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Comparative transcript profiling of apricot (Prunus armeniaca L.) fruit development and on-tree ripening

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Abstract

Considering the high degree of sequence conservation within the Rosaceae family and, in particular, among the Prunus species, we employed the first available peach oligonucleotide microarray (μPEACH 1.0) for studying the transcriptomic profile during apricot (cv. ‘Goldrich’) fruit development. Apricot fruits were harvested at three distinct developmental stages, corresponding to immature green (6 weeks before fully ripe stage), mature firm ripe (change of peel colour, 1 week before fully ripe stage) and fully ripe, namely T1, T2 and T3, respectively. When applied to μPEACH1.0, apricot target cDNAs showed significant hybridization with an average of 43% of spotted probes, validating the use of μPEACH1.0 to profile the transcriptome of apricot fruit. Microarray analyses carried out separately on peach (cv. ‘Fantasia’) and apricot fruit to profile transcriptome changes during fruit development showed that 70% of genes had the same expression pattern in both species. Such data indicate that the transcriptome is quite similar in apricot and peach fruit and also highlight the presence of species-specific transcript changes. In apricot, 400 and 74 differentially expressed genes were found during the transition from T1 to T2 and from T2 to T3, respectively. Among these, a considerable number of genes encoding IAA protein in action regulators (Aux/IAA) and heat shock proteins (HSPs) were highly up-regulated at early and late ripening, respectively. Intriguingly, the expression profiles of all considered HSPs and some of IAA protein /IAA genes showed different patterns between apricot and peach during the last stages of on-tree fruit development, suggesting the presence of diverse mechanism regulating ripening in these two close phylogenetically related species.

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Acknowledgments

This paper was produced within the framework of a Marie Curie individual fellowship held by GAM (Grant MEIF-CT-2006-038997). PT was in part supported by the DRUPOMICS project (MIPAF). The primers for auxin genes were a gift from Dr. Livio Trainotti., Dept of Biology, University of Padova, Italy. We thank Prof. Barry McGlasson (Centre for Plants and the Environment, University of Western Sydney, Australia) for helpful comments and critical reading of the manuscript.

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Authors and Affiliations

  1. Department of Environmental Agronomy and Crop Science, University of Padova, Viale dell’Università 16, 35020, Legnaro, Padua, Italy

    George A. Manganaris, Angela Rasori, Angelo Ramina & Claudio Bonghi

  2. Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, 3603, Cyprus

    George A. Manganaris

  3. Dipartimento di Produzione Vegetale, Università degli Studi di Milano, via Celoria 2, 20133, Milan, Italy

    Daniele Bassi & Filippo Geuna

  4. Scuola Superiore Sant’Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy

    Pietro Tonutti

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  1. George A. Manganaris
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  2. Angela Rasori
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  5. Angelo Ramina
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  6. Pietro Tonutti
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  7. Claudio Bonghi
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Correspondence to Claudio Bonghi.

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Communicated by A. Abbott

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Table S1

Physiological parameters of apricot fruit (DOC 29 kb)

Table S2

Sequences of the oligonucleotides used in qRT-PCR experiments. The “sequence name” refers to the peach contig number in the database used to prepare the oligo probes of the μPEACH1.0 microarray. The primers used for Aux/IAA genes are the same as those used and reported in supplementary data by Trainotti et al. (2007) (DOC 48 kb)

