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Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison.

Pilati S, Perazzolli M, Malossini A, Cestaro A, Demattè L, Fontana P, Dal Ri A, Viola R, Velasco R, Moser C - BMC Genomics (2007)

Bottom Line: From these analyses a core set of 1477 genes was found which was similarly modulated in all seasons.Between the two phases, at véraison, an oxidative burst and the concurrent modulation of the anti-oxidative enzymatic network was observed.The large number of regulatory genes we have identified represents a powerful new resource for dissecting the mechanisms of fruit ripening control in non-climacteric plants.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics and Molecular Biology; IASMA Research Center, Via E, Mach 1, 38010 S, Michele a/Adige (TN), Italy. stefania.pilati@iasma.it

ABSTRACT

Background: Grapevine (Vitis species) is among the most important fruit crops in terms of cultivated area and economic impact. Despite this relevance, little is known about the transcriptional changes and the regulatory circuits underlying the biochemical and physical changes occurring during berry development.

Results: Fruit ripening in the non-climacteric crop species Vitis vinifera L. has been investigated at the transcriptional level by the use of the Affymetrix Vitis GeneChip which contains approximately 14,500 unigenes. Gene expression data obtained from berries sampled before and after véraison in three growing years, were analyzed to identify genes specifically involved in fruit ripening and to investigate seasonal influences on the process. From these analyses a core set of 1477 genes was found which was similarly modulated in all seasons. We were able to separate ripening specific isoforms within gene families and to identify ripening related genes which appeared strongly regulated also by the seasonal weather conditions. Transcripts annotation by Gene Ontology vocabulary revealed five overrepresented functional categories of which cell wall organization and biogenesis, carbohydrate and secondary metabolisms and stress response were specifically induced during the ripening phase, while photosynthesis was strongly repressed. About 19% of the core gene set was characterized by genes involved in regulatory processes, such as transcription factors and transcripts related to hormonal metabolism and signal transduction. Auxin, ethylene and light emerged as the main stimuli influencing berry development. In addition, an oxidative burst, previously not detected in grapevine, characterized by rapid accumulation of H2O2 starting from véraison and by the modulation of many ROS scavenging enzymes, was observed.

Conclusion: The time-course gene expression analysis of grapevine berry development has identified the occurrence of two well distinct phases along the process. The pre-véraison phase represents a reprogramming stage of the cellular metabolism, characterized by the expression of numerous genes involved in hormonal signalling and transcriptional regulation. The post-véraison phase is characterized by the onset of a ripening-specialized metabolism responsible for the phenotypic traits of the ripe berry. Between the two phases, at véraison, an oxidative burst and the concurrent modulation of the anti-oxidative enzymatic network was observed. The large number of regulatory genes we have identified represents a powerful new resource for dissecting the mechanisms of fruit ripening control in non-climacteric plants.

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Real time RT-PCR validation of the expression profiles of six genes highly influenced by the season. A: 1615199_at, Cryptochrome 1; B: 1616872_at, Pseudo response regulator 9; C: 1614764_at, VvHT2, hexose transporter 2; D: 1606663_at, VvChs3, chalcone synthase isoform 3; E: 1607732_at, VvChs2: chalcone synthase isoform 2; F: 1620424_at, VvChi2, chalcone isomerase isofom 2. 2003 profiles are represented in red, 2005 in blue and 2006 in green. Relative expression data of the array hybridization experiments were centered on the average of the log2 values of each season. Expression profiles measured by RT-PCR experiments (insets) were first centered on the mean Ct value calculated on the three seasons for each gene and then log2 transformed. RT-PCR data are reported as means ± SE of three technical replicates.
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Figure 8: Real time RT-PCR validation of the expression profiles of six genes highly influenced by the season. A: 1615199_at, Cryptochrome 1; B: 1616872_at, Pseudo response regulator 9; C: 1614764_at, VvHT2, hexose transporter 2; D: 1606663_at, VvChs3, chalcone synthase isoform 3; E: 1607732_at, VvChs2: chalcone synthase isoform 2; F: 1620424_at, VvChi2, chalcone isomerase isofom 2. 2003 profiles are represented in red, 2005 in blue and 2006 in green. Relative expression data of the array hybridization experiments were centered on the average of the log2 values of each season. Expression profiles measured by RT-PCR experiments (insets) were first centered on the mean Ct value calculated on the three seasons for each gene and then log2 transformed. RT-PCR data are reported as means ± SE of three technical replicates.

Mentions: The influence on gene expression by environmental conditions is well reported in literature [77] and was evident in our PCA analysis (Fig. 2). The comparison of the three sampling years highlighted a large number of genes modulated only during one or two seasons, and thus excluded by the core set of ripening-specific genes: 938 genes in 2003, 2530 in 2005 and 2143 in 2006. Two examples are the isoform 2 of the phenylpropanoid biosynthetic genes chalcone synthase and chalcone isomerase whose expression profiles are depicted in Fig. 8E and 8F; such discrepancy in their modulation is indeed expected for non-ripening specific isoforms. Although these genes are probably highly affected by changes in the environment their GO functional categories distribution was not significantly different to that of the core set genes (data not shown). This result suggests that, on a long time frame, the plant reacts to the seasonal variations by adjusting the whole metabolism, and not just a part of it, to maintain homeostasis.


Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison.

