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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

Characteristics of homology search of unigenes aligned by BLASTx to the nr database. (A)E-value distribution of unigenes annotated in the nr database. (B) Species distribution of the first BLAST hits for each sequence with a cut-off E-value of 1.0E−5.
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Figure 4: Characteristics of homology search of unigenes aligned by BLASTx to the nr database. (A)E-value distribution of unigenes annotated in the nr database. (B) Species distribution of the first BLAST hits for each sequence with a cut-off E-value of 1.0E−5.

Mentions: All unigenes were aligned to five protein databases including Nr, Swiss-Prot, COG, GO, KEGG and one Nt nucleotide database. A total of 38,507 unigenes were annotated, which contained 37,776 (70.37%) unigenes identified from Nr, 27,087 (50.46%) from Nt, 27,316 (50.86%) from Swiss-Prot, 17,201 (32.04%) from COG, 28,014 (52.19%) from GO, 25,092 (46.74%) from KEGG (Table 2). E-value indicated the extent of sequence homology, and E-value is smaller, the sequence homology is higher. For E-value distribution of unigenes blastx hits in the Nr database which had the largest number of annotated unigenes, 44% homolog sequences ranged between 1E−5 and 1E−45, while 56% sequences had a threshold E-value less than 1E−45 that showed strong homology (Figure 4A). Species distribution of the first blastx hits of each unigene in the Nr database indicated that Vitis vinifera provided the best blastx matches with 24.6% unigenes in L. LA hybrid, and Oryza sativa was the second closest species, which had 8.7% homology with L. LA hybrid (Figure 4B).


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)

Characteristics of homology search of unigenes aligned by BLASTx to the nr database. (A)E-value distribution of unigenes annotated in the nr database. (B) Species distribution of the first BLAST hits for each sequence with a cut-off E-value of 1.0E−5.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Characteristics of homology search of unigenes aligned by BLASTx to the nr database. (A)E-value distribution of unigenes annotated in the nr database. (B) Species distribution of the first BLAST hits for each sequence with a cut-off E-value of 1.0E−5.
Mentions: All unigenes were aligned to five protein databases including Nr, Swiss-Prot, COG, GO, KEGG and one Nt nucleotide database. A total of 38,507 unigenes were annotated, which contained 37,776 (70.37%) unigenes identified from Nr, 27,087 (50.46%) from Nt, 27,316 (50.86%) from Swiss-Prot, 17,201 (32.04%) from COG, 28,014 (52.19%) from GO, 25,092 (46.74%) from KEGG (Table 2). E-value indicated the extent of sequence homology, and E-value is smaller, the sequence homology is higher. For E-value distribution of unigenes blastx hits in the Nr database which had the largest number of annotated unigenes, 44% homolog sequences ranged between 1E−5 and 1E−45, while 56% sequences had a threshold E-value less than 1E−45 that showed strong homology (Figure 4A). Species distribution of the first blastx hits of each unigene in the Nr database indicated that Vitis vinifera provided the best blastx matches with 24.6% unigenes in L. LA hybrid, and Oryza sativa was the second closest species, which had 8.7% homology with L. LA hybrid (Figure 4B).

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