Comparative Transcriptome and Metabolome Profiling Revealed Molecular Cascade Events During the Enzymatic Browning of Potato Tubers After Cutting

Abstract

Enzymatic browning is a major issue in potato processing, causing a decline in both nutritional value and quality. Although there are numerous studies on the mechanism of enzymatic browning of potato tubers, few relevant reports are available on the changes at the transcriptome level during enzymatic browning as well as on the differences in the browning process of potato tubers with differing degrees of enzymatic browning potential. To gain insights into the molecular mechanism of enzymatic browning after cutting, this study presents the transcriptional characterization of temporal molecular events during enzymatic browning of browning-resistant (BR) and browning-susceptible (BS) potato tubers. RNA-sequencing (RNA-seq) analysis detected 19,377 and 13,741 differentially expressed genes (DEGs) in BR and BS tubers, respectively, with similar function enrichment observed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Up-regulated DEGs were significantly enriched in the pathways related to phenol and lipid biosynthesis, while the down-regulated DEGs were significantly enriched in the pathways related to programmed cell death. Significant redox-related pathways occurred earlier in BS tubers compared to the BR tubers. Further analysis revealed that the BS tubers had a stronger phenolic synthesis ability compared to the BR tubers. However, the BR tubers showed a stronger free radical scavenging ability compared to the BS tubers. The results of our study provide insights into the temporal molecular events that occur during the enzymatic browning of potato tubers after cutting and the potential molecular mechanisms for different degrees of enzymatic browning.

Keywords: cut-wounding; enzymatic browning; metabolome; potato tubers; transcriptome.

Figure 1

Enzymatic browning phenotype and related enzyme activity of potato tubers. (a) Enzymatic browning phenotype of potato tubers during 0–24 h after cutting. (b–d).Color change of potato tubers during 0–24 h after cutting. (e–g) PPO, POD, and total phenol content of potato tubers. D6, susceptible-browning cultivar; X2, resistant-browning cultivar. The mean value and standard error were obtained from three biological replicates, and the significance difference level p ≤ 0.01 (**).

Figure 2

Statistical analysis of all identified differentially expressed genes (DEGs) in response to cut-wounding at different times. (a) Statistical chart of DEGs of transcriptome in response to cut-wounding at 4 h, 12 h, and 24 h after cutting; (b) Venn diagram of DEGs at different times after cut-wounding. D6, susceptible-browning cultivar; X2, resistant-browning cultivar.

Figure 3

KEGG enrichment analysis of shared differentially expressed genes (DEGs) of X2 and D6 tubers after cutting.

Figure 4

Gene expression pattern and KEGG analysis of 1248 overlapping DEGs. (a) Gene expression pattern analysis was performed by Short Time-series Expression Miner software (STEM version 1.3.13); (b) KEGG analysis of up- and down-regulated differentially expressed genes. D6, susceptible-browning cultivar; X2, resistant-browning cultivar.

Figure 5

Venn diagram of differentially expressed genes (DEGs) of potato tubers at different times after cutting–wounding between X2 and D6 cultivars.

Figure 6

Expression patterns of differentially expressed genes (DEGs) in the pathway of phenylpropanoid biosynthesis response to cut-wounding in potato tubers at different times. Red represents a high transcript level and white represents a low transcript level. PAL: phenylalanine ammonia lyase; C4H: Cinnamate 4-hydroxylase; 4CL: 4-coumaroyl: CoA ligase; CCR: cinnamoyl CoA reductase; CAD: cinnamyl-alcohol dehydrogenase; POD: peroxidase; HCT: shikimate O-hydroxycinnamoyltransferase; C3′H: cytochrome P450 98A3-like; CCoAOMT: caffeoyl-CoA O-methyltransferase.

Figure 7

Expression patterns of DEGs-related antioxidant activity of potato tubers. Red represents a high transcript level and white represents a low transcript level. PPO: polyphenol oxidase; CAT: catalase; SOD: superoxide dismutase.

Figure 8

The enzymy activity and content of H₂O₂. The mean value and standard error were obtained from three biological replicates.

Figure 9

Heat map of DEGs involved in plant hormone signal transduction during enzymatic browning of potato tubers. Red represents a high transcript level and white represents a low transcript level. Dark gray areas represent missing values. BAK1: ETR: ethylene receptor; EBF1/2: EIN3-binding F-box protein; EIN3:ethylene-insensitive protein 3; ERF1/2: ethylene-responsive transcription factor 1; AUX1: auxin transporter-like protein; TIR1: TRANSPORT INHIBITOR RESPONSE 1-like; AUX/IAA: auxin/indole-3-acetic acid 3; GH3: indole-3-acetic acid-amido synthetase; SAUR: auxin-induced protein 15A-like; PYR/PYL: abscisic acid receptor PYL8-like; CPP2C: protein phosphatase 2; SnRK2: serine/threonine-protein kinase SAPK1-like; ABF: ABRE binding factor; AHP: histidine kinase 3; B-ARR: two-component response regulator ARR2-like; A-ARR: two-component response regulator ARR17-like; DID1: gibberellin receptor GID1; DELLA: DELLA protein RGL2-like; TF: transcription factor PIF4; BAK1: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1-like; BKI1: systemin receptor SR160; BSK: serine/threonine-protein kinase; BZR1/2: BES1/BZR1 homolog protein 2-like; CYCD3: cyclin D3; JAR1: jasmonic acid-amino synthetase; JAZ: jasmonate ZIM domain-containing protein; NPR1: regulatory protein NPR1; TGA: transcription factor TGA.

Figure 10

The KEGG enrichment analyses of DMAs. (a) Up-regulated DAMs; (b) down-regulated DAMs.