Keywords

1 Introduction

Coffee is one of the most widely consumed beverages in the world and one of the most traded commodities globally. The main coffee-producing countries are Brazil, Vietnam, and Colombia, while the European Union and the United States of America are the largest consuming and importing markets globally (FAO 2022).

The two cultivated species, Coffea arabica L. (Arabica) and Coffea canephora Pierre ex A. Froehner (Robusta) accounted in 2020, on average, for about 60% and 40% of the world’s coffee production, respectively (ICO 2020). C. arabica is predominantly cultivated in the highlands and preferred by consumers due to its low bitterness, its aromatic characteristics, and its low caffeine content. C. canephora is more suitable for intertropical lowlands and characterized by a stronger bitterness and higher caffeine content (Lécolier et al. 2009).

Coffee, like other crops, is affected by several factors, including diseases, which may cause considerable yield losses. Moreover, there is clear evidence that the geographical distribution of several pathogens is expanding due to climate change and increasing global trade (Nnadi and Carter 2021). There are several ways to control diseases, ranging from chemical and biological control to good cropping practices. However, breeding for disease resistance is considered the most efficient and sustainable disease control strategy (Silva et al. 2022 and references therein).

Following a brief description of the most common coffee diseases, this review focuses on the advances in coffee leaf rust (CLR) research, mainly regarding pathogen infection, pathogen genetic diversity and population dynamics, and plant defense mechanisms. This knowledge is of utmost importance as an informed base to breed efficiently for durable resistance and devise innovative crop protection approaches.

2 Coffee’s Main Diseases

A plant disease results from the interaction between a susceptible host plant, a virulent pathogen, and favorable environmental conditions (Agrios 2005). Diseases caused by fungi, bacteria, and viruses (Table 1) are the major limiting factors in coffee production. According to Maghuly et al. (2020), approximately 26% of the global annual coffee production is lost due to diseases, threatening the income of nearly 125 million people worldwide.

Table 1 List of the main diseases of Coffea spp.
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Coffee leaf rust (CLR), caused by the biotrophic fungus Hemileia vastatrix Berkeley & Br. (phylum Basidiomycota, class Pucciniomycetes, order Pucciniales), is the major disease affecting Arabica coffee (Talhinhas et al. 2017; Silva et al. 2022 and references therein) inducing losses of over $1 billion annually (Kahn 2019). CLR was first recorded in 1861 near Lake Victoria (East Africa), but its first major outbreak was in 1869 in Ceylon (now Sri Lanka), leading to the eradication of coffee cultivation in this country, with devastating social and economic consequences. Nowadays, CLR is present in all the coffee-growing regions (Wellman 1952; Rodrigues Jr. et al. 1975; McCook and Peterson 2020; Keith et al. 2021). In the last decade, the epidemic resurgence of CLR, known as “the big rust”, had strong economic and social impacts on several countries across Latin America and the Caribbean (Baker 2014; Avelino et al. 2015). Moreover, CLR has been reported to have expanded its area of distribution to regions of higher altitude where previously it was not detected, namely above 1000–1100 m in Central America and above 1600 m in Colombia (Rozo et al. 2012; Avelino et al. 2015). It has led to food security issues as a result of the high dependence on coffee production by most coffee farmers and laborers (Avelino et al. 2015). There is little evidence that the big rust was caused by the evolution of new virulence in H. vastatrix. Rather, a combination of more conducive weather patterns, changing climatic conditions, and recurring economic shocks appear to be responsible (Rhiney et al. 2021 and references therein).

H. vastatrix infects the lower surface of the leaves, where it produces chlorotic spots preceding the differentiation of suprastomatal, bouquet-shaped, orange-coloured uredinia (Fig. 1a). Infected leaves fall off, leaving long expanses of twigs without any foliage (Fig. 1b). Another coffee rust [powdery rust (or grey rust) of coffee] is caused by the fungus Hemileia coffeicola Maublanc and Roger. Both H. vastatrix and H. coffeicola have C. arabica and other Coffea species as hosts, but H. coffeicola is only of local importance in some West African countries (Rodrigues Jr. 1990; Ritschel 2005). The symptoms of the disease are characterised by a dusty or powdery coating of yellow uredosori covering the underside of the coffee leaves (Rodrigues Jr. 1990).

