenic transition. Relevantly, a significant increase in the IAA content was reported to accompany early SE induction in different plants including carrot [48], sunflower [49], robusta coffee [50][51][52], alfalfa [53], pineapple guava [54], Arabidopsis [36], cotton [55] and Norway spruce [56]. Besides in vitro culture conditions, transgenic plants of Arabidopsis that produced somatic embryos in planta as a result of the overexpression of the LEAFY COTYLEDON2 (LEC2) gene were also found to accumulate IAA [57].…”

Section: Biosynthesis and Accumulation Of Auxin During Sementioning

confidence: 99%

Current Perspectives on the Auxin-Mediated Genetic Network that Controls the Induction of Somatic Embryogenesis in Plants

Wójcik

Wójcikowska

Gaj

2020

IJMS

109

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Auxin contributes to almost every aspect of plant development and metabolism as well as the transport and signalling of auxin-shaped plant growth and morphogenesis in response to endo- and exogenous signals including stress conditions. Consistently with the common belief that auxin is a central trigger of developmental changes in plants, the auxin treatment of explants was reported to be an indispensable inducer of somatic embryogenesis (SE) in a large number of plant species. Treating in vitro-cultured tissue with auxins (primarily 2,4-dichlorophenoxyacetic acid, which is a synthetic auxin-like plant growth regulator) results in the extensive reprogramming of the somatic cell transcriptome, which involves the modulation of numerous SE-associated transcription factor genes (TFs). A number of SE-modulated TFs that control auxin metabolism and signalling have been identified, and conversely, the regulators of the auxin-signalling pathway seem to control the SE-involved TFs. In turn, the different expression of the genes encoding the core components of the auxin-signalling pathway, the AUXIN/INDOLE-3-ACETIC ACIDs (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs), was demonstrated to accompany SE induction. Thus, the extensive crosstalk between the hormones, in particular, auxin and the TFs, was revealed to play a central role in the SE-regulatory network. Accordingly, LEAFY COTYLEDON (LEC1 and LEC2), BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15) and WUSCHEL (WUS) were found to constitute the central part of the complex regulatory network that directs the somatic plant cell towards embryogenic development in response to auxin. The revealing picture shows a high degree of complexity of the regulatory relationships between the TFs of the SE-regulatory network, which involve direct and indirect interactions and regulatory feedback loops. This review examines the recent advances in studies on the auxin-controlled genetic network, which is involved in the mechanism of SE induction and focuses on the complex regulatory relationships between the down- and up-stream targets of the SE-regulatory TFs. In particular, the outcomes from investigations on Arabidopsis, which became a model plant in research on genetic control of SE, are presented.

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“…More recently, RNA deep-sequencing technology has provided a platform for analysis of differences in gene expression 17 . There are reports demonstrating that hormonal signaling pathways such as auxin and cytokinin 16 , as well as stress-responsive pathways are critical during cotton SE development 18 . However, the initial SE molecular mechanisms have not been thoroughly studied and are still unclear in different dedifferentiated cotton cultivars.…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome Analysis of SE initial dedifferentiation in cotton of different SE capability

Cao

Zheng

et al. 2017

Sci Rep

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Somatic embryogenesis (SE) is a critical transition from vegetative to embryogenic growth in higher plants; however, few studies have investigated the mechanism that regulates SE initial differentiation. Most cotton varieties have not undergone regeneration by SE, so only a few varieties can be used in genetic engineering. Here, two varieties of cotton with different SE capabilities (HD, higher differentiation and LD, lower differentiation) were analyzed by high throughout RNA-Seq at the pre-induction stage (0h) and two induction stages (3h and 3d) under callus-induction medium (CIM). About 1150 million clean reads were obtained from 98.21% raw data. Transcriptomic analysis revealed that “protein kinase activity” and “oxidoreductase activity” were highly represented GO terms during the same and different treatment stages among HD and LD. Moreover, several stress-related transcription factors might play important roles in SE initiation. The SE-related regulation genes (SERKs) showed different expression patterns between HD and LD. Furthermore, the complex auxin and ethylene signaling pathway contributes to initiation of differentiation in SE. Thus, our RNA-sequencing of comparative transcriptome analysis will lay a foundation for future studies to better define early somatic formation in cotton with different SE capabilities.

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De novo transcriptome analysis reveals insights into dynamic homeostasis regulation of somatic embryogenesis in upland cotton (G. hirsutum L.)

Cited by 31 publications

References 53 publications

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Dose IBA-Induced Embryogenic Redifferentiation in Cotton

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Dose IBA-Induced Embryogenic Redifferentiation in Cotton

Current Perspectives on the Auxin-Mediated Genetic Network that Controls the Induction of Somatic Embryogenesis in Plants

Comparative Transcriptome Analysis of SE initial dedifferentiation in cotton of different SE capability

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