Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening

Abstract

Chili pepper (Capsicum annuum) is one of the most important crops worldwide. Its fruits contain metabolites produced over the maturation process like capsaicinoids and carotenoids. This metabolic process produces internal changes in flavor, color, texture, and aroma in fruits to make them more attractive for seed dispersal organisms. The chiltepin (C. annuum L. var. glabriusculum) is a wild variety of the C. annuum L. species that is considered a source of genetic resources that could be used to improve the current chili crops. In this study, we performed a transcriptomic analysis on two fruit maturation stages: immature stage (green fruit) and mature stage (red fruit) of a wild and a cultivated pepper variety. We found 19,811 genes expressed, and 1,008 genes differentially expressed (DEGs) in at least one of the five contrast used; 730 DEGs were found only in one contrast, and most DEGs in all contrasts were downregulated. GO enrichment analysis showed that the majority of DEGs are related to stress responses. KEGG enrichment analysis detected differences in expression patterns in metabolic pathways related to phenylpropanoid biosynthesis, secondary metabolites, plant hormone signal transduction, carotenoid biosynthesis and sesquiterpenoid and triterpenoid biosynthesis. We selected 105 tomato fruit ripening-related genes, and found 53 pepper homologs differentially expressed related to shape, size, and secondary metabolite biosynthesis. According to the transcriptome analysis, the two peppers showed very similar gene expression patterns; differences in expression patterns of genes related to shape, size, ethylene and secondary metabolites biosynthesis suggest that changes produced by domestication of chilli pepper could be very specific to the expression of genes related to traits desired in commercial fruits.

Transcriptional Regulation of Ripening in Chili Pepper Fruits (Capsicum spp.)

“…These results might suggest that activation of ethylene signaling and the subsequent alteration of ethylene sensitivity could be conserved in non-climacteric fruits [18,19]. In contrast, upregulation of ethylene receptor-like protein (ETR), a key regulator of the ethylene transcription pathway, was detected in a transcriptomic analysis of C. frutescens and C. annuum performed at different stages of ripening, suggesting that at least some species of chili pepper exhibit climacteric behavior [20,25].…”

“…Metabolic changes that occur during the ripening process of chili p transformations in flavor, color, texture and aroma. Accordingly, different profiles of genes that encode key enzymes of metabolite biosynthetic pathw tinct antioxidant activity patterns during chili pepper ripening have been de early (16)(17)(18)(19)(20)(21)(22)(23)(24)(25), breaker (36-28 DPA) and later stages (43)(44)(45)(46)(47)(48). For production of glycosides (quercetin, luteolin and apigenin) characterized th while the production of other metabolites, such as shikimic acid, putrescin butyric acid (GABA), which were highly accumulated, gradually decreased stage.…”

“…Additionally, a comparison between the transcription patterns of C. annuum L. ('Tampiqueño 74', a domesticated variety) and C. annuum L. var. glabriusculum (chiltepin wild variety) resulted in 53 differentially expressed genes associated with size, shape and secondary metabolite biosynthesis, suggesting that these differences could be related to the domestication process [20].…”

“…The gene expression profile and yeast twohybrid assays suggested that the interaction of two transcription factors (CaMADS, subfamily Some transcription factors have been identified and proposed as regulators of the transcription of structural genes that encode proteins involved in the ripening process of chili pepper fruits. Among the differentially expressed genes (DEGs) identified in the transcriptomic analysis conducted in immature and mature chili pepper fruits, only four genes encoding TFs were upregulated (FUL2, two bZIPs and one homeobox TF), while 25 TF genes were downregulated [20].…”

Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid

“…Several studies reported the presence of intra and interspecific diversity of fruit traits, metabolites content, and other agronomic traits in Capsicum species ( Ahmad et al., 2021a , 2021b ; Araceli et al., 2009 ; Chhapekar et al., 2020 ; Liu et al., 2020 ; Sarpras et al, 2016 ; Sarpras et al., 2019 ). Furthermore, many studies on marker development, QTL/gene(s) mapping of economically important traits, whole transcriptome, and genome sequencing have been reported on Capsicum species ( Ahn et al., 2014 ; Chhapekar et al., 2021 ; Dubey et al., 2019 ; Jaiswal et al., 2020 ; Kim et al., 2020 ; Liu et al., 2019 ; Martínez et al., 2021 ; Razo-Mendivil et al., 2021 ). Few studies reported that inter- and intraspecific hybrids of cultivated Capsicum species i.e.…”