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Global Transcriptome Profiling Analysis of Inhibitory Effects of Paclobutrazol on Leaf Growth in Lily (Lilium Longiflorum-Asiatic Hybrid).

Zhu X, Chai M, Li Y, Sun M, Zhang J, Sun G, Jiang C, Shi L - Front Plant Sci (2016)

Bottom Line: By analyzing dynamic changes of differentially expressed genes, nine metabolic pathways and signal transduction pathways were significantly enriched and many potentially interesting genes were identified that encoded putative regulators or key components of cell division, cell expansion, GA metabolism and signaling transduction and these genes were highlighted to reveal their importance in regulation of plant size.These results will provide a better understanding of the molecular mechanism on lily dwarfism and some potential genes related to lily organ size, which will lay the foundation for molecular breeding of potted lilies.These transcriptome data will also serve as valuable public genomic resources for other genetic research in lily.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China; University of Chinese Academy of SciencesBeijing, China.

ABSTRACT
As a popular ornamental flower, potted lily is an important object of lily breeding. Paclobutrazol, a chemical growth retardation compound, is often used to dwarf plant in producing potted lilies. However, in recent years, the plants with inherited dwarf traits by using genetic engineer breeding technology are being developed. The studies on molecular basis of lily dwarfism will offer some target genes which have profound dwarf effect for genetic engineer breeding. Here, we confirmed that paclobutrazol inhibited plant height and leaf size in Lilium Longiflorum-Asiatic hybrid, and then RNA-Seq technique was employed to analyze gene transcripts of Lilium Longiflorum-Asiatic hybrid leaves by paclobutrazol treatment in order to get a deeper insight into dwarfism mechanism of lily. Approximately 38.6 Gb data was obtained and assemble into 53,681 unigenes. Annotation, pathways, functional classification and phylogenetic classification of these data were analyzed based on Nr, Nt, Swiss-Prot, KEGG, COG, and GO databases. 2704 differentially expressed genes were screened by comparing paclobutrazol-treated samples with untreated samples and quantitative real-time PCR was performed to validate expression profiles. By analyzing dynamic changes of differentially expressed genes, nine metabolic pathways and signal transduction pathways were significantly enriched and many potentially interesting genes were identified that encoded putative regulators or key components of cell division, cell expansion, GA metabolism and signaling transduction and these genes were highlighted to reveal their importance in regulation of plant size. These results will provide a better understanding of the molecular mechanism on lily dwarfism and some potential genes related to lily organ size, which will lay the foundation for molecular breeding of potted lilies. These transcriptome data will also serve as valuable public genomic resources for other genetic research in lily.

No MeSH data available.


Related in: MedlinePlus

Statistics of the DEG numbers and verification of expression profiles of 12 selected DEGs using qRT-PCR. CK, controls; T3, PBZ-treated samples at 3 h; T24, PBZ-treated samples at 24 h; T72, PBZ-treated samples at 72 h. (A) The DEG numbers are counted. The black columns showed the upregulated DEGs and the gray columns showed the downregulated DEGs compared with controls. (B–D) Close correlations (r = 0.92, 0.91, and 0.96) were observed between relative expression levels measured with RNA-Seq and qRT-PCR. The x-axis represented unigene ID, and the y-axis showed expression levels (fold difference).
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Figure 7: Statistics of the DEG numbers and verification of expression profiles of 12 selected DEGs using qRT-PCR. CK, controls; T3, PBZ-treated samples at 3 h; T24, PBZ-treated samples at 24 h; T72, PBZ-treated samples at 72 h. (A) The DEG numbers are counted. The black columns showed the upregulated DEGs and the gray columns showed the downregulated DEGs compared with controls. (B–D) Close correlations (r = 0.92, 0.91, and 0.96) were observed between relative expression levels measured with RNA-Seq and qRT-PCR. The x-axis represented unigene ID, and the y-axis showed expression levels (fold difference).

Mentions: With Q-value ≥ 0.8 and an absolute log2ratio (treatment/control) ≥1 based on the NOISeq method, a total of 2704 genes were found to be differentially expressed among the three PBZ-treated samples compared with control group. Among these DEGs, 648 genes were quickly induced by PBZ, while 712 genes were downregulated at 3 h. At 24 h, 815 genes were found, of which 560 genes were upregulated and 256 genes were downregulated. At 72 h, 674 genes were upregulated and 644 genes were downregulated (Figure 7A). These results indicated that both up- and down-regulation of gene expression occurred, and the transcript abundance of genes changed dynamically over time of PBZ treatment.