Fig. 1
2 photos. A. It exhibits branched leaves with colored spots on the lower surface. B. A plant with minimal leaves. C. A cyclic diagram of the Hemileia infection with germinated urediniospores and appressorium present over the stomata penetrates the hyphae and forms the bouquet-shaped stomata.

Coffee leaf rust (CLR) symptoms and urediniospore infection. a Chlorotic spots and uredosporic sori on the lower leaves surface; b severe defoliation associated with CLR in one coffee plant contrasting with resistant ones in the background; c Hemileia vastatrix infection process. Photos taken by the authors. Created with Biorender.com

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Coffee berry disease (CBD) caused by the hemibiotrophic fungus Colletotrichum kahawae J.M. Waller & P.D. Bridge (phylum Ascomycota, class Sordariomycetes, order Glomerellales) is the most devastating disease affecting Arabica coffee production in Africa at high altitudes (Silva et al. 2006; van der Vossen and Walyaro 2009; Loureiro et al. 2012; Maghuly et al. 2020). It was first reported in 1922 in Kenya (McDonald 1926) and is still restricted to Africa, but represents a threat to high-altitude coffee areas of Latin America and Asia (Silva et al. 2006 and references therein; van der Vossen and Walyaro 2009). C. kahawae infects all stages of the crop, but maximum crop losses occur following infection of green berries with the formation of dark sunken lesions with sporulation causing their mummification and premature dropping. Under adequate climatic conditions and if no control measures are applied, this disease can destroy 50–80% of the developing green berries (Firman and Waller 1977; Silva et al. 2006; Hindorf and Omondi 2011).

Cercosporiosis, or brown eye spot (BES), is currently one of the main diseases of coffee in Brazil. It is caused by Cercospora coffeicola Berk. and Cooke (phylum Ascomycota, class Dothideomycetes, order Mycosphaerellales). The pathogen causes lesions on leaves and fruits, resulting in defoliation, decreased productivity, diminished coffee quality, and yield loss. In the nursery, this defoliation reduces the seedling’s growth rate, which becomes inappropriate for planting and marketing. Also, in field conditions, the disease could be harmful to young trees (Botelho et al. 2017 and references therein). BES can appear as two distinct symptoms on leaves and in field conditions, the ‘brown eye spot’ and the ‘black spot’ (Andrade et al. 2021). The first one is the typical symptom caused by C. coffeicola on coffee leaves, which can be described as small necrotic spots consisting of a light-colored center and sometimes surrounded by a purple, brown ring with yellow edges, giving rise to the name brown eye spot. The atypical symptom is characterized by a black spot with the lesions being black, without the yellow halo.

Coffee wilt disease (CWD), or tracheomycosis, is caused by the vascular wilt pathogen Fusarium xylarioides Steyaert (teleomorph = Gibberella xylarioides R. Heim & Saccas) (phylum Ascomycota, class Sordariomycetes, order Hypocreales). CWD spreads across Africa, destroying coffee trees, reducing yields, and significantly impacting producer livelihoods. (Pinard et al. 2016; Maghuly et al. 2020; Flood 2021). It is frequently found in older and densely planted coffee trees (Assefaa et al. 2022). Through systematic sanitation and the establishment of breeding programs in affected countries, CWD appeared to have declined. However, in the 1990s, the disease re-emerged and increased to epidemic proportions affecting Robusta coffee in the Democratic Republic of the Congo, Uganda, and Tanzania and Arabica coffee in Ethiopia (Flood 2021). The first symptoms of CWD are yellowing of the leaves, which then wilt and develop brown necrotic lesions. The leaves then curl, dry up and fall off. This process may start on one part of the tree but eventually spreads to the rest of the plant. Once a tree is infected, there is no remedy other than to uproot the tree and burn it in situ to reduce the chances of spreading the infection. No new trees should be planted in the same place for at least six months to prevent remnants of the root system in the soil, which retain viable spores of the disease, from reinfecting new plants (Phiri and Baker 2009).

