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. 2024 May 30;25(11):5994.
doi: 10.3390/ijms25115994.

Transcriptome Analysis of Potato Leaves under Oxidative Stress

Juping Liu  1   2 , Xun Tang  1   2 , Huanhuan Zhang  1   3 , Meng Wei  2 , Ning Zhang  1   2 , Huaijun Si  1   2
Affiliations

Transcriptome Analysis of Potato Leaves under Oxidative Stress

Juping Liu et al. Int J Mol Sci. .

Abstract

Potato (Solanum tuberosum L.) is a major global food crop, and oxidative stress can significantly impact its growth. Previous studies have shown that its resistance to oxidative stress is mainly related to transcription factors, post-translational modifications, and antioxidant enzymes in vivo, but the specific molecular mechanisms remain unclear. In this study, we analyzed the transcriptome data from potato leaves treated with H2O2 and Methyl viologen (MV), and a control group, for 12 h. We enriched 8334 (CK vs. H2O2) and 4445 (CK vs. MV) differentially expressed genes (DEGs), respectively, and randomly selected 15 DEGs to verify the sequencing data by qRT-PCR. Gene ontology (GO) enrichment analysis showed that the DEGs were mainly concentrated in cellular components and related to molecular function, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that most of the DEGs were related to metabolic pathways, plant hormone signal transduction, MAPK-signaling pathway, and plant-pathogen interactions. In addition, several candidate transcription factors, mainly including MYB, WRKY, and genes associated with Ca2+-mediated signal transduction, were also found to be differentially expressed. Among them, the plant hormone genes Soltu.DM.03G022780 and Soltu.DM.06G019360, the CNGC gene Soltu.DM.06G006320, the MYB transcription factors Soltu.DM.06G004450 and Soltu.DM.09G002130, and the WRKY transcription factor Soltu.DM.06G020440 were noticeably highly expressed, which indicates that these are likely to be the key genes in the regulation of oxidative stress tolerance. Overall, these findings lay the foundation for further studies on the molecular mechanisms of potato leaves in response to oxidative stress.

Keywords: Solanum tuberosum L.; differentially expressed genes; oxidative stress; reactive oxygen species; transcriptome.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Physiological indexes of potato leaves’ SOD, CAT, and POD activities were determined under oxidative stress. The values are means ± SD of three replicates (p < 0.05). The a, b, and c represent significant differences.
Figure 2
Figure 2
Differentially expressed genes (DEGs) analysis. (A) The number of up- and down-regulated DEGs among T1 vs. T2, T1 vs. T3, and T2 vs. T3 comparisons. (B) Venn diagram comparison of the number of DEGs.
Figure 3
Figure 3
GO classification analysis of DEGs in (A) T1 vs. T2 and (B) T1 vs. T3.
Figure 4
Figure 4
KEGG enrichment analysis of DEGs in (A) T1 vs. T2 and (B) T1 vs. T3.
Figure 5
Figure 5
Heatmaps of EDGs encoding genes about SOD, POD, CAT, GPX, APX, and GST. Each column represents the mean expression value (log2 FPKM, T2 sample is divided by T1 and T3 sample is divided by T1 and T2, respectively) of three biological replicates obtained from RNA-Seq data.
Figure 6
Figure 6
Heatmaps of EDGs involved in plant hormone signaling, including IAA, ethelene, and ABA. Each column represents the mean expression value (log2 FPKM, T2 sample is divided by T1, T3 sample is divided by T1 and T2, respectively) of three biological replicates obtained from RNA-Seq data.
Figure 7
Figure 7
Heatmaps of DEGs encoding genes related to Ca2+ signal transduction during oxidative stress of potato plants. Each column represents the mean expression value (log2 FPKM, T2 sample is divided by T1, T3 sample is divided by T1 and T2, respectively) of three biological replicates obtained from RNA-Seq data.
Figure 8
Figure 8
Heatmaps of DEGs encoding transcription factors. (A) The transcription factor of MYB. (B) The transcription factor of WRKY. Each column represents the mean expression value (log2 FPKM, T2 sample is divided by T1, T3 sample is divided by T1 and T2, respectively) of three biological replicates obtained from RNA-Seq data.
Figure 9
Figure 9
Verification of RNA-Seq results with qRT-qPCR in (A) T1 vs. T2 and (B) T1 vs. T3.
Figure 10
Figure 10
The model of pathways in response to oxidative stress (↑ representative up regulation; ↓ representative down regulation).
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