Comparative transcriptomic profiling of peach and nectarine cultivars reveals cultivar-specific responses to chilled postharvest storage

Abstract

Introduction: Peach (Prunus persica (L.) Batsch,) and nectarine fruits (Prunus persica (L.) Batsch, var nectarine), are characterized by a rapid deterioration at room temperature. Therefore, cold storage is widely used to delay fruit post-harvest ripening and extend fruit commercial life. Physiological disorders, collectively known as chilling injury, can develop typically after 3 weeks of low-temperature storage and affect fruit quality.

Methods: A comparative transcriptomic analysis was performed to identify regulatory pathways that develop before chilling injury symptoms are detectable using next generation sequencing on the fruits of two contrasting cultivars, one peach (Sagittaria) and one nectarine, (Big Top), over 14 days of postharvest cold storage.

Results: There was a progressive increase in the number of differentially expressed genes between time points (DEGs) in both cultivars. More (1264) time point DEGs were identified in 'Big Top' compared to 'Sagittaria' (746 DEGs). Both cultivars showed a downregulation of pathways related to photosynthesis, and an upregulation of pathways related to amino sugars, nucleotide sugar metabolism and plant hormone signal transduction with ethylene pathways being most affected. Expression patterns of ethylene related genes (including biosynthesis, signaling and ERF transcription factors) correlated with genes involved in cell wall modification, membrane composition, pathogen and stress response, which are all involved later during storage in development of chilling injury.

Discussion: Overall, the results show that common pathways are activated in the fruit of 'Big Top' nectarine and 'Sagittaria' peach in response to cold storage but include also differences that are cultivar-specific responses.

Keywords: ERF transcription factors; Prunus; ethylene; postharvest; transcriptome.

Figure 1

Effects of cold storage on ‘Sagittaria’ peaches and ‘BigTop’ nectarines at 1°C followed by 36 h recovery at ambient temperature (22 °C). (A, B) maturity index (total soluble solids/titratable acidity) (n=3); (C, D) firmness (kg) (n=10). (E, F) ethylene emission (n=6). Mean ± SD; letters indicate significant differences between time points based on ANOVA and Tukey’s rank test (P < 0.05). Asterisks indicate significant differences between ‘Sagittaria’ and ‘Big Top’ values for each day (*** <0.001, * < 0.05).

Figure 2

Gene expression changes during cold storage. Principal Component Analysis (PCA) of normalised raw gene expression counts in SAG peach (A) and BT nectarine (B) for each day of cold storage at 1 °C (+36 h at ambient temperature (AT) 22 °C). Differentially expressed genes (DEGs) among successive storage time points for each cultivar: Sagittaria (SAG) peach (C) and Big Top (BT) nectarine (D). Gene expression level values were normalized by the DESEQ2 software (pvalue corrected < 0.05 andlog2FC> 1.5).

Figure 3

Expression profiling of time course transcriptome data using ImpulseDE2 (Fischer et al., 2018) to identify clusters of genes that are continuously up- or down-regulated MONOTONOUS INCREASE (MI) and DECREASE (MD) genes and transiently up- or down-regulated, TRANSIENT INCREASE (TI) and DECREASE (TD) (A); numbers of differentially expressed genes (DEGs) in the MI, MD, TI and TD clusters for SAG peach and BT nectarine (B).

Figure 4

Differential expression in the two cultivars. Venn diagrams of shared and unique genes related to temporal profiles in the two cultivars, in the four different clusters MONOTONOUS INCREASE (MI) (A), MONOTONOUS DECREASE (MD) (B), TRANSIENT INCREASE (TI) (C) and TRANSIENT DECREASE (TD) (D). GO enrichment analysis of MI and MD cluster genes in the two cultivars: MI genes in SAG (174) (E), and BT (468) (F); MD cluster genes in SAG (403) (G) and BT (456) (H), including C, cellular components; F, molecular functions and B, biological processes. The pathway enrichment analysis was performed with KOBASS, online tool, and the detailed information is presented as a bubble chart. The size of the bubbles represents the number of assigned genes, and the color of bubbles represents the -log10 (Q-value).

Figure 5

Real-time PCR analysis of selected DEGs related to ethylene and auxin signalling in SAG peach and BT nectarine, during cold storage treatment (1°C) at day 0, 1, 5, 7 and 14 followed by 36 h recovery at ambient temperature (22 °C). in two seasons 2017 (A, C, E, G, I) and 2018 (B, D, F, H, J). PRUPE_3G062800 (ERF) (A, B); PRUPE_2G272500 (ERF) (C, D); PRUPE_3G209900 (ACO) (E, F); PRUPE_1G208300 (AUX/IAA) (G, H); PRUPE_6G343800 (AUX/IAA) (I, J). Different letters indicate significant differences among cultivars considering all time points and both years. Statistical analyses were performed using ANOVA and Tukey’s ranked test (P < 0.05). Data are the mean ± SE; n=3.

Figure 6

Module-Day trait association identified by WGCNA in SAG peach (A) and BT nectarine (B). Each row corresponds to a module. The number of genes in each module is indicated on the left. The heat map indicates the correlation of each module with days of storage with the score and significance (P values in brackets) according to a Pearson analysis.

Figure 7

Gene structure and conserved motifs within thirteen peach ERF proteins identified through WGCNA as correlating in expression with downstream genes containing ERF binding motifs in their promoter sequences. Motifs identified using the MEME suite.