American leaf spot disease, also known as “Ojo de Gallo” is caused by the fungus Mycena citricolor (Berk. & M.A. Curtis) Sacc. (Phylum Basidiomycota, class Agaricomycetes, order Agaricales) and has been reported in Latin America. This fungus can grow on all plant organs, including leaves, stems, and fruits. Subcircular spots, initially brown, becoming pale-brown to straw-colored, are produced mainly on leaves. The spots have a distinct margin and are 6–13 mm in diameter but with no halo. The centers of older leaf spots may disintegrate, giving a shot-hole appearance. The main effect of the disease is leaf fall, with a consequent reduction in the growth and yield of the coffee plants (Wang and Avelino 1999; Krishnan 2017).

The bacterial halo blight (BHB) of coffee caused by the Gram-negative bacterium Pseudomonas syringae pv. garcae (Psgc) Young, Dye & Wilkie of the family Pseudomonadaceae, was first described in 1955 by Amaral et al. (1956) in the municipality of Garça in the Brazilian state of São Paulo, and later in Paraná and Minas Gerais states (Badel and Zambolim 2019 and references therein). Bacterial halo blight has been reported in the African Continent, in Kenya, Ethiopia, and Uganda (Ramos and Shavdia 1976; Korobko and Wondinagegne 1997) and in China (Bai et al. 2013). It has been estimated that BHB can cause losses up to 70% in nurseries and in the field, predominantly in regions above 1000 m in the presence of severe wind (Zoccoli et al. 2011). Necrotic spots surrounded or not by chlorotic haloes in leaf borders are the most common symptoms of BHB disease. However, flowers, fruits, and branches can also be affected (Badel and Zambolim 2019). The bacterium survives mainly as an epiphyte associated with plant debris. It penetrates the host tissue through natural openings (stomata) or wounds and is disseminated by water and wind-driven aerosol particles (Zoccoli et al. 2011). A recent study suggests that seeds may also be a source of inoculum (Belan et al. 2016).

Coffee leaf scorch (CLS), also referred to as atrophy of branches, is caused by Xylella fastidiosa subsp. pauca (Xfp), a Gram-negative bacterium belonging to the family Xanthmonadaceae. CLS has been reported in Brazil, Costa Rica, and Porto Rico (Beretta et al. 1996; Rodriguez et al. 2001; Bolaños et al. 2015). Strains of the bacterium isolated from coffee and citrus are closely related, and both share the sharpshooter insect of the Cicadellidae family as a dissemination vector. The bacterium colonizes the xylem vessels of host plants, as well as the foregut of its insect vectors (Badel and Zambolim 2019). CLS symptoms include apical and marginal leaf scorch, defoliation, reduction of the internode length, the leaf size, the plant height, fruit size and quantity, terminal clusters of small chlorotic and deformed leaves, lateral shoot dieback, and overall stunting (Li et al. 2001). CLS disease is widespread and often occurs if coffee is adjacent to citrus orchards affected by X. fastidiosa (citrus variegated chlorosis disease). Although there appears to be some degree of host specialization within the subspecies of X. fastidiosa, cross-infection has been reported in commercial grapevine cultivars and olive trees (Badel and Zambolim 2019).

Coffee ringspot virus (CoRSV), currently classified as Coffee ringspot dichorhavirus by the International Committee on Taxonomy of Viruses (ICTV), belong to the genus Dichorhavirus, of Rhabdoviridae family (Genus: Dichorhavirus, ICTV). CoRSV has been reported in the main coffee-growing states of Minas Gerais (Brazil) (Ramalho et al. 2014, 2016) and some regions of Costa Rica (Rodrigues et al. 2002). The virus is transmitted by Brevipalpus phoenicis (Geijskes) (Acari: Tenuipalpidae) and can infect coffee leaves and fruits. Symptoms on leaves are typical concentric chlorotic rings, sometimes forming bands on the veins. On coffee berries, CoRSV develops chlorotic or necrotic lesions that are frequently invaded by secondary fungal or bacterial opportunists. In severely affected trees, leaves fall and fruit drops, which can affect coffee production and quality (Ramalho et al. 2014). The severity of the disease has been attributed to ecological disturbances associated with expanding coffee areas and to chemical pest control favoring the vector.

