Limits...
Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality.

Vizoso P, Meisel LA, Tittarelli A, Latorre M, Saba J, Caroca R, Maldonado J, Cambiazo V, Campos-Vargas R, Gonzalez M, Orellana A, Silva H - BMC Genomics (2009)

Bottom Line: These differentially expressed genes reveal the complex biological processes that are associated with these factors, as well as a large number of putative gene families that may participate differentially in these processes.Additionally, these results suggest that the mitochondria and plastids play a major role in these processes.The EST sequences and full-length cDNA clones developed in this work, combined with the large population of differentially expressed genes may serve as useful tools and markers that will enable the scientific community to better define the molecular processes that affect fruit quality in response to post-harvest conditions and the organelles that participate in these processes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile.

ABSTRACT

Background: Cold storage is used to inhibit peach fruit ripening during shipment to distant markets. However, this cold storage can negatively affect the quality of the fruit when it is ripened, resulting in disorders such as wooliness, browning or leathering. In order to understand the individual and combined biological effects that factors such as cold storage and ripening have on the fruit and fruit quality, we have taken a comparative EST transcript profiling approach to identify genes that are differentially expressed in response to these factors.

Results: We sequenced 50,625 Expressed Sequence Tags (ESTs) from peach mesocarp (Prunus persica O'Henry variety) stored at four different postharvest conditions. A total of 10,830 Unigenes (4,169 contigs and 6,661 singletons) were formed by assembling these ESTs. Additionally, a collection of 614 full-length and 1,109 putative full-length cDNA clones within flanking loxP recombination sites was created. Statistically analyzing the EST population, we have identified genes that are differentially expressed during ripening, in response to cold storage or the combined effects of cold storage and ripening. Pair-wise comparisons revealed 197 contigs with at least one significant difference in transcript abundance between at least two conditions. Gene expression profile analyses revealed that the contigs may be classified into 13 different clusters of gene expression patterns. These clusters include groups of contigs that increase or decrease transcript abundance during ripening, in response to cold or ripening plus cold.

Conclusion: These analyses have enabled us to statistically identify novel genes and gene clusters that are differentially expressed in response to post-harvest factors such as long-term cold storage, ripening or a combination of these two factors. These differentially expressed genes reveal the complex biological processes that are associated with these factors, as well as a large number of putative gene families that may participate differentially in these processes. In particular, these analyzes suggest that woolly fruits lack the increased boost of metabolic processes necessary for ripening. Additionally, these results suggest that the mitochondria and plastids play a major role in these processes. The EST sequences and full-length cDNA clones developed in this work, combined with the large population of differentially expressed genes may serve as useful tools and markers that will enable the scientific community to better define the molecular processes that affect fruit quality in response to post-harvest conditions and the organelles that participate in these processes.

Show MeSH

Related in: MedlinePlus

Gene clusters with inverse expression profiles exclusively in woolly fruits. Cluster 1 (left) contains 94 genes that have increased expression exclusively in fruits that are wooly (E4: R+, C+), whereas cluster 9 (right) contains 95 genes with decreased expression exclusively in these same fruits. The Gene Ontology annotations of the genes in these clusters are represented below each cluster. The number of genes associated with each GO term is represented by the color of the bars, as depicted in the scale presented in this figure. The dashed line indicates non-ripe fruits, E1 (R-, C-). To the left of the dashed line is the expression levels for ripe, juicy fruits, E2 (R+, C-). To the right of the dashed line are E3 (R-, C+) and E4 (R+, C+) fruits, non-ripe and ripe fruits that have undergone long-term cold storage, respectively. E4 (R+, C+) fruits are wooly. Annotations correspond to the parental plant GO Slim terms.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2748099&req=5

Figure 5: Gene clusters with inverse expression profiles exclusively in woolly fruits. Cluster 1 (left) contains 94 genes that have increased expression exclusively in fruits that are wooly (E4: R+, C+), whereas cluster 9 (right) contains 95 genes with decreased expression exclusively in these same fruits. The Gene Ontology annotations of the genes in these clusters are represented below each cluster. The number of genes associated with each GO term is represented by the color of the bars, as depicted in the scale presented in this figure. The dashed line indicates non-ripe fruits, E1 (R-, C-). To the left of the dashed line is the expression levels for ripe, juicy fruits, E2 (R+, C-). To the right of the dashed line are E3 (R-, C+) and E4 (R+, C+) fruits, non-ripe and ripe fruits that have undergone long-term cold storage, respectively. E4 (R+, C+) fruits are wooly. Annotations correspond to the parental plant GO Slim terms.

