Comparative Transcriptome Analysis Identified Genes Associated with Fruit Size in Pepper (Capsicum annuum L.)

Abstract

Pepper (Capsicum annuum L.) is one of the most widely grown vegetable crops in China, with widespread cultivation worldwide. Fruit weight (size) is a complex trait controlled by multiple factors and is an essential determinant of pepper yield. In this study, we analyzed the transcriptome of two pepper recombinant lines with different fruit weights, ‘B302’ and ‘B400’, at five developmental stages to reveal some of the differentially expressed genes and mechanisms controlling fruit weight. The results showed that 21,878 differential genes were identified between the two specimens. Further analysis of the differentially expressed genes revealed that Boron transporter 4 was significantly highly expressed in the large-fruited pepper and almost not expressed at all in the small-fruited pepper. CaAUX1, CaAUX/IAA, CaGH3, CaSAUR, and other related genes in the Auxin signal transduction pathway were highly expressed in the large-fruited pepper but significantly reduced in the small-fruited pepper. In addition, a comparison of differentially expressed transcription factors at different times revealed that transcription factors such as CaMADS3, CaAGL8, CaATHB13, and CaATHB-40 were highly differentially expressed in the large-fruited pepper, and these transcription factors may be related to pepper fruit expansion. Through weighted gene co-expression network analysis (WGCNA), the MEorangered4 module was shown to have a highly significant correlation with fruit weight, and the key modules were analyzed by constructing the hub core gene network interactions map and core genes regulating fruit weight such as APETALA 2 were found. In conclusion, we find that the expression of relevant genes at different developmental stages was different in ‘B302’ and ‘B400’, and it was hypothesized that these genes play essential roles in the development of fruit size and that the interactions occurring between transcription factors and phytohormones may regulate the development of fruit size.

Estimating Transcriptome Diversity and Specialization in Capsicum annuum L.

“…The two TFs exclusively found in W accessions and shown in Table 1, "B3 domaincontaining transcription factor ABI3" (XP_016577487.1) and "Zinc finger BED domaincontaining protein RICESLEEPER" (XP_016582130.1), have been associated with molecular mechanisms for tolerance to abiotic and biotic stresses [41] and fruit size [42], respectively. However, genes for TF exclusively expressed in D or W accessions in Table 1 do not present a fully coherent expression pattern in all D or W accessions, which suggests that variations in genotypes are very important in the expression pattern of these genes, and the only common denominator found among them is their role in tolerance to various forms of stress.…”