Lipid metabolism and actin Cytoskeleton regulation underlie yield and disease resistance in two coffea canephora breeding populations

Authors: Ahn, Ezekiel; Park, Sunchung; BHATT, JISHNU - Orise Fellow; LIM, SEUNGHYUN - Orise Fellow; Meinhardt, Lyndel

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/1/2025
Publication Date: 12/3/2025
Citation: Ahn, E.J., Park, S., Bhatt, J., Lim, S., Meinhardt, L.W. 2025. Lipid metabolism and actin Cytoskeleton regulation underlie yield and disease resistance in two coffea canephora breeding populations. Plants. https://doi.org/10.3390/plants14233675.
DOI: https://doi.org/10.3390/plants14233675

Interpretive Summary: Robusta coffee is a globally important crop, valued for its high yield and disease resistance. However, improving robusta through traditional breeding is a slow process. This study used genomic tools to accelerate breeding by investigating the genetic differences between two distinct robusta populations, "Premature" and "Intermediate," focusing on three key traits: coffee bean production, resistance to the devastating coffee leaf rust disease, and the yield of usable green coffee beans. We analyzed existing genetic and trait data, applying statistical and machine learning methods to identify links between specific genetic markers and variations in these traits. A major finding was the striking difference in the genetic control of these traits between the two populations. The Premature population showed numerous genetic associations with all three traits, whereas the Intermediate population showed far fewer, primarily for leaf rust resistance. For leaf rust resistance, we identified genes known to play roles in plant defense, including those involved in recognizing fungal pathogens and triggering immune responses. For green bean yield in the Premature population, we discovered a novel association with a gene potentially involved in caffeine synthesis, suggesting a link between caffeine metabolism and the quantity of usable beans. We also identified the genes with roles in cell wall formation, and intracellular signaling. The identified candidate genes provide valuable targets for future research to confirm their functions and develop tools for marker-assisted selection, ultimately contributing to more efficient and targeted coffee breeding programs.

Technical Abstract: This study investigated the genetic architecture of coffee bean production, leaf rust incidence, and green bean yield in two Coffea canephora populations (Premature and Intermediate) using single-SNP association analysis and machine learning. We re-analyzed a publicly available dataset comprising phenotypic data from multiple years and locations, and Genotyping-by-Sequencing (GBS) derived SNP data. Single-SNP association analysis with a False Discovery Rate (FDR)-adjusted p-value threshold of 0.01, revealed substantial population-specific differences. The Premature population exhibited numerous significant SNP associations for all three traits, while the Intermediate population showed significantly fewer associations, primarily for leaf rust incidence. Candidate genes were identified near significant SNPs from the single-SNP analysis and the top five most important SNPs from the Bootstrap Forest models. For leaf rust incidence in the Premature population, candidate genes included RPP13-like, NB-ARC, and CERK1, consistent with known plant defense mechanisms. In contrast, the Intermediate population implicated a TPR_REGION-containing protein and a nitrate regulatory gene2 protein. For coffee bean production, a prominent region on chromosome 6 was identified in the Premature population, including an alpha/beta-hydrolase superfamily protein and an IPPc domain-containing protein. For green bean yield in the Premature population, a putative caffeine synthase 3 gene (Cc09t06990.1). Overlapping genes between the single-SNP and Bootstrap Forest analyses included Cc06t03050.1 (IPPc domain-containing protein), Cc05t02930.1 (TAF domain-containing protein), Cc11t13960.1 (TORTIFOLIA1-like protein 4), Cc02t25100.1 (Nitrate regulatory gene2 protein), and Cc05t15840.1 (TPR_REGION domain-containing protein).