Genome-wide association analysis of traits related to development, abiotic and biotic stress resistance in Coffea canephora

• One hundred fifteen SNPs with significant associations were identified within or near genes related to early development and resistance to pests and diseases. • A population derived from genetic resources introduced in Espírito Santo, Brazil, plays a significant role in the improvement of Coffea canephora . • Four SNPs associated with more than one trait were identified. • The chromosomal regions that were detected could be used for selection assisted by molecular markers to help and accelerate the coffee improvement process. Genome-wide association studies (GWAS) investigate the relationship between genomic variants and traits of interest. The objective of this study was to identify genomic regions with significant associations between SNP (Single Nucleotide Polymorphism) markers and agronomic traits in Coffea canephora . A total of 251 Conilon plants, derived from seeds of old seminal crops in the southern region of Espírito Santo, Brazil, were evaluated. The plants were phenotyped for traits related to early development, biotic and abiotic stresses and genotyped using DArTseqTM methodology. After filtering, 2,542 SNPs were used in the GWAS analysis, which identified 115 SNPs with significant associations ( p < 0.05) for the traits: plant height, mean height growth rate, stem diameter, mean diameter growth rate, incidence of mealybug, rust and leaf miner. Additionally, a genomic search was conducted to identify SNPs located within or near candidate genes, as well as their putative functions related to the studied traits. Studies applying the GWAS methodology to C. canephora are rare. Therefore, these findings provide preliminary insights into associated SNPs, which can be validated for use in future research. This approach enables the identification of potential candidate genes and supports marker-assisted selection in coffee breeding programs.