Transcriptome Analysis Reveals Candidate Genes Involved in Low Temperature Stress in Bell Pepper
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Transcriptome Analysis Reveals Candidate Genes Involved in Low Temperature Stress in Bell Pepper L. Jia, P. Lia, Zh. Sub, M. Lib, and H. Wangc,* aCollege
of Pharmacy, Liaocheng University, Liaocheng City, Shandong Province, China of Life Science, Liaocheng University, Liaocheng City, Shandong Province, China c College of Horticulture, Zhejiang A&F University, Hangzhou City, Zhejiang Province, China *e-mail: [email protected] bCollege
Received December 12, 2019; revised March 25, 2020; accepted May 12, 2020
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. Keywords: Capsicum annuum, bell pepper, low temperature stress response, transcriptome, differentially expressed genes, time series clustering analysis, functional enrichment analysis DOI: 10.1134/S1021443720060084
INTRODUCTION Bell pepper (also known as sweet pepper) is a cultivar group of the Capsicum annuum species, which is valued for their plentiful vitamin C and nutritional content. The estimated value of cash receipts for bell peppers in a year is $247.5 million [1]. The sweet pepper is native to North and South American and is adapted to warm and dry climates, thus the optimum temperature for growth of bell peppers ranges from 21 to 29°C [2]. In addition, bell peppers are sensitive to low temp
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