3 CLR Causal Agent: Hemileia vastatrix

3.1 Life Cycle and Infection Process

Hemileia vastatrix is a hemicyclic fungus producing urediniospores, teliospores, and basidiospores. Urediniospores and teliospores are produced in the same sorus but at different times. Urediniospores are dikaryotic and represent the asexual cycle, reinfecting the leaves whenever environmental conditions are favorable. Teliospores rarely occur and germinate in situ, producing a promycelium from which four basidiospores are formed. Basidiospores cannot infect coffee, but no other host plant has been identified (Talhinhas et al. 2017 and references therein).

As an obligate biotroph, H. vastatrix can only feed, grow and reproduce on living coffee leaves by the differentiation of a specific hypha called haustorium. This organ forms after penetration of the wall of a live host cell, expanding on the inner side of the cell wall while invaginating the surrounding host plasma membrane (Garnica et al. 2014). In addition to their role in nutrient uptake, haustoria are actively involved in establishing and maintaining the biotrophic relationship through the secretion of effector proteins (Voegele and Mendgen 2011; Kemen et al. 2005; Bozkurt and Kamoun 2020).

The H. vastatrix infection process on coffee leaves (Fig. 1c), like other rust fungi (Heath 1997; Voegele and Mendgen 2011), involves specific events, including urediniospore germination, appressorium formation over stomata, penetration, and inter- and intracellular colonization (Rodrigues Jr. et al. 1975; Silva et al. 1999, 2006 and references therein). Urediniospore germination requires water and is optimal at about 24 °C. After appressorium formation, the fungus penetrates, forming a penetration hypha that grows into the substomatal chamber. This hypha produces at the advancing tip two thick lateral branches; each hypha and its branches resemble an anchor. From each lateral branch of the anchor is borne a hypha, the haustorial mother cell (HMC), that gives rise to a haustorium, which primarily infects the stomatal subsidiary cells. The fungus pursues its growth with the formation of more intercellular hyphae, including HMCs, and many haustoria in the spongy and palisade parenchyma cells and even of the upper epidermis. A dense mycelium is observed below the penetration area, and a uredosporic sorus protrudes like a “bouquet” through the stomata about 21 days after inoculation.

3.2 Genetic and Physiological Diversity

The first experimental evidence for the physiological specialization of H. vastatrix was identified in India by Mayne (1932), who differentiated the local rust samples into four physiologic races. The world surveys of coffee rust races initiated in the 1950s at the Coffee Rusts Research Center (Centro de Investigação das Ferrugens do Cafeeiro—CIFC) in Portugal enabled the characterization of more than 55 rust races from about 4000 rust samples received from different coffee-growing countries. These races have been identified according to their spectra of virulence on a set of 27 coffee plant differentials (Silva et al. 2022 and references therein).

Coffee rust race identification relies on applying Flor’s gene-to-gene theory to the Coffea sp.–H. vastatrix interaction (Noronha-Wagner and Bettencourt 1967). The resistance genes characterized on coffee plants were designated by “SH genes”. Major genes SH1, SH2, SH4, and SH5 were found in C. arabica, the gene SH3 is considered to derive from C. liberica, and SH6, SH7, SH8, and SH9 were only found in “Timor hybrid”—HDT (natural Coffea arabica × canephora hybrid) derivatives, therefore coming from the Robusta side of the hybrid (Rodrigues Jr. et al. 1975; Bettencourt and Rodrigues Jr. 1988). Concomitantly, it was possible to infer nine virulence genes (v1–v9) on H. vastatrix.