Global Transcriptome Profiling Analysis of Inhibitory Effects of Paclobutrazol on Leaf Growth in Lily (Lilium Longiflorum-Asiatic Hybrid).

Zhu X, Chai M, Li Y, Sun M, Zhang J, Sun G, Jiang C, Shi L - Front Plant Sci (2016)

Statistics of the DEG numbers and verification of expression profiles of 12 selected DEGs using qRT-PCR. CK, controls; T3, PBZ-treated samples at 3 h; T24, PBZ-treated samples at 24 h; T72, PBZ-treated samples at 72 h. (A) The DEG numbers are counted. The black columns showed the upregulated DEGs and the gray columns showed the downregulated DEGs compared with controls. (B–D) Close correlations (r = 0.92, 0.91, and 0.96) were observed between relative expression levels measured with RNA-Seq and qRT-PCR. The x-axis represented unigene ID, and the y-axis showed expression levels (fold difference).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4835717&req=5

Figure 7: Statistics of the DEG numbers and verification of expression profiles of 12 selected DEGs using qRT-PCR. CK, controls; T3, PBZ-treated samples at 3 h; T24, PBZ-treated samples at 24 h; T72, PBZ-treated samples at 72 h. (A) The DEG numbers are counted. The black columns showed the upregulated DEGs and the gray columns showed the downregulated DEGs compared with controls. (B–D) Close correlations (r = 0.92, 0.91, and 0.96) were observed between relative expression levels measured with RNA-Seq and qRT-PCR. The x-axis represented unigene ID, and the y-axis showed expression levels (fold difference).
Mentions: With Q-value ≥ 0.8 and an absolute log2ratio (treatment/control) ≥1 based on the NOISeq method, a total of 2704 genes were found to be differentially expressed among the three PBZ-treated samples compared with control group. Among these DEGs, 648 genes were quickly induced by PBZ, while 712 genes were downregulated at 3 h. At 24 h, 815 genes were found, of which 560 genes were upregulated and 256 genes were downregulated. At 72 h, 674 genes were upregulated and 644 genes were downregulated (Figure 7A). These results indicated that both up- and down-regulation of gene expression occurred, and the transcript abundance of genes changed dynamically over time of PBZ treatment.

Bottom Line: By analyzing dynamic changes of differentially expressed genes, nine metabolic pathways and signal transduction pathways were significantly enriched and many potentially interesting genes were identified that encoded putative regulators or key components of cell division, cell expansion, GA metabolism and signaling transduction and these genes were highlighted to reveal their importance in regulation of plant size.These results will provide a better understanding of the molecular mechanism on lily dwarfism and some potential genes related to lily organ size, which will lay the foundation for molecular breeding of potted lilies.These transcriptome data will also serve as valuable public genomic resources for other genetic research in lily.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China; University of Chinese Academy of SciencesBeijing, China.

ABSTRACT
As a popular ornamental flower, potted lily is an important object of lily breeding. Paclobutrazol, a chemical growth retardation compound, is often used to dwarf plant in producing potted lilies. However, in recent years, the plants with inherited dwarf traits by using genetic engineer breeding technology are being developed. The studies on molecular basis of lily dwarfism will offer some target genes which have profound dwarf effect for genetic engineer breeding. Here, we confirmed that paclobutrazol inhibited plant height and leaf size in Lilium Longiflorum-Asiatic hybrid, and then RNA-Seq technique was employed to analyze gene transcripts of Lilium Longiflorum-Asiatic hybrid leaves by paclobutrazol treatment in order to get a deeper insight into dwarfism mechanism of lily. Approximately 38.6 Gb data was obtained and assemble into 53,681 unigenes. Annotation, pathways, functional classification and phylogenetic classification of these data were analyzed based on Nr, Nt, Swiss-Prot, KEGG, COG, and GO databases. 2704 differentially expressed genes were screened by comparing paclobutrazol-treated samples with untreated samples and quantitative real-time PCR was performed to validate expression profiles. By analyzing dynamic changes of differentially expressed genes, nine metabolic pathways and signal transduction pathways were significantly enriched and many potentially interesting genes were identified that encoded putative regulators or key components of cell division, cell expansion, GA metabolism and signaling transduction and these genes were highlighted to reveal their importance in regulation of plant size. These results will provide a better understanding of the molecular mechanism on lily dwarfism and some potential genes related to lily organ size, which will lay the foundation for molecular breeding of potted lilies. These transcriptome data will also serve as valuable public genomic resources for other genetic research in lily.

No MeSH data available.


Related in: MedlinePlus