Transcriptome sequence and physiological analysis revealed the roles of carotenoids and photosynthesis under low temperature combined with low-light stress on pepper (Capsicum annuum L.)

Low temperature combined with low light (LL) is an adverse factor seriously affecting pepper productivity and quality. However, little is known about the molecular mechanisms related to LL stress responses. Therefore, transcriptome and physiological changes in Hangjiao No. 2 (H2) and Xiangtela No. 2 (X2) pepper were studied under normal conditions and LL. We found 8,392 and 8,028 differentially expressed genes in H2 and X2, respectively, significantly associated with photosynthesis, photosynthesis antenna proteins, and carotenoids, were enriched in 27 and 40 gene ontology terms in H2 and X2, respectively, and 14 and 16 Kyoto Encyclopedia of Gene and Genomes pathways. The accuracy and reliability of the RNA-Seq results were confirmed by qRT-PCR. Furthermore, carotenoid-related genes ZDS, CA1, CA2, NCED, LOC107840293, and LOC107850059 functioned in response to LL. Additionally, LL significantly decreased photosynthesis capacity, photosynthetic pigment contents, as well as maximum quantum efficiency, and changed carotenoid-related compounds, revealing photosynthesis and carotenoids were involved in LL stress response. Our findings provide insight into LL stress-induced transcriptional expression patterns.