‘Celeste’ and ‘Bing’ are described as early- and mid-season varieties24. Both varieties were characterized for fruit growth and phenology in two seasons (Fig. 1A and Fig. S1A and Tables S1 to S4). In the 2017–2018 season, the slow growth period was more prolonged in the mid-season variety, in which growth resumption occurred from 39 DAFB (Fig. 1A). On the other hand, pink color initiation started at 40 DAFB in the early-season variety (Fig. 1B), whereas in the mid-season variety, it started at 50 DAFB (Fig. 1A and Table S2). GA4 and GA1 were detected in the fruits of both varieties from 34 to 44 DAFB (Fig. S1B).
Several GAs are present at the time of fruit color initiation in sweet cherry and other non-climacteric fruits5,10; therefore, we aimed to investigate the role of GA in ripening triggering by altering GA homeostasis. For this, GA3 treatment was performed when both varieties transitioned from light green to straw yellow fruit color (35 DAFB the 2017–2018 season and 34 DAFB the 2018–2019 season). At the time of GA3 application, both varieties were phenologically similar (Fig. 1; Tables S1 to S4).
GA3 affected ripening parameters at fully ripeness in both varieties, in the 2017–2018 seasons (Table 1), including firmness in both varieties, early-season variety fruit weight, and mid-season variety SSC. Similar results were observed in the 2018–2019 season (Table S5).
Table 1
Ripening related parameters in control- and GA3-treated fruit samples at harvest in early- and mid-season varieties, during 2017–2018 season. d.u., durometer units; SSC, soluble solids content; M.A., malic acid.
Season | Variety | Treatment | Weight (g) | Firmness (d.u.) | SSC (ºBrix) | Acidity (M.A. %) |
2017–2018 | Early-season var., Celeste | Control | 9.03ª** | 55.63a | 15.19a | 2.12a |
GA3* | 9.71b | 58.33b | 15.26a | 1.92a |
Mid-season var., Bing | Control | 8.70a | 54.06a | 19.85a | 3.24a |
GA3 | 8.61a | 63.21b | 18.91b | 3.19a |
* GA3 was applied as the commercial product ProGibb ® 40% SG to individual branches a rate of 30 ppm. GA3 treatment was at the light green-to-straw yellow transition of fruits at 35 DAFB in Celeste and Bing. |
**For each ripening related parameter, the significance of variation between control- and GA3-treated fruits was tested by one-way ANOVA analysis with Tukey's post hoc test, whereby different letters are significantly different means (p < 0.05). |
GA3 treatment produced less color in both varieties at harvest, decreased the percentage of dark fruits, and increased the percentage of light fruits in the 2017–2018 season (Figs. 2A-2D), which also occurred the following season (Figs. S2A-S2D). Estimated anthocyanins were significantly reduced in both varieties at harvest (Figs. 2E and 2F).
To further characterize the effect of GA3, IAD was measured from the date of the GA3 treatment in both varieties (Fig. 3).
IAD is a non-destructive ripening index utilized in sweet cherry, correlated with the anthocyanin content25. It reveals the presence of phenolic compounds that act as a screen for chlorophyll absorbance by measuring absorbance differences between 560 nm, 640 nm, and the 750 nm reference26. After the GA3 treatment, the early-season variety had a lower IAD value only at harvest in both seasons (Fig. 3A and Fig. S3A), whereas the mid-season variety had a delayed increase in the IAD values (Fig. 3B and Fig. S3B). This delay observed in the mid-season variety was accompanied by color differences between control- and GA3-treated fruits as soon as 15 days after the treatment (50 DAFB), whereas control- and GA3-treated fruits of the early-season variety had no differences in color at the same date (Fig. 3C).
As both varieties were differentially affected by GA3, we explored the transcriptomic effect produced by GA3 treatment through RNA-seq analysis. For this, we analyzed fruit samples collected minutes before the GA3 treatment in the 2017–2018 season (T0, 35 DAFB), and control- and GA3-treated fruit samples collected four days after the GA3 treatment (CT4 and GT4, respectively, 39 DAFB). In total, 18 samples were sequenced, nine per variety (three points: T0, CT4 and GT4, and three replicates) that yielded a total of 859 million filtered reads (84 Gb of data), with an average length of 98 bp, and a similar quantity of mapped reads to the P. avium transcriptome reference that was ca. 68% of the total filtered read count (Table S6).