Pilati S, Perazzolli M, Malossini A, Cestaro A, Demattè L, Fontana P, Dal Ri A, Viola R, Velasco R, Moser C - BMC Genomics (2007)

Real time RT-PCR validation of the expression profiles of six genes highly influenced by the season. A: 1615199_at, Cryptochrome 1; B: 1616872_at, Pseudo response regulator 9; C: 1614764_at, VvHT2, hexose transporter 2; D: 1606663_at, VvChs3, chalcone synthase isoform 3; E: 1607732_at, VvChs2: chalcone synthase isoform 2; F: 1620424_at, VvChi2, chalcone isomerase isofom 2. 2003 profiles are represented in red, 2005 in blue and 2006 in green. Relative expression data of the array hybridization experiments were centered on the average of the log2 values of each season. Expression profiles measured by RT-PCR experiments (insets) were first centered on the mean Ct value calculated on the three seasons for each gene and then log2 transformed. RT-PCR data are reported as means ± SE of three technical replicates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2228314&req=5

Figure 8: Real time RT-PCR validation of the expression profiles of six genes highly influenced by the season. A: 1615199_at, Cryptochrome 1; B: 1616872_at, Pseudo response regulator 9; C: 1614764_at, VvHT2, hexose transporter 2; D: 1606663_at, VvChs3, chalcone synthase isoform 3; E: 1607732_at, VvChs2: chalcone synthase isoform 2; F: 1620424_at, VvChi2, chalcone isomerase isofom 2. 2003 profiles are represented in red, 2005 in blue and 2006 in green. Relative expression data of the array hybridization experiments were centered on the average of the log2 values of each season. Expression profiles measured by RT-PCR experiments (insets) were first centered on the mean Ct value calculated on the three seasons for each gene and then log2 transformed. RT-PCR data are reported as means ± SE of three technical replicates.
Mentions: The influence on gene expression by environmental conditions is well reported in literature [77] and was evident in our PCA analysis (Fig. 2). The comparison of the three sampling years highlighted a large number of genes modulated only during one or two seasons, and thus excluded by the core set of ripening-specific genes: 938 genes in 2003, 2530 in 2005 and 2143 in 2006. Two examples are the isoform 2 of the phenylpropanoid biosynthetic genes chalcone synthase and chalcone isomerase whose expression profiles are depicted in Fig. 8E and 8F; such discrepancy in their modulation is indeed expected for non-ripening specific isoforms. Although these genes are probably highly affected by changes in the environment their GO functional categories distribution was not significantly different to that of the core set genes (data not shown). This result suggests that, on a long time frame, the plant reacts to the seasonal variations by adjusting the whole metabolism, and not just a part of it, to maintain homeostasis.

Bottom Line: From these analyses a core set of 1477 genes was found which was similarly modulated in all seasons.Between the two phases, at véraison, an oxidative burst and the concurrent modulation of the anti-oxidative enzymatic network was observed.The large number of regulatory genes we have identified represents a powerful new resource for dissecting the mechanisms of fruit ripening control in non-climacteric plants.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics and Molecular Biology; IASMA Research Center, Via E, Mach 1, 38010 S, Michele a/Adige (TN), Italy. stefania.pilati@iasma.it

ABSTRACT

Background: Grapevine (Vitis species) is among the most important fruit crops in terms of cultivated area and economic impact. Despite this relevance, little is known about the transcriptional changes and the regulatory circuits underlying the biochemical and physical changes occurring during berry development.

Results: Fruit ripening in the non-climacteric crop species Vitis vinifera L. has been investigated at the transcriptional level by the use of the Affymetrix Vitis GeneChip which contains approximately 14,500 unigenes. Gene expression data obtained from berries sampled before and after véraison in three growing years, were analyzed to identify genes specifically involved in fruit ripening and to investigate seasonal influences on the process. From these analyses a core set of 1477 genes was found which was similarly modulated in all seasons. We were able to separate ripening specific isoforms within gene families and to identify ripening related genes which appeared strongly regulated also by the seasonal weather conditions. Transcripts annotation by Gene Ontology vocabulary revealed five overrepresented functional categories of which cell wall organization and biogenesis, carbohydrate and secondary metabolisms and stress response were specifically induced during the ripening phase, while photosynthesis was strongly repressed. About 19% of the core gene set was characterized by genes involved in regulatory processes, such as transcription factors and transcripts related to hormonal metabolism and signal transduction. Auxin, ethylene and light emerged as the main stimuli influencing berry development. In addition, an oxidative burst, previously not detected in grapevine, characterized by rapid accumulation of H2O2 starting from véraison and by the modulation of many ROS scavenging enzymes, was observed.

Conclusion: The time-course gene expression analysis of grapevine berry development has identified the occurrence of two well distinct phases along the process. The pre-véraison phase represents a reprogramming stage of the cellular metabolism, characterized by the expression of numerous genes involved in hormonal signalling and transcriptional regulation. The post-véraison phase is characterized by the onset of a ripening-specialized metabolism responsible for the phenotypic traits of the ripe berry. Between the two phases, at véraison, an oxidative burst and the concurrent modulation of the anti-oxidative enzymatic network was observed. The large number of regulatory genes we have identified represents a powerful new resource for dissecting the mechanisms of fruit ripening control in non-climacteric plants.

Show MeSH
Related in: MedlinePlus