Mentions: Groups of clusters that correlate the gene expression profiles with the different post-harvest conditions are clearly visible when these groups are analyzed and compared (Figure 4, 5, and 6). One group (Figure 4) is represented by two clusters of genes (Clusters 4 and 12) whose expression profiles are inversely related in juicy, ripe fruits (E2: R+, C-), when compared to the other post harvest stages. Cluster 4 contains 107 genes with reduced expression exclusively in juicy, ripe fruits (E2: R+, C-), whereas cluster 12 contains 112 genes with increased expression exclusively in these same fruits. It is important to note this comparison is not a pair-wise comparison, rather a comparison between all four post-harvest conditions (E1: R-, C-; E2: R+, C-; E3: R-, C+; E4: R+, C+). Clusters 4 and 12 reveal a decrease and increase in gene expression in juicy fruits, respectively, which is not present in woolly fruits. Genes that are differentially expressed in juicy fruits and not woolly fruits are genes that may be participating in the woolly phenotype. Analyses of these sequences and their corresponding Gene Ontology annotations reveal that ripe peaches have an increase in metabolic processes, especially processes associated with the metabolism of carbohydrates, nucleic acids, amino acids, lipids and secondary metabolites (Figure 4). In contrast, there is a decrease in translation, transport, and signal transduction processes. According to the GO annotations, it appears as though there is an increase in the expression of genes that are associated with mitochondria and plastids, as well as a decrease in those associated with ribosomes and the plasma membrane. Many of the metabolic process described earlier are carried out in the mitochondria and plastids, supporting this trend. The decrease in translation also correlates with the decrease in processes associated with the ribosome. These analyses suggest that woolly fruits lack the increased boost of metabolic processes necessary for ripening, such as the expression of cell wall modifying enzymes as well as the production of sugars and aromatic secondary metabolites. The changes in expression of cell wall modifying enzymes is consistent with what has been reported previously [1,9-13,39,48,51,55,56]. However, these cluster analyses reveal the organelles that may actively participate in these processes as well as a large number of genes and gene families that should be analyzed for their participation in the altered metabolic processes present in woolly fruits.


Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality.

Vizoso P, Meisel LA, Tittarelli A, Latorre M, Saba J, Caroca R, Maldonado J, Cambiazo V, Campos-Vargas R, Gonzalez M, Orellana A, Silva H - BMC Genomics (2009)

Gene clusters with inverse expression profiles exclusively in woolly fruits. Cluster 1 (left) contains 94 genes that have increased expression exclusively in fruits that are wooly (E4: R+, C+), whereas cluster 9 (right) contains 95 genes with decreased expression exclusively in these same fruits. The Gene Ontology annotations of the genes in these clusters are represented below each cluster. The number of genes associated with each GO term is represented by the color of the bars, as depicted in the scale presented in this figure. The dashed line indicates non-ripe fruits, E1 (R-, C-). To the left of the dashed line is the expression levels for ripe, juicy fruits, E2 (R+, C-). To the right of the dashed line are E3 (R-, C+) and E4 (R+, C+) fruits, non-ripe and ripe fruits that have undergone long-term cold storage, respectively. E4 (R+, C+) fruits are wooly. Annotations correspond to the parental plant GO Slim terms.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2748099&req=5

