Peer-review publications

Abstract

Coffee is one of the most consumed beverages in the world. It is also one of the most globally traded commodities. Coffee leaf rust (CLR), caused by the biotrophic fungus Hemileia vastatrix, is the most important disease affecting Arabica coffee growing worldwide, leading to significant yield losses if no control measures are applied. A deep understanding of the complex mechanisms involved in coffee-H. vastatrix interactions, such as the pathogen variability and the mechanisms governing plant resistance and susceptibility, is required to breed efficiently for durable resistance and design new approaches for crop protection. Here we summarize our current understanding across multiple areas related to pathogen infection, variability and candidate effectors, breeding for disease resistance, and the various components of the coffee immune system, by reviewing a comprehensive body of research on CLR and the advances recently made. We also update information about the defense responses activated by the application of plant resistance inducers, a promising alternative to fungicides in the control of CLR. Moreover, we identify and discuss future directions for further research

Agronomy 2022, 12(2), 326; https://doi.org/10.3390/agronomy12020326

Abstract

The devastating disease Coffee Leaf Rust, caused by Hemileia vastatrix (Hv), has been the major constraint to worldwide coffee production. Recently, Hv populations were shown to be structured into three divergent genetic lineages with marked host specialization (C1, C2 and C3). However, there is yet no overall understanding on the population dynamics and adaptation of the most widespread and epidemiological relevant Hv group (C3). We used RAD sequencing to generate 13,804 SNPs across a worldwide collection of 99 Hv isolates. Phylogenetic analyses uncovered a well-supported structuring within C3, with three main subgroups (SGI, SGII and SGIII), which seem to reflect the historical distribution, breeding and exchange of coffee cultivars. SGI shows a ladder-like diversification pattern and occurs across all 4 continents sampled, SGII is mainly restricted to Africa and SGIII is only observed in Timor, revealing a higher genetic differentiation. Outlier and association tests globally identified 112 SNPs under putative positive selection which impacted population structure. In particular, 29 overlapping SNPs per se seemed to have an extremely strong effect on Hv population divergence. We also found exclusive and fixed alleles associated to the SGs supporting local adaptation. Functional annotation revealed that transposable elements may play a role in host adaptation. Our study provides a higher-resolution perspective on the evolutionary history of Hv on cultivated coffee, showing its strong ability to adapt and the strength of the selective force imposed by coffee hosts, which should be taken into account when designing strategies for both pathogen dissemination control and selective breeding.

Phytopatology 2022; https://doi.org/10.1094/PHYTO-09-21-0376-R