Expression profiles of organogenesis-related genes over the time course of one-step de novo shoot organogenesis from intact seedlings of kohlrabi

Ćosić﻿﻿﻿, Tatjana; Raspor, Martin; Savić﻿﻿﻿, Jelena; Cingel, Aleksandar; Matekalo, Dragana; Zdravković-Korać, Snežana; Ninković﻿﻿﻿, Slavica

doi:10.1016/j.jplph.2018.11.004

Cited by 12 publications

(19 citation statements)

References 80 publications

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“…Arabidopsis rgd3 mutants of this gene showed impairment in root development at high temperatures if the mutation was localized in the middle of protein, between conserved domains, while seedlings with the mutation within HEAT repeats exhibited such phenotype constitutively [ 39 ]. Expression of that gene can be both up- and down-regulated by cytokinins during de novo shoot organogenesis in Arabidopsis , depending on the developmental stage [ 40 ]. Differential expression of the carrot DcBTAF1 among thick- and thin-rooted cultivars and cultivated and wild carrots may suggest its involvement in the dose-related regulation of expression of downstream genes involved in storage root formation.…”

Section: Discussionmentioning

confidence: 99%

Mining for Candidate Genes Controlling Secondary Growth of the Carrot Storage Root

Macko-Podgórni

Stelmach

Kwolek

et al. 2020

IJMS

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Background: Diverse groups of carrot cultivars have been developed to meet consumer demands and industry needs. Varietal groups of the cultivated carrot are defined based on the shape of roots. However, little is known about the genetic basis of root shape determination. Methods: Here, we used 307 carrot plants from 103 open-pollinated cultivars for a genome wide association study to identify genomic regions associated with the storage root morphology. Results: A 180 kb-long region on carrot chromosome 1 explained 10% of the total observed phenotypic variance in the shoulder diameter. Within that region, DcDCAF1 and DcBTAF1 genes were proposed as candidates controlling secondary growth of the carrot storage root. Their expression profiles differed between the cultivated and the wild carrots, likely indicating that their elevated expression was required for the development of edible roots. They also showed higher expression at the secondary root growth stage in cultivars producing thick roots, as compared to those developing thin roots. Conclusions: We provided evidence for a likely involvement of DcDCAF1 and/or DcBTAF1 in the development of the carrot storage root and developed a genotyping assay facilitating the identification of variants in the region on carrot chromosome 1 associated with secondary growth of the carrot root.

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Section: Discussionmentioning

confidence: 99%

Mining for Candidate Genes Controlling Secondary Growth of the Carrot Storage Root

Macko-Podgórni

Stelmach

Kwolek

et al. 2020

IJMS

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“…The identification of cytokinin pathway genes, GRAS family gene, AP2/ERF family gene, KNOX, CDK, YABBY, and YUCCA as DEGs, and the further expression validation of them using qRT-PCR, are likely to promise their consistent roles in shoot regeneration with P. euphratica. Taking CDK as an example, which is essential to regulate G1/S and G2/M transformation in cell division during all stages of cell cycle, is equally indispensable for cell expansion in leaf, plant cell signal transduction, and regulation of differentiation [30]. In this study, the up-regulated expression of CDK in LD group potentially indicates that CDK overexpression causes plants lose the ability to form callus or regenerate shoots.…”

Section: Discussionmentioning

confidence: 71%

Identification of Shoot Differentiation-Related Genes in Populus euphratica Oliv.