The race genotypes comprise v1–v9 virulence genes from isolates derived from C. arabica and tetraploid interspecific hybrids, whereas the virulence genes from some isolates that attack diploid coffee species are not known due to the unavailability of genetic studies in these plants (Rodrigues Jr. et al. 1975; Bettencourt and Rodrigues Jr. 1988; Talhinhas et al. 2017). However, virulence profiling, particularly of isolates infecting tetraploid interspecific hybrids, like HDT derivatives, can only go as far as the available collection of coffee differential genotypes allows, leaving many virulence profiles incomplete or entirely unidentified (Talhinhas et al. 2017; Silva et al. 2022).

Work carried out at CIFC allowed to find rust races with the ability to infect all known coffee genotypes of C. arabica, as well as some genotypes of HDT, like CIFC HDT 832/1 and CIFC HDT 832/2 used as sources of resistance in the coffee populations of Catimor and Sarchimor that were spread to the coffee world (Talhinhas et al. 2017; Silva et al. 2022; CIFC records).

The evolution of virulence in H. vastatrix is parallel to the existent resistance genotypes. For example, in a coffee country that grows only pure Arabica like Geisha (SH1), Kent’s (SH2), Agaro (SH4), and Bourbon and Typica (SH5), the probability of finding different associations of v1, v2, v4, v5 is 100%. Contrarily, the probability of finding the virulence genes v6, v7, v8, and v9 associated with the interspecific tetraploid hybrids, like HDT, is very low or inexistent (CIFC records).

3.3 Implications of Rust Molecular Diversity and Population Dynamics in Coffee Breeding

The global dissemination of H. vastatrix across continents seems to be intimately linked to the historical evolution of the global coffee industry. It is no surprise that coffee hosts act as a major selective pressure shaping the geographical distribution and local prevalence of rust races, leading to the recorded large spectrum of virulence profiles and the recurrent emergence of new ones. However, it is puzzling how H. vastatrix can so rapidly evolve to overcome resistance in coffee cultivars, considering that no sexual phase in the pathogen’s life cycle has yet been identified. Numerous studies have been engaged to characterize population genetic variability in coffee rust, failing to detect any clear genetic structuring pattern or a direct link between phenotypic diversity and molecular diversity (Talhinhas et al. 2017 and references therein; Kosaraju et al. 2017; Santana et al. 2018; Quispe-Apaza et al. 2021; Bekele et al. 2022). Those studies using several kinds of DNA markers (AFLP, RFLP, rDNA-ITS, SRAP, SSRs) and mainly addressing local populations reported different levels of genetic variability, from low to high, but consistently no evidence of population structure could be found, either relating to race, host or geographical origin. The first insights on the population evolutionary history of this pathogen arouse only recently from efforts on genomic research with the analysis of genome-wide SNP data. For the first time, H. vastatrix populations were found to be clearly structured into three divergent genetic lineages with marked host specialization, differentiating rusts infecting diploid coffee species from those infecting tetraploid coffee species (Silva et al. 2018). Moreover, evidences of recombination and footprints of introgression were also found, alerting to the possibility of virulence factors exchange between rust lineages. Episodes of introgression by hybridization have probably been rare in time, but the risk of having different rust lineages within cruising range should be taken into account to guide disease control and breeding strategies. While recombination has been detected both from DNA marker and genomic data (Maia et al. 2013; Cabral et al. 2016; Silva et al. 2018), albeit through unknown mechanisms, probably of a parasexual nature. Both these events may, however, be contributing to virulence increase and could explain the high pace of pathotype emergence. More recently, additional genomic data allowed to further discover a population genetic subdivision in a worldwide sampling of rusts from C. arabica and interspecific hybrids, revealing three divergent genetic subgroups: a low differentiated and globally distributed rust lineage, as well as two other highly differentiated rust lineages, one occurring specifically in Africa and the other in East Timor (Rodrigues et al. 2022). Most interestingly, the divergence of these lineages could be explained by only a small set of SNP loci putatively under the effect of positive selection (Rodrigues et al. 2022). These results suggest that genetic variation underlying host adaptation relies on a small portion of the genome and that the genes associated with these loci may be critically important for the species to survive in novel environments/coffee hosts. Important genome reference assemblies for H. vastatrix have been created in the last years (Cristancho et al. 2014; Porto et al. 2019). The recent availability of a chromosome-level genome resource for H. vastatrix (Tobias et al. 2022) offers renewed prospects for characterizing virulence loci, envisioning the future development of candidate diagnostic markers associated with rust pathotypes and alternative strategies for selective breeding.