Clustering of the 100 genes having the highest expression levels revealed that samples behaved as expected, i.e., replicates grouped, except for one replicate of T0 of early-season variety (Sample_ID: CT0_3) that was excluded from subsequent analysis (Fig. S4).
DEGs analysis was performed on the genes that changed between T0 and CT4 (CT4-T0) and between T0 and GT4 (GT4-T0) with a cutoff value of two-fold change and FDR < 0.05. Up and downregulated genes were identified in both varieties (Fig. 4). In the early-season variety, 381 and 808 genes changed only in GT4-T0 and CT4-T0, respectively (Fig. 4A). In mid-season variety, 249 and 495 genes changed only in GT4-T0 and CT4-T0, respectively (Fig. 4B). There were 482 and 729 genes in the early-season variety, and 563 and 314 genes in the mid-season variety, that changed independently of the GA3 treatment (they are in the intercepts of the diagrams). In contrast, the 381 GT4-T0 genes plus the 808 CT4-T0 genes in the early-season variety, and the 249 GT4-T0 genes plus the 495 CT4-T0 genes in the mid-season variety, were GA3-modulated. Therefore, they were used in the subsequent GO enrichment analysis focused on the Biological Process categories.
In the early-season variety, 'response to stimulus', 'response to hormone' and 'response to auxin' were some of the overrepresented GO terms (FDR < 0.05) in the GT4-T0 comparison. On the contrary, 'protein phosphorylation' and 'photosynthesis' were some of the overrepresented GO terms (FDR < 0.05) in the CT4-T0 comparison (Table 2).
Table 2
Gene ontology (GO) enrichment analysis performed on the DEGs that are modulated by GA3 in early- and mid-season varieties. The biological process function ontologies with the lowest p-value and FDR less than 0.05 are shown.
Variety | Comparisons | GO ID | GO description | p-value |
Early-season var., Celeste | GT4-T0 total (381) | GO:0050896 | response to stimulus | 2.284E-06 |
GO:0042221 | response to chemical | 6.317E-06 |
GO:0010033 | response to organic substance | 1.107E-05 |
GO:0009725 | response to hormone | 1.519E-05 |
GO:0009719 | response to endogenous stimulus | 1.647E-05 |
GO:0009733 | response to auxin | 2.071E-05 |
CT4-T0 total (808) | GO:0055114 | oxidation-reduction process | 9.47E-08 |
GO:0006468 | protein phosphorylation | 1.62E-07 |
GO:0008152 | metabolic process | 2.65E-07 |
GO:0016310 | phosphorylation | 2.09E-05 |
GO:0019419 | sulfate reduction | 2.57E-05 |
GO:0015979 | photosynthesis | 4.86E-05 |
Mid-season var., Bing | GT4-T0 up* (168) | GO:0005975 | carbohydrate metabolic process | 5.293E-04 |
CT4-T0 down* (306) | GO:0055114 | oxidation-reduction process | 3.986E-08 |
GO:0009607 | response to biotic stimulus | 3.269E-05 |
GO:0005975 | carbohydrate metabolic process | 4.311E-05 |
GO:0006950 | response to stress | 4.565E-05 |
*GT4-T0 up and CT4-T0 down comparisons of mid-season variety had more overrepresented categories than GT4-T0 total and CT4-T0 total, respectively; therefore, they were included as these comparisons are more informative. |
Regarding the mid-season variety, the GO term 'carbohydrate metabolic process' was overrepresented (FDR < 0.05) in the GT4-T0 comparison with upregulated genes, whereas 'oxidation-reduction process' and 'response to stress', among others, were overrepresented GO terms (FDR < 0.05) in the CT4-T0 comparison that includes downregulated genes (Table 2).
