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Transcriptome Analysis Reveals Candidate Genes Involved in Low Temperature Stress in Bell Pepper

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Abstract

Despite cold stress is a critical environmental condition that influences the growth and development of bell pepper (Capsicum annuum L.), the underlying molecular mechanism remains unclear. This study aimed to explore the genes associated with the low temperature stress response in bell pepper. Bell pepper ‘Zhongjiao NO.4’ (CRC, cold resistance cultivar) and ‘Zhong 30’ (WT, cold sensitive variety) was used in this study. CRC was grown under 4°C for 0 h (Low), 8 h (Low 8), 16 h (Low 16), and 24 h (Low 24), as well as WT was also grown under 4°C. The transcriptome profile of bell pepper was obtained through Illumina RNA-sequencing. The differentially expressed genes (DEGs) between Low and WT groups were explored, and DEGs between every two groups of Low, Low8, Low16, and Low24 were also screened. Time series clustering analysis of DEGs among Low groups was performed. Functional enrichment analysis of DEGs was conducted by using cluster Profiler package, followed by protein-protein interaction (PPI) analysis. The results showed that DEGs in CRC were involved in flavonoid biosynthesis and phenylalanine metabolism. Functional enrichment analysis of time-course related DEGs indicated that genes were mainly associated with metabolic process, photosynthesis, and lipid metabolic process. LOC107864131, LOC107857080, and LOC107855212 were considered as hub genes, and played vital role in cold stress in bell pepper. Meanwhile, the expression level of ribosomal proteins-related genes was significantly down-regulated during cold treatment. The dynamic expression changes revealed the regulatory role of genes in cold stress response of bell pepper. Our findings might shed light on the molecular mechanisms related to cold tolerance in bell pepper and provide useful candidate genes for genetic improvement.

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Funding

This work was supported by the National Natural Science Foundation of China (project no. 30671242) and the Natural Science Foundation of Shandong Province Mayor (project no. ZR2017CM009).

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    Authors and Affiliations

    1. College of Pharmacy, Liaocheng University, Liaocheng City, Shandong Province, China

      L. Ji & P. Li

    2. College of Life Science, Liaocheng University, Liaocheng City, Shandong Province, China

      Zh. Su & M. Li

    3. College of Horticulture, Zhejiang A&F University, Hangzhou City, Zhejiang Province, China

      H. Wang

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    L. Ji and P. Li are co-first authors.

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    Correspondence to H. Wang.

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    Abbreviations: ACT1—Actin gene 1; BH—Benjamini and Hochberg; BP—biological process; CBF1—C-repeat binding factor 1; CRC—cold resistance cultivar; DEGs—differentially expressed genes; FPKM—Fragments Per Kilobase Million; GO—Gene ontology; Hsp70s—heat shock proteins 70; KEGG—Kyoto Encyclopedia of Genes and Genomes; PCA—principal component analysis; PPI—protein-protein interaction.

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    Ji, L., Li, P., Su, Z. et al. Transcriptome Analysis Reveals Candidate Genes Involved in Low Temperature Stress in Bell Pepper. Russ J Plant Physiol 67, 1116–1125 (2020). https://doi.org/10.1134/S1021443720060084

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