Identification of shoot differentiation-related genes in populus euphratica oliv.

Yaru Fu, Tianyu Dong, Lizhi Tan, Danni Yin, Miaomiao Zhang, Guomiao Zhao, Meixia Ye, Rongling Wu

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Article number1034
JournalGenes
Volume10
Issue number12
DOIs
StatePublished - Dec 2019

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Populus
Regeneration
Genes
Indoleacetic Acids
Plant Shoots
Plant Growth Regulators
Organogenesis
Genetic Selection
Ubiquitin
Transcriptome
Arabidopsis
Proteolysis
Embryonic Development
Cluster Analysis
Real-Time Polymerase Chain Reaction
Cell Differentiation
Signal Transduction

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Fu, Yaru ; Dong, Tianyu ; Tan, Lizhi ; Yin, Danni ; Zhang, Miaomiao ; Zhao, Guomiao ; Ye, Meixia ; Wu, Rongling. / Identification of shoot differentiation-related genes in populus euphratica oliv. In: Genes. 2019 ; Vol. 10, No. 12.
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abstract = "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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Fu, Y, Dong, T, Tan, L, Yin, D, Zhang, M, Zhao, G, Ye, M & Wu, R 2019, 'Identification of shoot differentiation-related genes in populus euphratica oliv.', Genes, vol. 10, no. 12, 1034. https://doi.org/10.3390/genes10121034

Identification of shoot differentiation-related genes in populus euphratica oliv. / Fu, Yaru; Dong, Tianyu; Tan, Lizhi; Yin, Danni; Zhang, Miaomiao; Zhao, Guomiao; Ye, Meixia; Wu, Rongling.

In: Genes, Vol. 10, No. 12, 1034, 12.2019.

Research output: Contribution to journalArticle

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