Figure 5. Heat map with the number of DEGs that are modulated by GA3 in each Gene Ontology (GO) category. A, Number of genes in GT4-T0 and CT4-T0 comparisons that are up or downregulated in the early-season variety. B, Number of genes in GT4-T0 and CT4-T0 comparisons that are up or downregulated in the mid-season variety. For A and B, biological processes with p < 0.001.
In general, GO terms were specific to a particular comparison, except for the GO category 'oxidation-reduction process' in the early-season variety (Fig. 5A) and 'carbohydrate metabolic process' in the mid-season variety (Fig. 5B), with downregulated genes in CT4-T0 and upregulated genes in the GT4-T0. The GO term 'metabolic process' had the highest number of DEGs modulated by GA3 in the mid-season variety (Fig. 5B). In the early-season variety, this GO term and 'cellular process' were the most abundant (Fig. 5A).
CT4-T0 up and down comparisons contain GA-modulated genes that up or downregulated from T0 to T4, but they no longer changed after the GA3 treatment. In the early-season variety, the CT4-T0 down comparison contained DEGs in 'photosynthesis', 'protein phosphorylation', and 'transmembrane transport' GO categories, among others (Fig. 5A). In contrast, in the mid-season variety, it contained DEGs in the 'response to stress' and 'plant-type secondary cell wall biogenesis' GO categories, among others (Fig. 5B). On the other hand, the 'carotenoid metabolism' GO category contained GA-modulated genes that upregulated from T0 to T4 in the early-season variety.
GT4-T0 up and down comparisons contain GA-modulated genes that did not change from T0 to T4 but are up or downregulated by GA3. DEGs in the 'auxin response' and 'putrescine biosynthetic process' GO categories were present in the GT4-T0 up comparison, in the early-season variety. In contrast, several GO categories related to negative regulation of gene expression were found in the GT4-T0 down comparison in this variety (Fig. 5A). In the mid-season variety, DEGs in the 'cell wall organization or biogenesis' and 'reactive oxygen species metabolic process' GO categories were present in the comparison containing upregulated genes (GT4-T0 up), whereas 'xylan biosynthetic process' had DEGs in the GT4-T0 down comparison in this variety (Fig. 5A)
After that, we investigated the variety-specific genes that respond to GA3 treatment (Fig. 6). In the GT4-T0 comparison of the early-season variety, 436 and 652 genes were up and downregulated, respectively. On the other hand, 477 and 145 genes were up and downregulated in the mid-season variety.
As shown in Table 3, the GO terms 'response to auxin', 'response to stress', and 'DNA packaging', among others, were overrepresented (FDR < 0.01), with genes that exclusively changed in the early-season variety. On the other hand, in the mid-season variety, 'regulation of transcription, DNA-templated' and 'regulation of nucleic acid-templated transcription' were some of the overrepresented GO terms (FDR < 0.01) in the upregulated DEGs that were exclusive of this variety
Table 3
GO enrichment analysis performed on the DEGs that are modulated by GA3 and unique to each variety. The biological process function ontologies with the lowest p-value and FDR less than 0.05 are shown.
Variety | Comparisons | GO ID | GO description | p-value |
Early-season var., Celeste | GT4-T0 total (1088) | GO:0050896 | response to stimulus | 1.34E-13 |
GO:0055114 | oxidation-reduction process | 1.31E-11 |
GO:0042221 | response to chemical | 2.90E-10 |
GO:0009733 | response to auxin | 7.08E-10 |
GO:0006950 | response to stress | 6.87E-09 |
GO:0006323 | DNA packaging | 9.67E-09 |
Mid-season var., Bing | GT4-T0 total (622) | GO:0006355 | regulation of transcription, DNA-templated | 2.90E-06 |
GO:1903506 | regulation of nucleic acid-templated transcription | 3.48E-06 |
GO:2001141 | regulation of RNA biosynthetic process | 3.48E-06 |
GO:0009409 | response to cold | 4.13E-06 |
GO:2000112 | regulation of cellular macromolecule biosynthetic process | 5.81E-06 |
GO:0051252 | regulation of RNA metabolic process | 5.94E-06 |
In Fig. 7, the enriched GO terms that had more DEGs unique to early-season variety were 'response to stimulus', 'oxidation-reduction' process', 'cellular component organization or biogenesis', 'chromosome organization', 'cell cycle', 'response to hormone', 'response to auxin', among others. In contrast, the GO terms that had more DEGs unique to mid-season variety were 'biological regulation', 'aromatic compound biosynthetic process', 'regulation of transcription, DNA-templated', and 'regulation of nucleic acid-templated transcription', among others (Fig. 7).
