Wild Coffea spp.: Comparative Transcriptome Analysis, Metabolic Diversification, and Perspectives in Genetic Resource Exploration

• Grant number: 24/23401-5
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: June 01, 2025
• End date: March 31, 2029
• Field of knowledge: Agronomical Sciences - Agronomy
• Principal Investigator: Douglas Silva Domingues
• Grantee: Joana Nascimento Oliveira Zeist
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated research grant: 23/03353-3 - Bridging gaps between biological resources in Coffea genus and future crop improvement facing global changes: BRIDGES-COFFEA, AP.R

Abstract

Climate change and the growing demand for coffees with differentiated sensory profiles highlight the importance of exploring the genetic diversity of wild Coffea species to support breeding strategies. This study aims to develop high-resolution transcriptomes for Coffea stenophylla, C. liberica, and C. salvatrix, with the goal of identifying differentially expressed genes and characterizing biosynthetic pathways related to economically and sensorially relevant compounds, such as caffeine, diterpenes, lipids, and sugars. Leaf and fruit samples at different phenological stages will be processed for RNA analysis using large-scale sequencing technologies, employing both short-read and long-read platforms. Gene expression data will be analyzed to identify regulatory patterns and metabolic pathways associated with the bioactive compounds of interest, with the most relevant genes validated through RT-qPCR. In parallel, metabolites of interest will be quantified, and a correlation analysis between transcripts and metabolites will be performed.The expected outcomes include the assembly of high-quality transcriptomes and the functional annotation of genes involved in key metabolic pathways, contributing to the molecular understanding of metabolic and sensory adaptations in these species. This study will provide a foundation for the sustainable utilization of the Coffea genus's biodiversity, enhancing scientific knowledge of wild species and their applications in the development of innovative breeding strategies. Additionally, it will strengthen Brazil's leadership in coffee research and innovation within the coffee production chain.