Identification of Key Genes Associated with Lycopene Accumulation in Red Carrot Taproots Based on WGCNA

Lycopene (carotenoid) is a natural pigment with strong antioxidant properties. The taproots of red carrots (Daucus carota L.) exhibit red coloration due to the presence of high levels of lycopene. However, the candidate genes responsible for regulating lycopene accumulation in red carrots have yet to be identified. In this study, the variations in carotenoid content were assessed at five different stages of taproot development. The results showed a rapid accumulation of lycopene in the taproots between 45 and 60 days after sowing, peaking at its highest level by 75 days. Weighted Gene Co-expression Network Analysis (WGCNA) was used to construct co-expression modules associated with lycopene accumulation. Notably, two of the identified modules (red and mediumpurple3) exhibited significant correlations with lycopene content. A total of 24 differentially expressed genes (DEGs) were enriched by both Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and one carotenoid pathway gene was only enriched by KEGG analysis. Among these genes, five genes associated with photosynthesis (DCAR_016944 [DcCHL27], DCAR_021505 [DcFNR2], DCAR_000568 [DcPSB28], DCAR_030558 [DcBPG1], and DCAR_030562 [DcBPG1]) and one carotenoid pathway gene (DCAR_013459 [DcCRTISO-1]) were highly connected hub genes. These six genes were significantly up-regulated at 60 and 75 days after sowing, when the taproots accumulated high lycopene content, and were identified as candidate genes. These findings contribute valuable insights into the molecular mechanisms underlying the modulation of lycopene.