4 Coffee Rust Resistance

4.1 Concepts of Plant Disease Resistance

Plants’ perception and response to pathogen invasion evolved alongside the pathogen infection strategy as a sophisticated multilayer surveillance system leading to complete host immunity, partial resistance, or susceptibility (Bettgenhaeuser et al. 2014; Li et al. 2020). Plant defenses are structured in constitutive/passive and induced responses. The first comprises preformed barriers, such as waxy epidermal cuticles, rigid cell walls, and antimicrobial secondary metabolites that offer protection against pathogens. The second one results from a suite of plasma membrane receptors that detect the pathogens or their molecules and is based on the recognition of conserved microbe-associated or pathogen-associated molecular patterns (MAMPs/PAMPs) and host danger-associated molecular patterns (DAMPs) by pattern recognition receptors (PRRs) that activate PAMP-triggered immunity (PTI) (Delplace et al. 2022). Alongside this broad-range defense system, plants developed intracellular resistance proteins to detect specific effector proteins secreted by pathogens activating the effector-trigger immunity (ETI) (Andersen et al. 2018). This two-branch immunity system (PTI and ETI) leads to the induction of a continuous and overlapping downstream response, such as mitogen-activated protein kinase (MAPK) cascades, G-proteins, calcium flux, reactive oxygen species (ROS), transcriptional reprogramming, phytohormones, pathogenesis-related (PR) genes/proteins and epigenetic modifications (Meng and Zhang 2013; Zhang et al. 2012; Lecourieux et al. 2006; Robert-Seilaniantz et al. 2011; Amorim et al. 2017; Zhu et al. 2016). These responses seem stronger and more prolonged during ETI when compared to PTI. ETI is typically associated with the hypersensitive reaction (HR), a form of programmed plant cell death localized at the infection sites (Torres et al. 2006; Jones and Dangl 2006). HR is one of the most important factors in the restriction of pathogen growth, particularly of obligate biotrophs (Heath 2000; Andersen et al. 2018) such as rust fungi (Periyannan et al. 2017).

ROS can trigger HR (Torres et al. 2006; Martins et al. 2020) and may act as a damaging or signaling molecule depending on the balance between ROS production and scavenging mechanisms. When the ROS-scavenging mechanisms fail, this leads to an excess of ROS accumulation responsible for oxidative damage, promoting lipid peroxidation, and damaging macromolecules (e.g., proteins, lipids, and sugars) and DNA (Das and Roychoudhury 2014). Membrane damage by peroxidation of polyunsaturated fatty acids (e.g., linoleic acid) can be initiated not only by ROS but also by lipid radicals or by lipoxygenases (LOXs) during the HR. Also associated with the rapid loss of cell membrane integrity during HR is an increase in oxidizing enzymes, such as superoxide dismutase (SOD) and peroxidases (Heath 2000; Daudi et al. 2012).

Plant peroxidases (POD) function in plant defense against pathogens through the production of antimicrobial quantities of H2O2, as well as in cell wall lignification or cross-linking with cell wall proteins (Penel 2000; Torres et al. 2006).

Moreover, several studies suggest that plant phenolic compounds are strongly involved in plant–pathogen interaction and may restrict pathogen spread (Vermerris and Nicholson 2006). As well phenylalanine ammonia-lyase (PAL), a key enzyme of the phenylpropanoid pathway, catalyzes the deamination of phenylalanine to trans-cinnamic acid, a precursor for several phenolic compounds such as salicylic acid (SA), phenylpropanoids, flavonoid, and lignin seems to be involved in immunity responses (Bagal et al. 2012).

