Transcriptomic analysis reveals cold responsive genes implicated in
peach low temperature tolerance
V. Falara1, G.A. Manganaris2,3, F. Ziliotto3, A. Manganaris4, C. Bonghi3*, A.
Ramina3, A.K. Kanellis1*
1
Group of Biotechnology of Pharmaceutical Plants, Lab of Pharmacognosy, Department of
Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
2
Cyprus University of Technology, Department of Agricultural Production and Food Science and
Technology, Lemessos, 50329, Cyprus
3
Department of Environmental Agronomy and Crop Science, University of Padova, Viale
dell’Università 16, 35020, Legnaro (Padova), Italy
4
Department of Crop Production, Technological Educational Institute, 57400, Sindos-Thessaloniki,
Greece
*Corresponding authors
Angelos K. Kanellis
Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124
Thessaloniki, Greece
Tel: +302310997656
FAX: +302310997662
E-mail: kanellis@pharm.auth.gr
Claudio Bonghi
Department of Environmental Agronomy and Crop Science, University of Padova,
Viale dell’Università 16, 35020, Legnaro (Padova), Italy
Tel: +390498272844
FAX:+390498272850
E-mail: claudio.bonghi@unipd.it
Supplementary Tables
Table S1. Gene names, their abbreviations along with the number of contig
characterised in the dedicated peach database and the set of primers used to obtain the
cDNA fragment used as probe in northern analyses as supplementary table.
Gene name
Abbreviation
Heat shock protein 17.4 [Quercus
suber]
HSP_3065*
small heat shock protein - soybean
HSP_3067
Dehydrin [Prunus persica]
Dhd_1528
Dehydration-induced protein RD22like protein [Gossypium hirsutum]
RD-22_974
Pathogenesis-related protein PR-4B
precursor [Nicotiana tabacum]
PR-4B_1026
Lipoxygenase (EC 1.13.11.12) loxD tomato
LOX_4304
Putative beta-D-xylosidase (PpAz152) Xyl_1031
Expansin [Prunus persica]
Exp_676**
Forward
Reverse
Primers
Size
(bp)
705
-
CTGCAATGGAGAATGGGGTTCT
GTGCTTCCACAGAGTTTGTAG
GATGGAATGGATCATCATTTGGAC
CCAAGGCTCCTACCTTTCCTC
GCAGGAATATAGGATTGCGAGG
147
343
181
CGGTTGCTGTTTGCCACAGC
CTACGACTTTGTTGACTGTGGC
GCTTCTGGAGTAAATGATCATTTGCAT
T
GACCCTCCAAAGTTAATCTCTGG
177
194
GGAGGAGCATATAATAGGCCATC
GCCCACAATCTGGCACATGGG
149
CCTGGACGTACACGTGGATGT
-
*HSP_3065 was gift from Dr. Ann Callahan,** Exp_676 was a gift from Dr.Hiroko Hayamα,
*HSP_3065 was gift from Dr. Ann Callahan,** Exp_676 was a gift from Dr.Hiroko Hayamα,
1340
Legend to Table S2
Table S2. List of probes showing significant expression values after Significant
Analysis for Microarrays (SAM analysis) in each of the four comparisons performed
in the trial. A total of 444 probes showed significant expression values after SAM
analysis in at least two of the four (4 w + 1d vs. 0 w + 1 d ‘Morettini No2’; 6w + 1 d
vs. 0 w + 1d ‘Morettini No2’; 4 w + 1d vs. 0 w + 1 d ‘Royal Glory’4 w + 1d vs. 0 w +
1 d ‘Royal Glory’) hybridizations performed in the trial. “Ctg” refers to the peach
contig number present in the database and used to synthesize the oligo probes for the
µPEACH1.0 microarray. “Oligo ID” is the code assigned to each transcript (444 out
of 4,806) by the manufacturer (Operon). “At gene” is the AGI Locus (ATH AGI code
TAIR 7) of the Arabidopsis gene best hit for each peach contigs obtained using
BLASTX against the TAIR protein 7 database. “Description” is the name assigned to
Arabidopsis gene best hit for peach contigs. “Mapman BIN” is the BIN and subBIN
(http://www.gabipd.org/projects/MapMan/) assigned to the Arabidopsis gene best hit
for peach contigs. The following eight columns report the microarray results: 4 w
(0°C) + 1 d (25°C)/1 d (25°C) ‘Morettini No2’ and stdev report [log2 (intensity
4weeks/intensity T0 and relative standard deviation value]; 6weeks (0°C) + 1 day
(25°C) /1 day (25°C) ‘Morettini No2’ and stdev report reports [log2 (intensity 6
weeks (0°C) + 1 day (25°C)/intensity 1 day (25°C)) and relative standard deviation
value]; 4weeks (0°C) + 1 day (25°C) /1 day (25°C) ‘Royal Glory’ and stdev report
[log2 (intensity 4weeks (0°C) + 1 day (25°C)/intensity 1 day (25°C)) and relative
standard deviation value]; 6weeks/1 day (25°C) ‘Royal Glory’ and stdev reports [log2
(intensity 6 weeks(0°C) + 1 day (25°C)/intensity 1 day (25°C)) 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). Ns and NA indicate probes that
were not significant at SAM analysis and data not available, respectively.
Legend to Figure 1S
Fig. 1S. Differentially expressed transcripts in peach fruit of cultivars ‘Morettini No2’
and ‘Royal Glory’ after 4 and 6 weeks of cold storage (0°C) plus 1 day shelf life
(25°C). Numbers associated to light-grey bars represent up- (above) and dark grey
represent down- (bottom) regulated transcripts identified via microarray analysis in
the four samples compared to fruit 1 day after harvest. A total of 185 and 355
transcripts have been considered for ‘Morettini No2’ (left) and ‘Royal Glory’ (right)
comparisons, respectively, according to SAM (Table S2, supplementary material).
Numbers of the up- and down-regulated transcripts in the 4 weeks samples showing
the same expression pattern with the 6 weeks samples are indicated within the dotted
lines. Numbers associated with the white bars indicate constitutively expressed
mRNA after 4 and 6 weeks cold storage plus 1 day shelf life.
In sensitive cultivar ‘Morettini No2’, among the 100 up-regulated transcripts after 4
weeks at 0°C + 1 day at 25°C, only 53 remained still induced after 2 additional weeks
in storage. In the same sample an additional set of 12 genes, not differentially
expressed after 4 weeks at 0°C + 1 day at 25°C, were induced leading to a total
number of 65 up-regulated genes. Similar trend was also observed in ‘Royal Glory’,
where among the 158 up-regulated messages after 4 weeks cold storage plus 1 day
shelf life; only 38 were still induced after 6 weeks cold storage and 1 day shelf life,
with an additional set of 18 transcripts not differentially expressed after 4 weeks cold
storage + 1 day at room temperature, for a total of 56 genes. Considering the downregulated genes, among the 155 ones observed after 4 weeks at 0°C + 1 day at 25°C,
only 33 were still down-regulated after 6 weeks at 0°C + 1 day at 25°C, in addition to
a set of 24 transcripts, whose expression did not change after removal from 4 weeks
of cold storage and subsequent maintenance at room temperature for 1 day.