As 'response to hormone' was an overrepresented GO, a directed search of hormone-related genes was performed in the CT4-T0 and GT4-T0 comparisons of each variety (Table 4).
Table 4
Differential gene expression as fold change of genes related to hormone pathways in pairwise comparisons CT4-T0 and GT4-T0 of each variety. In gray, comparisons having genes whose absolute fold change value was at least two.
| | | Early-season variety | Mid-season variety |
Name | ID | GO Biological Process | CT4-T0 | GT4-T0 | CT4-T0 | GT4-T0 |
gibberellin-regulated protein 11-like | Pav_sc0001364.1_g150.1.mk | Not identified GO | -19.5 | | -8.4 | -9.4 |
gibberellin-regulated protein 1-like | Pav_sc0000044.1_g560.1.mk | Not identified GO | | | | 2.2 |
gibberellin-regulated protein 4-like | Pav_sc0000766.1_g050.1.mk | Not identified GO | | | | 2.9 |
gibberellin-regulated protein 9 | Pav_sc0000350.1_g1060.1.mk | Not identified GO | -5.8 | -3.8 | | |
gibberellin 2-beta-dioxygenase-like | Pav_sc0003135.1_g610.1.mk | Not identified GO | -5.1 | | | |
gibberellin 2-beta-dioxygenase 1 | Pav_sc0000143.1_g470.1.mk | Not identified GO | -4.2 | -2.0 | | |
gibberellin 2-beta-dioxygenase 1-like | Pav_sc0000095.1_g1110.1.mk | Not identified GO | -2.6 | | | |
DELLA protein GAI-like | Pav_sc0000704.1_g110.1.mk | Not identified GO | | 2.2 | | |
gibberellin receptor GID1B-like | Pav_sc0000848.1_g080.1.mk | Response to endogenous stimulus | . | -3.1 | | |
Name | ID | GO Biological Process | CT4-T0 | GT4-T0 | CT4-T0 | GT4-T0 |
phytoene synthase 2 chloroplastic | Pav_sc0001124.1_g480.1.mk | Metabolic proces | 2.3 | | | |
9-cis epoxycarotenoid dioxygenase NCED1 chloroplastic-like | Pav_sc0000095.1_g1080.1.mk | Metabolic proces | 4.0 | | | |
probable carotenoid cleavage dioxygenase 4 chloroplastic | Pav_sc0000354.1_g230.1.mk | Metabolic proces | -4.2 | -2.1 | -2.9 | -3.9 |
abscisic acid 8'-hydroxylase 2 isoform X1 | Pav_sc0000563.1_g270.1.mk | Metabolic proces | -4.9 | | | |
abscisic acid 8'-hydroxylase 4 | Pav_sc0002234.1_g030.1.mk | Metabolic proces | -5.1 | -2.5 | | |
abscisic stress ripening | Pav_sc0005261.1_g020.1.br | Not identified GO | 2.8 | 2.3 | | |
abscisic stress-ripening protein 2 | Pav_sc0002659.1_g070.1.br | Not identified GO | 2.9 | | | |
abscisic acid stress ripening protein homolog | Pav_sc0000863.1_g110.1.m | Not identified GO | 3.1 | 2.8 | | |
abscisic stress-ripening protein 2 | Pav_sc0000863.1_g060.1.br | Not identified GO | 3.3 | 2.5 | | |
abscisic acid receptor PYL4 | Pav_sc0001341.1_g250.1.mk | Not identified GO | | 2.1 | 2.6 | 2.6 |
protein C2-DOMAIN ABA-RELATED 4-like | Pav_sc0000464.1_g320.1.mk | Not identified GO | | | 2.2 | 2.0 |
protein C2-DOMAIN ABA-RELATED 7 | Pav_sc0000221.1_g240.1.mk | Not identified GO | 2.1 | 2.2 | | |
probable protein phosphatase 2C 12 | Pav_sc0000852.1_g1120.1.mk | Cellular protein modification process | 2.1 | | 2.9 | 3.3 |
