Putative Transcription Factor Genes Associated with Regulation of Carotenoid Biosynthesis in Chili Pepper Fruits Revealed by RNA-Seq Coexpression Analysis
10 de octubre de 2022
Les invitamos a leer el artículo: "Putative Transcription Factor Genes Associated with Regulation of Carotenoid Biosynthesis in Chili Pepper Fruits Revealed by RNA-Seq Coexpression Analysis" en el que colaboró el Dr. Octavio Martínez de la Vega, Investigador de la UGA-Langebio junto con por el Dr. Neftalí Ochoa Alejo, Investigador de Cinvestav Irapuato.
Autores: Maria Guadalupe Villa-Rivera1, Octavio Martínez2 and Neftalí Ochoa-Alejo1.
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36824, Mexico
- Unidad de Genómica Avanzada, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36824, Mexico
Felicitamos al estudiantado y profesorado que contribuyeron en esta investigación por su arduo trabajo.
Abstract: During the ripening process, the pericarp of chili pepper (Capsicum spp.) fruits accumulates large amounts of carotenoids. Although the carotenoid biosynthesis pathway in the Capsicum genus has been widely studied from different perspectives, the transcriptional regulation of genes encoding carotenoid biosynthetic enzymes has not been elucidated in this fruit. We analyzed RNA-Seq transcriptomic data from the fruits of 12 accessions of Capsicum annuum during the growth, development, and ripening processes using the R package named Salsa. We performed coexpression analyses between the standardized expression of genes encoding carotenoid biosynthetic enzymes (target genes (TGs)) and the genes of all expressed transcription factors (TFs). Additionally, we analyzed the promoter region of each biosynthetic gene to identify putative binding sequences for each selected TF candidate. We selected 83 TFs as putative regulators of the carotenogenic structural genes. From them, putative binding sites in the promoters of the carotenoid-biosynthesis-related structural genes were found for only 54 TFs. These results could guide the search for transcription factors involved in the regulation of the carotenogenic pathway in chili pepper fruits and might facilitate the collection of corresponding experimental evidence to corroborate their participation in the regulation of this biosynthetic pathway in Capsicum spp.
Keywords: chili pepper; carotenoids; transcriptional regulation; RNA-Seq; transcription factors.