Other proteins also reported as being involved in plant resistance are hydrolases, particularly sugar hydrolases (GH) and peptidases/proteases. The proteases (together with phosphatases) can lead to a complex regulation of cell wall proteins through post-translational modification and GHs confer high plasticity to cell wall polysaccharides and/or are directly involved in antifungal activity (Guerra-Guimarães et al. 2015). Indeed, ß-1,3-glucanase and chitinase (considered as PR-proteins) hydrolyze ß-1,3-glucan and chitin, respectively, the cell wall components of most fungal pathogens (as revised by Silva et al. 1999). Additionally, Germins and germin-like proteins (GLPs) which are homohexamer glycoproteins, have also been implicated in biotic and abiotic stress responses (Liao et al. 2021). Studies related to GLP and plant immunity showed their association with jasmonic acid (JA)-mediated defense response (Liu et al. 2016; Pei et al. 2019) or the connection between GLP overexpression and the improved resistance to fungal pathogens and the accumulation of ROS (Beracochea et al. 2015; Sultana et al. 2016).

4.2 Mechanisms of Coffee Resistance to H. vastatrix

Over the years, there has been considerable progress in understanding the mechanisms of coffee’s complete resistance to H. vastatrix at the cellular and biochemical levels, and more recently via analytical chemistry, gene expression analysis, and the use of omics approaches.

Coffee resistance to H. vastatrix is characterized by the arrest of fungal growth, which may occur at pre-haustorial stages (pre-haustorial resistance) or after the formation of at least one haustorium (post-haustorial resistance). In both types of resistance, the hypersensitive reaction (HR) is one of the first cytological responses induced by H. vastatrix. This response occurs initially in stomatal cells associated with pre-haustorial fungal stages and later in plant cells invaded by haustoria, and spreads to adjacent noninvaded cells (Silva et al. 2006, and references therein; Silva et al. 2008; Diniz et al. 2012; Guerra-Guimarães et al. 2015).

The early perception of the pathogen invasion by a repertoire of recognition kinases at the plasma membrane, such as RLK and LRR-RLK2, or intracellularly by nucleotide-binding site–leucine-rich repeat (NBS-LRR) are successful steps in triggering host defense (Fernandez et al. 2004; Guzzo et al. 2009; Diniz et al. 2012; Diola et al. 2013; McCook and Peterson 2020). During coffee resistance to H. vastatrix, the up-regulation of two MAPKs (MAPK2—Mitogen-activated protein kinase 2 and MEK2—Dual specificity mitogen-activated protein kinase kinase 2) suggests that they are important signaling elements of the defense response during the infection process (Diola et al. 2013). In addition, two calcium-related genes, calcium-dependent protein kinase 5 (CDPK5) and calmodulin-binding protein (CaMBP) have been associated as part of the Ca2+ signaling in coffee resistance response (Diola et al. 2013). In coffee plants, a small list of transcriptional factors has been associated with resistance to H. vastatrix: Ap2 (AP2 type transcription factor) (Fernandez et al. 2004), bHLH (basic helix-loop-helix DNA-binding protein) (Florez et al. 2017), and bZIP56 (bZIP transcription factor) (Diola et al. 2013). However, the WRKY family is the most well-studied transcriptional regulators in coffee plants, with 17 out of 22 genes that seem to be linked to H. vastatrix resistance. Of all known coffee WRKYs, CaWRKY1 (CaWRKY1a and CaWRKY1b) is activated as early as H. vastatrix penetration into host tissues and deployment of HR (Ganesh et al. 2006; Petitot et al. 2008, 2013a; Diniz et al. 2012). The role of phytohormones, like JA and ethylene (ET), in coffee defense against H. vastatrix, remains unclear (Guzzo et al. 2009; Ramiro et al. 2010; Diniz et al. 2012; Diola et al. 2013; Florez et al. 2017). However, several studies point out that SA is a key hormone in coffee defense against H. vastatrix, by the increased expression of SA pathway-related genes, such as SA-biosynthesis gene PAL, by SA-induce PR genes, CaPR1, CaPR2, CaPR5, CaPR10 (Couttolenc-Brenis et al. 2020; Diniz et al. 2012, 2021; Diola et al. 2013; Guzzo et al. 2009; Ramiro et al. 2009) and by SA-mediated protein–protein interactions gene NPR1 (Non-expressor of pathogenesis-related) (Diniz et al. 2012; Petitot et al. 2013b; Couttolenc-Brenis et al. 2020). NPR1 is a transcription co-factor and a bone fide SA receptor and, consequently, a positive regulator of several SA downstream responses such as HR (Saleem et al. 2021).