probable protein phosphatase 2C 39 | Pav_sc0000975.1_g200.1.mk | Cellular protein modification process | . | | | 2.2 |
probable phosphatase 2C-like protein 44 | Pav_sc0000119.1_g610.1.mk | Cellular protein modification process | . | -3.0 | -4.4 | |
Name | ID | GO Biological Process | CT4-T0 | GT4-T0 | CT4-T0 | GT4-T0 |
auxin-responsive protein SAUR50 | Pav_sc0000480.1_g730.1.mk | Response to endogenous stimulus | 10.8 | 13.8 | 6.8 | 4.7 |
auxin-responsive protein IAA29 | Pav_co4052989.1_g010.1.mk | Response to endogenous stimulus | 2.8 | 3.5 | | |
auxin-responsive protein IAA29 | Pav_sc0000311.1_g1160.1.mk | Response to endogenous stimulus | 5.9 | 5.3 | | |
auxin-responsive protein IAA13 | Pav_sc0002717.1_g060.1.br | Response to endogenous stimulus | 2.6 | | | |
auxin-responsive protein IAA11 isoform X1 | Pav_sc0002181.1_g160.1.mk | Response to endogenous stimulus | 2.6 | | | |
auxin-responsive protein IAA8-like isoform X2 | Pav_sc0002327.1_g560.1.mk | Response to endogenous stimulus | 4.3 | 3.4 | 2.9 | |
auxin-induced protein IAA6 | Pav_sc0000716.1_g200.1.mk | Response to endogenous stimulus | 2.3 | 2.0 | 2.3 | 2.5 |
protein kinase PINOID | Pav_sc0000481.1_g260.1.mk | Response to endogenous stimulus | 3.4 | 4.3 | 4.4 | 6.5 |
probable indole-3-pyruvate monooxygenase YUCCA10 | Pav_sc0000382.1_g010.1.mk | Response to endogenous stimulus | 6.2 | 3.0 | 4.2 | |
auxin-induced protein 15A | Pav_sc0006480.1_g020.1.br | Response to endogenous stimulus | 7.3 | 10.6 | | |
auxin-induced protein 15A | Pav_sc0006480.1_g030.1.br | Response to endogenous stimulus | 3.9 | 5.4 | | |
auxin-induced protein 15A-like | Pav_sc0007626.1_g030.1.br | Response to endogenous stimulus | 10.8 | 15.0 | | |
auxin-induced protein 15A-like | Pav_sc0008108.1_g010.1.mk | Response to endogenous stimulus | 5.1 | 8.4 | | |
auxin-induced protein 15A-like | Pav_sc0004469.1_g010.1.br | Response to endogenous stimulus | . | | -2.7 | -3.0 |
auxin-induced protein 15A-like | Pav_sc0004655.1_g020.1.br | Response to endogenous stimulus | . | | -3.7 | -3.0 |
auxin-induced protein 15A-like | Pav_sc0004655.1_g010.1.br | Response to endogenous stimulus | . | | -3.4 | |
Name | ID | GO Biological Process | CT4-T0 | GT4-T0 | CT4-T0 | GT4-T0 |
1-aminocyclopropane-1-carboxylate oxidase | Pav_sc0001084.1_g100.1.mk | Metabolic process | 3.0 | 2.8 | | |
1-aminocyclopropane-1-carboxylate oxidase | Pav_sc0002206.1_g340.1.mk | Metabolic process | 6.6 | 5.3 | | |
1-aminocyclopropane-1-carboxylate oxidase homolog 1-like | Pav_sc0000583.1_g270.1.mk | Metabolic process | | | -12.5 | |
ethylene-responsive transcription factor ERF003-like | Pav_sc0000890.1_g720.1.mk | Nucleobase-containing compound metabolic process | 7.0 | 5.2 | 22.3 | 25.3 |