Table S3

List of probes showing significant expression values after SAM analysis in the fully ripe vs immature fruit of apricot (T3 vs T1) and peach (S4 vs S1) comparisons performed in the trial. “Oligo ID” is the code assigned to each transcript (220 out of 4,806) by the manufacturer (Operon). “Contig_name” refers to the peach contig number present in the database and used to synthesize the oligo probes for the μPEACH1.0 microarray. “Description” is the name assigned to Arabidopsis gene best hit for each peach contigs on the basis of the best hit obtained by a BLAST search against the plant proteome database. “At gene” is the AGI Locus (ATH AGI code TAIR 8) of the Arabidopsis gene best hit for each peach contigs obtained using BLASTX against the TAIR protein 8 database. “BINCODE” is the BIN and subBIN (http://www.gabipd.org/projects/MapMan/) assigned to the Arabidopsis gene best hit for peach contigs. “BIN NAME” is the description assigned to each BIN and SubBIN. The following four columns report the microarray results: apricot T3 (fully ripe) vs T1 (immature green) and st. dev. report [log2 (intensity T3/intensity T1 and relative standard deviation value)] and peach S4 (fully ripe) vs S1 (early growth stage) and st. dev. report [log2 (intensity S4/intensity S1 and relative standard deviation value)]. “Cluster” reports the letter that identifies the cluster to which the probes were assigned on the basis of the hybridization ratio value, expressed as log2, considering for down-regulated genes (log2 ratio ≤ −1.0, green colour), for up-regulated genes (log2 ratio ≥1.0, red colour) and for genes showing no differential expression (log2 ratio > −1 and <1, white colour). Cluster A and H included gene more expressed in ripe and immature fruit respectively, shared by apricot and peach. In clusters C and G and in clusters D and E were falling genes differentially expressed only in apricot and or in peach, respectively. In clusters B and F were grouped genes with an opposite trend in both species (e.g. cluster B was more expressed in ripe apricot and immature peach) (XLS 353 kb)

Table S4

List of probes showing significant expression values after Significant Analysis for Microarrays (SAM analysis) in the mature firm ripe fruit vs immature (T2 vs T1) and fully ripe vs mature firm ripe (T3 vs T2) of apricot comparisons performed in the trial. “Oligo ID” is the code assigned to each transcript (452 out of 4,806) by the manufacturer (Operon). “Contig_name” refers to the peach contig number present in the database and used to synthesize the oligo probes for the μPEACH1.0 microarray. “Description” is the name assigned to each peach contig on the basis of best hit obtained by a BLAST search against plant proteome database. “At gene” is the AGI Locus (ATH AGI code TAIR 8) of the Arabidopsis gene best hit for each peach contig obtained using BLASTX against the TAIR protein 8 database. “BINCODE” is the BIN and subBIN (http://www.gabipd.org/projects/MapMan/) assigned to the Arabidopsis gene best hit for peach contigs. “BIN NAME” is the description assigned to each BIN and SubBIN. The following four columns report the microarray results: T2 (mature firm ripe) vs T1 (immature green) and st. dev. report [log2 (intensity T2/intensity T1 and relative standard deviation value)] and T3 (fully ripe) vs T2 (mature firm fruit) and st. dev. report [log2 (intensity S4/intensity S3 and relative standard deviation value)]. Green is used to highlight down-regulated genes (log2 ratio ≤ −1.0), red to highlight up-regulated genes (log2 ratio ≥1.0) and yellow for genes showing no differential expression (log2 ratio > −1 and <1) (XLS 150 kb)

Table S5

Overrepresentation analysis of functional categories, carried out by using PageMan, in the comparison of mature firm ripe fruit vs immature (T2 vs T1) of apricot. “BINCODE” is the BIN and subBIN (http://www.gabipd.org/projects/MapMan/) assigned to the Arabidopsis gene best hit for peach contigs. “BIN NAME” is the description assigned to each BIN and SubBIN. Fisher’s exact test was used to test whether significantly more genes in a given category were present, on the basis of their count in the μPEACH 1.0 (column D), when T2 and T1 apricot fruit transcriptomes were compared (column C). Highlighted in yellow are BIN and subBIN significant in Fisher’s exact test (XLS 75.5 kb)

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Manganaris, G.A., Rasori, A., Bassi, D. et al. Comparative transcript profiling of apricot (Prunus armeniaca L.) fruit development and on-tree ripening. Tree Genetics & Genomes 7, 609–616 (2011). https://doi.org/10.1007/s11295-010-0360-4

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