Dong

Li-zhi

et al. 2019

Genes

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De novo shoot regeneration is one of the important manifestations of cell totipotency in organogenesis, which reflects a survival strategy organism evolved when facing natural selection. Compared with tissue regeneration, and somatic embryogenesis, de novo shoot regeneration denotes a shoot regeneration process directly from detatched or injured tissues of plant. Studies on plant shoot regeneration had identified key genes mediating shoot regeneration. However, knowledge was derived from Arabidopsis; the regeneration capacity is hugely distinct among species. To achieve a comprehensive understanding of the shoot regeneration mechanism from tree species, we select four genetic lines of Populus euphratica from a natural population to be sequenced at transcriptome level. On the basis of the large difference of differentiation capacity, between the highly differentiated (HD) and low differentiated (LD) groups, the analysis of differential expression identified 4920 differentially expressed genes (DEGs), which were revealed in five groups of expression patterns by clustering analysis. Enrichment showed crucial pathways involved in regulation of regeneration difference, including "plant hormone signal transduction", "cell differentiation", "cellular response to auxin stimulus", and "auxin-activated signaling pathway". The expression of nine genes reported to be associated with shoot regeneration was validated using quantitative real-time PCR (qRT-PCR). For the specificity of regeneration mechanism with P. euphratica, large amount of DEGs involved in "plant-pathogen interaction", ubiquitin-26S proteosome mediated proteolysis pathway, stress-responsive DEGs, and senescence-associated DEGs were summarized to possibly account for the differentiation difference with distinct genotypes of P. euphratica. The result in this study helps screening of key regulators in mediating the shoot differentiation. The transcriptomic characteristic in P. euphratica further enhances our understanding of key processes affecting the regeneration capacity of de novo shoots among distinct species.

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“…For certain plant species, either direct and/or indirect shoot organogenesis can be carried out in one step, without the need for pre-incubation on CIM. The requirement for CIM is dependent on plant species and genotype, but the same sequence of molecular events that accompany the stages of DNSO is likely to take place in competent explants regardless of whether they are physically incubated on CIM or not [22,[28][29][30]. The morphogenic events that are part of DNSO occur within a unique, highly organized cellular and genetic framework, for which the presence of plant growth regulators in the regeneration media is merely a condition that enables certain developmental events to switch on.…”

Section: The Course Of Dnso: From Pluripotent Primordia To Developing Shootsmentioning

confidence: 99%

“…An important circumstance that differentiates DNSO from the embryogenic development of the SAM is the presence of exogenous growth regulators-notably CK-in the regeneration media. It has been suggested before that both the phytohormone content of the explants and the expression of CK-responsive genes can be triggered by the CKs present in the regeneration media [28,29,108]. Because CK is already present in the regeneration media and being taken up by the explants, it can trigger the expression of WUS more efficiently compared to the factors that act upstream of WUS during embryogenic development-hence, during DNSO WUS is being induced by CK rather than the other way around.…”

Section: Formation Of the Shoot Apical Meristem Is The Key Event In The Acquisition Of Shoot Identitymentioning

confidence: 99%

Integrating the Roles for Cytokinin and Auxin in De Novo Shoot Organogenesis: From Hormone Uptake to Signaling Outputs

Raspor

Motyka

Kaleri

et al. 2021

IJMS

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De novo shoot organogenesis (DNSO) is a procedure commonly used for the in vitro regeneration of shoots from a variety of plant tissues. Shoot regeneration occurs on nutrient media supplemented with the plant hormones cytokinin (CK) and auxin, which play essential roles in this process, and genes involved in their signaling cascades act as master regulators of the different phases of shoot regeneration. In the last 20 years, the genetic regulation of DNSO has been characterized in detail. However, as of today, the CK and auxin signaling events associated with shoot regeneration are often interpreted as a consequence of these hormones simply being present in the regeneration media, whereas the roles for their prior uptake and transport into the cultivated plant tissues are generally overlooked. Additionally, sucrose, commonly added to the regeneration media as a carbon source, plays a signaling role and has been recently shown to interact with CK and auxin and to affect the efficiency of shoot regeneration. In this review, we provide an integrative interpretation of the roles for CK and auxin in the process of DNSO, adding emphasis on their uptake from the regeneration media and their interaction with sucrose present in the media to their complex signaling outputs that mediate shoot regeneration.

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Expression profiles of organogenesis-related genes over the time course of one-step de novo shoot organogenesis from intact seedlings of kohlrabi

Cited by 12 publications

References 80 publications

Mining for Candidate Genes Controlling Secondary Growth of the Carrot Storage Root

Mining for Candidate Genes Controlling Secondary Growth of the Carrot Storage Root

Identification of Shoot Differentiation-Related Genes in Populus euphratica Oliv.

Integrating the Roles for Cytokinin and Auxin in De Novo Shoot Organogenesis: From Hormone Uptake to Signaling Outputs

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