Light and transmission electron microscopic observations further suggest the involvement of ROS, such as H2O2 and O2− in the HR of coffee-resistant genotypes. Additionally, deposition of phenolic-like compounds in cell walls and cytoplasmic contents, plant cell wall lignification, haustoria encasement with callose and β-1,4-glucans; accumulation of intercellular pectin-like material containing polysaccharides and phenols, and plant cell hypertrophy were also observed (Rodrigues Jr. et al. 1975; Silva et al. 2001, 2002, 2006, 2008; Ramiro et al. 2009; Diniz et al. 2012).

Biochemical studies with coffee-resistant genotypes, revealed the early increase in the activity of several oxidative enzymes associated with ROS homeostasis, namely, POD, LOX, and SOD, as well as the enzyme PAL (Rojas et al. 1993; Silva et al. 2002, 2008; Guerra-Guimarães et al. 2009a). The early increase in the SA levels, quantified by HPLC/ESI-MS/MS, reinforces the involvement of an SA-dependent pathway in coffee resistance to H. vastatrix (Sá et al. 2014). Additionally, the evaluation of chlorogenic acid, an abundant polyphenol in coffee, performed by HPLC-DAD and LC-MS also revealed an early and significant increase in its content associated with the resistance (Leitão et al. 2011). Chitin and β-1,3-glucan, are the main components of H. vastatrix cell walls, including those from intercellular hyphae (infection hyphae and HMCs) and haustoria (Silva et al. 1999). An early increase of β-1,3-glucanase (PR2) and chitinase (PR3) activity was observed in crude extracts and in the apoplast of resistant coffee leaves (Maxemiuc-Naccache et al. 1992; Guerra-Guimarães et al. 2009b). Furthermore, basic isoforms specific to class I chitinases were detected earlier and only in the resistance, suggesting its involvement in the defense response of the coffee plants (Guerra-Guimarães et al. 2009b).

Going deep into the study of the coffee leaf apoplast, a proteomic analysis was performed revealing the increase in abundance of several cell wall glycohydrolases (GH3, GH31, and GH38 family), PR proteins [PR1, PR2, PR3, thaumatin/osmotin (PR5), GPLs (PR15 and PR16)], proteases (serin, cysteine and aspartic peptidases) and other enzymes (e.g.; metallophosphatases) playing a role in the coffee defense response (Azinheira et al. 2013; Guerra-Guimarães et al. 2015; Possa et al. 2020; Silva et al. 2022).

The resistant and susceptible coffee genotypes share most of the described host responses when infected by H. vastatrix. However, they are observed earlier and with greater magnitude during the resistance response, particularly in pre-haustorial resistance.

5 Conclusions

This chapter reviews decades of scientific knowledge accumulated on coffee–H. vastatrix interactions. From the first studies back in the sixties until today, a wealth of data has been gathered about this binomial relationship. What we know today has evolved significantly from Flor’s gene-for-gene model to rust races’ candidate markers within the current “omics” era (genomics, transcriptomics, metabolomics, and proteomics). The income of new data continuously challenges what we know and raises further questions. What is the true nature of the coffee resistance genes, and how are they regulated? How are the recently discovered small non-coding RNA (sRNA, miRNAs) involved in gene regulation? How can miRNA be related to coffee resistance to H. vastatrix? The answer to these and more questions relies on our ability to continue to explore the coffee–H. vastatrix interaction and adventure ourselves to go deep into barely explored coffee resistance research fields such as functional characterization and epigenetics. Despite all the significant progress made to date, a thorough exploration of Coffea–Hemileia vastatrix interactions using advanced technologies remains critical for developing new and efficient disease control strategies.