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Transcriptomic analysis of differentially expressed genes in an orange-pericarp mutant and wild type in pummelo (Citrus grandis).

Guo F, Yu H, Xu Q, Deng X - BMC Plant Biol. (2015)

Bottom Line: The transcription factors and genes corresponding to effected metabolic pathways may involved in the carotenoid regulation was confirmed by the qRT-PCR analysis in the MT pericarp.This study has provided a global picture of the gene expression changes in a novel mutant with distinct color in the fruit pericarp of pummelo.Interpretation of differentially expressed genes (DEGs) revealed new insight into the molecular regulation of β-carotene accumulation in the MT pericarp.

View Article: PubMed Central - PubMed

ABSTRACT

Background: The external colour of fruit is a crucial quality feature, and the external coloration of most citrus fruits is due to the accumulation of carotenoids. The molecular regulation of carotenoid biosynthesis and accumulation in pericarp is limited due to the lack of mutant. In this work, an orange-pericarp mutant (MT) which showed altered pigmentation in the pericarp was used to identify genes potentially related to the regulation of carotenoid accumulation in the pericarp.

Results: High Performance Liquid Chromatography (HPLC) analysis revealed that the pericarp from MT fruits had a 10.5-fold increase of β-carotene content over that of the Wild Type (WT). Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of all downstream carotenogenic genes was lower in MT than in WT, suggesting that down-regulation is critical for the β-carotene increase in the MT pericarp. RNA-seq analysis of the transcriptome revealed extensive changes in the MT gene expression level, with 168 genes down-regulated and 135 genes up-regulated. Gene ontology (GO) and KEGG pathway analyses indicated seven reliable metabolic pathways are altered in the mutant, including carbon metabolism, starch and sucrose metabolism and biosynthesis of amino acids. The transcription factors and genes corresponding to effected metabolic pathways may involved in the carotenoid regulation was confirmed by the qRT-PCR analysis in the MT pericarp.

Conclusions: This study has provided a global picture of the gene expression changes in a novel mutant with distinct color in the fruit pericarp of pummelo. Interpretation of differentially expressed genes (DEGs) revealed new insight into the molecular regulation of β-carotene accumulation in the MT pericarp.

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RT-PCR analyses of differentially expressed genes corresponding to metabolic pathways and transcription factors in MT and WT. The transcript abundance from RNA-seq data was added on the top of each gene. RPKM, reads per kilo bases per million reads.
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Fig4: RT-PCR analyses of differentially expressed genes corresponding to metabolic pathways and transcription factors in MT and WT. The transcript abundance from RNA-seq data was added on the top of each gene. RPKM, reads per kilo bases per million reads.

Mentions: A total of 22 DEGs were selected for qRT-PCR verification. Among them, 10 were referred to as the differentially expressed transcription factors. The other 12 genes belonged to the affected pathways including sugar metabolism and amino acid metabolism. The results showed that 19 out of the 22 differentially expressed genes in MT and WT were in consistency with the RNA-seq data (Figure 4). Linear regression [(RNA-seq value) = a(qRT-PCR value) + b] analysis of these 19 DEGs showed an overall correlation coefficient of 0.78, indicating a good correlation between the transcription profile revealed by RNA-seq data and the transcript abundance assayed by qRT-PCR (Additional file 6). These results confirmed the reliability of the RNA-seq data.Figure 4


Transcriptomic analysis of differentially expressed genes in an orange-pericarp mutant and wild type in pummelo (Citrus grandis).

Guo F, Yu H, Xu Q, Deng X - BMC Plant Biol. (2015)

RT-PCR analyses of differentially expressed genes corresponding to metabolic pathways and transcription factors in MT and WT. The transcript abundance from RNA-seq data was added on the top of each gene. RPKM, reads per kilo bases per million reads.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4352283&req=5

Fig4: RT-PCR analyses of differentially expressed genes corresponding to metabolic pathways and transcription factors in MT and WT. The transcript abundance from RNA-seq data was added on the top of each gene. RPKM, reads per kilo bases per million reads.
Mentions: A total of 22 DEGs were selected for qRT-PCR verification. Among them, 10 were referred to as the differentially expressed transcription factors. The other 12 genes belonged to the affected pathways including sugar metabolism and amino acid metabolism. The results showed that 19 out of the 22 differentially expressed genes in MT and WT were in consistency with the RNA-seq data (Figure 4). Linear regression [(RNA-seq value) = a(qRT-PCR value) + b] analysis of these 19 DEGs showed an overall correlation coefficient of 0.78, indicating a good correlation between the transcription profile revealed by RNA-seq data and the transcript abundance assayed by qRT-PCR (Additional file 6). These results confirmed the reliability of the RNA-seq data.Figure 4

Bottom Line: The transcription factors and genes corresponding to effected metabolic pathways may involved in the carotenoid regulation was confirmed by the qRT-PCR analysis in the MT pericarp.This study has provided a global picture of the gene expression changes in a novel mutant with distinct color in the fruit pericarp of pummelo.Interpretation of differentially expressed genes (DEGs) revealed new insight into the molecular regulation of β-carotene accumulation in the MT pericarp.

View Article: PubMed Central - PubMed

ABSTRACT

Background: The external colour of fruit is a crucial quality feature, and the external coloration of most citrus fruits is due to the accumulation of carotenoids. The molecular regulation of carotenoid biosynthesis and accumulation in pericarp is limited due to the lack of mutant. In this work, an orange-pericarp mutant (MT) which showed altered pigmentation in the pericarp was used to identify genes potentially related to the regulation of carotenoid accumulation in the pericarp.

Results: High Performance Liquid Chromatography (HPLC) analysis revealed that the pericarp from MT fruits had a 10.5-fold increase of β-carotene content over that of the Wild Type (WT). Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of all downstream carotenogenic genes was lower in MT than in WT, suggesting that down-regulation is critical for the β-carotene increase in the MT pericarp. RNA-seq analysis of the transcriptome revealed extensive changes in the MT gene expression level, with 168 genes down-regulated and 135 genes up-regulated. Gene ontology (GO) and KEGG pathway analyses indicated seven reliable metabolic pathways are altered in the mutant, including carbon metabolism, starch and sucrose metabolism and biosynthesis of amino acids. The transcription factors and genes corresponding to effected metabolic pathways may involved in the carotenoid regulation was confirmed by the qRT-PCR analysis in the MT pericarp.

Conclusions: This study has provided a global picture of the gene expression changes in a novel mutant with distinct color in the fruit pericarp of pummelo. Interpretation of differentially expressed genes (DEGs) revealed new insight into the molecular regulation of β-carotene accumulation in the MT pericarp.

Show MeSH