ethylene-responsive transcription factor 1B-like | Pav_sc0000583.1_g510.1.mk | Nucleobase-containing compound metabolic process | -7.8 | -6.0 | | 12.6 |
ethylene-responsive transcription factor 12 | Pav_sc0001305.1_g990.1.mk | Nucleobase-containing compound metabolic process | 3.0 | 3.0 | 5.9 | 6.3 |
ethylene-responsive transcription factor ERF027-like | Pav_sc0000355.1_g370.1.mk | Nucleobase-containing compound metabolic process | 3.0 | | 6.3 | 8.1 |
ethylene-responsive transcription factor ERF106 | Pav_sc0001102.1_g230.1.mk | Nucleobase-containing compound metabolic process | 2.1 | | 3.1 | 3.6 |
ethylene-responsive transcription factor ERF109-like | Pav_sc0000071.1_g750.1.mk | Nucleobase-containing compound metabolic process | . | | 12.3 | 9.9 |
ethylene-responsive transcription factor ERF017 | Pav_sc0000129.1_g1460.1.mk | Nucleobase-containing compound metabolic process | . | | 9.9 | 5.1 |
Name | ID | GO Biological Process | CT4-T0 | GT4-T0 | CT4-T0 | GT4-T0 |
cytokinin dehydrogenase 4-like | Pav_sc0000129.1_g070.1.mk | Metabolic process | -6.2 | -14 | -20.2 | |
two-component response regulator ARR22-like | Pav_sc0000164.1_g090.1.mk | Signal transduction | -4.1 | -3.4 | -6.4 | -3.9 |
two-component response regulator ARR2 isoform X1 | Pav_sc0000174.1_g1950.1.mk | Signal transduction | | | 2.6 | 2.6 |
Several gibberellin 2-beta-dioxygenase related genes were downregulated in the CT4-T0 and GT4-T0 comparisons only in the early-season variety. Regarding the ABA biosynthetic pathway, two abscisic acid 8'-hydroxylase related genes were downregulated in the early-season variety. Concerning the ABA response, several abscisic stress ripening-related genes were upregulated in the CT4-T0 comparison only in the early-season variety, which was less marked in the GT4-T0 comparison. Regarding the auxin response, several genes that encode putative auxin AuxIAA response repressors were induced in the CT4-T0 comparison of the early-season variety, and they were less upregulated in the GT4-T0 comparison. Some genes coding for auxin-induced protein 15A and 15A-like were upregulated in CT4-T0 and were upregulated even more in GT4-T0, whereas other groups of auxin-induced protein 15A-like were downregulated in the mid-season variety. In contrast, several ethylene-responsive transcription factor genes were more upregulated in the mid-season variety than in the early-season variety.
Given that 'negative regulation of gene expression' and 'DNA packaging' and 'nucleosome assembly' GO terms were overrepresented, a directed search of genes related to these categories was performed (Table 5).
Table 5
Differential gene expression as fold change of genes related to transcriptional and epigenetic regulation in pairwise comparisons CT4-T0 and GT4-T0 of each variety. In gray, comparison having genes whose absolute fold change value was at least two.