Figure 5: Gene clusters with inverse expression profiles exclusively in woolly fruits. Cluster 1 (left) contains 94 genes that have increased expression exclusively in fruits that are wooly (E4: R+, C+), whereas cluster 9 (right) contains 95 genes with decreased expression exclusively in these same fruits. The Gene Ontology annotations of the genes in these clusters are represented below each cluster. The number of genes associated with each GO term is represented by the color of the bars, as depicted in the scale presented in this figure. The dashed line indicates non-ripe fruits, E1 (R-, C-). To the left of the dashed line is the expression levels for ripe, juicy fruits, E2 (R+, C-). To the right of the dashed line are E3 (R-, C+) and E4 (R+, C+) fruits, non-ripe and ripe fruits that have undergone long-term cold storage, respectively. E4 (R+, C+) fruits are wooly. Annotations correspond to the parental plant GO Slim terms.
Mentions: Groups of clusters that correlate the gene expression profiles with the different post-harvest conditions are clearly visible when these groups are analyzed and compared (Figure 4, 5, and 6). One group (Figure 4) is represented by two clusters of genes (Clusters 4 and 12) whose expression profiles are inversely related in juicy, ripe fruits (E2: R+, C-), when compared to the other post harvest stages. Cluster 4 contains 107 genes with reduced expression exclusively in juicy, ripe fruits (E2: R+, C-), whereas cluster 12 contains 112 genes with increased expression exclusively in these same fruits. It is important to note this comparison is not a pair-wise comparison, rather a comparison between all four post-harvest conditions (E1: R-, C-; E2: R+, C-; E3: R-, C+; E4: R+, C+). Clusters 4 and 12 reveal a decrease and increase in gene expression in juicy fruits, respectively, which is not present in woolly fruits. Genes that are differentially expressed in juicy fruits and not woolly fruits are genes that may be participating in the woolly phenotype. Analyses of these sequences and their corresponding Gene Ontology annotations reveal that ripe peaches have an increase in metabolic processes, especially processes associated with the metabolism of carbohydrates, nucleic acids, amino acids, lipids and secondary metabolites (Figure 4). In contrast, there is a decrease in translation, transport, and signal transduction processes. According to the GO annotations, it appears as though there is an increase in the expression of genes that are associated with mitochondria and plastids, as well as a decrease in those associated with ribosomes and the plasma membrane. Many of the metabolic process described earlier are carried out in the mitochondria and plastids, supporting this trend. The decrease in translation also correlates with the decrease in processes associated with the ribosome. These analyses suggest that woolly fruits lack the increased boost of metabolic processes necessary for ripening, such as the expression of cell wall modifying enzymes as well as the production of sugars and aromatic secondary metabolites. The changes in expression of cell wall modifying enzymes is consistent with what has been reported previously [1,9-13,39,48,51,55,56]. However, these cluster analyses reveal the organelles that may actively participate in these processes as well as a large number of genes and gene families that should be analyzed for their participation in the altered metabolic processes present in woolly fruits.

Bottom Line: These differentially expressed genes reveal the complex biological processes that are associated with these factors, as well as a large number of putative gene families that may participate differentially in these processes.Additionally, these results suggest that the mitochondria and plastids play a major role in these processes.The EST sequences and full-length cDNA clones developed in this work, combined with the large population of differentially expressed genes may serve as useful tools and markers that will enable the scientific community to better define the molecular processes that affect fruit quality in response to post-harvest conditions and the organelles that participate in these processes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile.

ABSTRACT

Background: Cold storage is used to inhibit peach fruit ripening during shipment to distant markets. However, this cold storage can negatively affect the quality of the fruit when it is ripened, resulting in disorders such as wooliness, browning or leathering. In order to understand the individual and combined biological effects that factors such as cold storage and ripening have on the fruit and fruit quality, we have taken a comparative EST transcript profiling approach to identify genes that are differentially expressed in response to these factors.

Results: We sequenced 50,625 Expressed Sequence Tags (ESTs) from peach mesocarp (Prunus persica O'Henry variety) stored at four different postharvest conditions. A total of 10,830 Unigenes (4,169 contigs and 6,661 singletons) were formed by assembling these ESTs. Additionally, a collection of 614 full-length and 1,109 putative full-length cDNA clones within flanking loxP recombination sites was created. Statistically analyzing the EST population, we have identified genes that are differentially expressed during ripening, in response to cold storage or the combined effects of cold storage and ripening. Pair-wise comparisons revealed 197 contigs with at least one significant difference in transcript abundance between at least two conditions. Gene expression profile analyses revealed that the contigs may be classified into 13 different clusters of gene expression patterns. These clusters include groups of contigs that increase or decrease transcript abundance during ripening, in response to cold or ripening plus cold.

Conclusion: These analyses have enabled us to statistically identify novel genes and gene clusters that are differentially expressed in response to post-harvest factors such as long-term cold storage, ripening or a combination of these two factors. These differentially expressed genes reveal the complex biological processes that are associated with these factors, as well as a large number of putative gene families that may participate differentially in these processes. In particular, these analyzes suggest that woolly fruits lack the increased boost of metabolic processes necessary for ripening. Additionally, these results suggest that the mitochondria and plastids play a major role in these processes. The EST sequences and full-length cDNA clones developed in this work, combined with the large population of differentially expressed genes may serve as useful tools and markers that will enable the scientific community to better define the molecular processes that affect fruit quality in response to post-harvest conditions and the organelles that participate in these processes.

Show MeSH
Related in: MedlinePlus