Integrated phenotypic, metabolic, and proteomic profiling to elucidate productivity and quality of C. Arabica cultivars from Cerrado Mineiro

Abstract

Brazil is the world's largest exporter of arabica coffee, with the State of Minas Gerais accounting for more than half of the national production. Within the state, the Cerrado Mineiro region is renowned for specialty coffee production and was the first Brazilian region to receive a designation of origin. For this reason, periodic field evaluations are essential to assess the performance of Coffea arabica L. cultivars that exhibit resilience and maintain consistent cup quality standards. In this study, leaf samples from five C. arabica cultivars were collected from two experimental sites within the Cerrado Mineiro region. These cultivars were selected based on their productivity, cup quality, and resistance to coffee leaf rust and nematodes. The material underwent comprehensive analysis, including anatomical analysis, specific leaf area, leaf water potential, and spectral indices determination and quantification of starch and total proteins. In addition, untargeted metabolomic, proteomic, and enzymatic activity analyses (particularly invertases) were performed. Climate data, soil characteristics, altitude, water regime, and agronomic traits of the cultivars (cup quality and mean productivity) were also retrieved. To analyze this complex dataset, a combination of statistical methods was applied, including univariate analyses and machine learning algorithms, to extract meaningful insights into the field performance of the cultivars. The analyzed cultivars showed higher metabolome and proteome profile variation than in leaf anatomy. Despite similar climatic conditions at the experimental sites, environmental variables and the leaf water status at the sampling time had more influence on plant metabolism. Metabolomic and proteomic analyses revealed stress- related metabolic pathways, particularly in the Catiguá MG2 and Paraíso 2 cultivars. Notably, Paraíso 2 demonstrated higher agronomic stability, maintaining high productivity and cup quality in both environments. This research enhances the understanding of coffee cultivar acclimation in field conditions, guiding management and breeding strategies to improve productivity, beverage quality, and resilience to future climate challenges.