| | | Early-season variety | Mid-season variety |
Name | ID | GO Biological Process | CT4-T0 | GT4-T0 | CT4-T0 | GT4-T0 |
dof zinc finger protein DOF1.2 | Pav_sc0001556.1_g080.1.mk | Nucleobase-containing compound metabolic process | 3.1 | 3.3 | 13.5 | 9.7 |
transcription factor MYB44 | Pav_sc0000625.1_g100.1.mk | Not identified GO | 3.8 | 3.9 | 20.0 | 13.4 |
transcription factor MYB44-like | Pav_sc0000800.1_g060.1.mk | Not identified GO | . | . | 13.5 | 12.8 |
transcription factor MYB44-like | Pav_sc0000852.1_g360.1.mk | Not identified GO | . | . | 6.4 | 5.5 |
transcription factor MYB44-like | Pav_sc0001807.1_g120.1.mk | Not identified GO | . | . | 4.3 | 3.8 |
transcription repressor MYB6-like | Pav_sc0000464.1_g910.1.mk | Not identified GO | -3.0 | -2.8 | -2.1 | -2.6 |
tannin-related R2R3 MYB transcription factor | Pav_sc0000129.1_g770.1.br | Not identified GO | -10.0 | -9.0 | -3.2 | -2.1 |
transcription factor bHLH94-like | Pav_sc0006212.1_g040.1.mk | Not identified GO | -6.8 | -10.0 | -2.7 | -4.4 |
transcription factor bHLH92 | Pav_sc0000998.1_g640.1.mk | Not identified GO | -6.7 | -8.6 | | |
probable WRKY transcription factor 13 | Pav_sc0002442.1_g080.1.mk | Nucleobase-containing compound metabolic process | -8.5 | . | | |
probable WRKY transcription factor 70 | Pav_sc0001582.1_g320.1.mk | Nucleobase-containing compound metabolic process | -3.4 | . | 3.9 | 5.3 |
probable WRKY transcription factor 46 | Pav_sc0000254.1_g030.1.mk | Nucleobase-containing compound metabolic process | -3.0 | . | 4.5 | 4.0 |
probable WRKY transcription factor 26 | Pav_sc0000375.1_g500.1.mk | Nucleobase-containing compound metabolic process | . | . | 2.4 | 3.2 |
probable WRKY transcription factor 11 | Pav_sc0000624.1_g520.1.mk | Nucleobase-containing compound metabolic process | . | . | 2.6 | 2.6 |
probable WRKY transcription factor 7 | Pav_sc0000852.1_g460.1.mk | Nucleobase-containing compound metabolic process | . | . | 2.8 | 3.2 |
probable WRKY transcription factor 40 isoform X1 | Pav_sc0000890.1_g500.1.mk | Nucleobase-containing compound metabolic process | . | . | 5.4 | 6.8 |
Name | ID | GO Biological Process | CT4-T0 | GT4-T0 | CT4-T0 | GT4-T0 |
DNA (cytosine-5)-methyltransferase 1-like Pav_sc0000113.1_g130.1.mk | Pav_sc0000113.1_g130.1.mk | DNA metabolic process | -5.2 | -4.4 | -2.1 | -2.4 |
homocysteine S-methyltransferase 1 Pav_sc0001051.1_g010.1.mk | Pav_sc0001051.1_g010.1.mk | Biosynthetic process | -2.2 | | -2.6 | |
histone-lysine N-methyltransferase ASHR3 Pav_sc0000065.1_g730.1.mk | Pav_sc0000065.1_g730.1.mk | Cellular protein modification process | -5.8 | -6.6 | -2.6 | -3.6 |
histone acetyltransferase KAT6B Pav_sc0001313.1_g160.1.mk | Pav_sc0001313.1_g160.1.mk | Not identified GO | -6.3 | -5.5 | -5.0 | -4.7 |
histone-lysine N-methyltransferase ATXR6 Pav_sc0000138.1_g1060.1.mk | Pav_sc0000138.1_g1060.1.mk | Cellular protein modification process | -2.4 | -2.9 | | |
histone-lysine N-methyltransferase SETD1B-like Pav_sc0000363.1_g430.1.mk | Pav_sc0000363.1_g430.1.mk | Not identified GO | -4.1 | -3.3 | | |
Many genes coding for MYB44-like transcription factor were upregulated in CT4-T0, but they were less induced in the GT4-T0 comparison in the mid-season variety. In contrast, other transcription factor genes were downregulated in the early-season variety, including a gene coding for a putative tannin-related R2R3 MYB. Finally, both varieties had downregulated genes encoding putative histone methyl transferases and a DNA (cytosine-5)-methyltransferase 1-like in the CT4-T0, which were slightly less expressed in the GT4-T0 comparison.