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Coffee is currently one of the most valuable export commodities. It is only superseded by petroleum in value (Lashermes and Anthony 2007). Retail sales of coffee are valued around $70 billion USD (Philippe 2009). This product is the seeds, frequently called 'beans', which come from plants of the genus Coffea in the Rubiaceae family. Approximately seventy percent of the world's coffee comes from cultivars of Coffea arabica (Vieira 2008). As a commodity, coffee is exported from its tropical farming areas to the sub-tropical and temperate areas where it is consumed primarily as a beverage. North America is the primary consumer of coffee, and hence the major importer of green coffee beans (Goddard and Akiyama 1989). Coffee rust, Hemileia vastatrix, is the most significant pest of coffee plants; it is also considered one of the seven most significant tropical plant diseases (Kushalappa and Eskes 1989). It is estimated that this pathogen costs coffee farmers in Africa, Asia, and South and Central America a combined $2 billion USD a year, and is responsible for a yield loss of approximately ten percent annually (Hein and Gatzweiler 2006). The significance of coffee economically, and thus the effects of its primary pest, warrant a concise review of the topic.
1.2 Where it matters
Coffee is a tropical plant native to the highlands of Ethiopia in northeast Africa (FAO, 1968). From there the plant has been cultivated in every major continent with a tropical region, and many islands. This includes, but is not limited to, Africa, Middle East, Asia, South and Central America, Australia, and Hawaii. Though the latter two areas are minor contributors to the production of coffee, they are significant in that coffee rust has not yet existed in those regions (Mahe 2007). The major world producers of coffee are the Americas (60%), Asia (24%), and Africa (14.5%) (Vieira 2008). Coffee rust is widespread in all major coffee growing areas. It is the opinion of most that its dissemination was accomplished through wind. Coffee cultivation in South America began as a significant crop in the early 1800's, and by the late 1800's South America had become a significant part of the world's coffee production (Hanley 1997). Interestingly, coffee rust was not a problem in South America until 1970 (Schieber 1975). Since South America grows the majority of the world's coffee, that particular region will receive the most emphasis.
2. Background Information
2.1 The plant
2.1.1 Biology of coffee plants
Coffea arabica is a shrub that grows up to five meters in height. Coffee plants take three to four years before they set fruit, and up to eight years before they are fully productive. Full productivity lasts up to twenty years, though the plants can live longer. The plant typically blooms multiple times a year (region-dependent), and fruit generally take more than six months to fully mature. Blooming takes place along the axis of the stem (Fig. 1 A). Fruit production occurs on last year's growth, so dieback caused by the rust fungus during the previous year can affect the next yield the following year. Most of the fruits, called coffee cherries, contain two greenish seeds (Fig. 1 B). As a beverage, coffee is prepared by removing the fruit, roasting the seeds, grinding them up, and running hot water through them. Typically, the coffee seeds are exported green, after the fruit has been removed. Coffee flowers are insect-pollinated (Roubik 2002) and, in the case of C. arabica, also self-fertile. C. arabica is an allotetraploid (2n = 44), while all of its close relatives (e.g. C. canephora) are diploid (2n = 22) and self-sterile.
Fig. 1. (A) Coffee tree in bloom. (B) Taxonomic diagram showing characteristic aspects of coffee plants. Modified from H. D. Vieira 'Coffee: The Plant and its Cultivation,' in Plant-Parasitic Nematodes of Coffee (2008).
The importance of these chromosomal differences will become clear later, as C. canephora is a significant source of resistance genes against coffee rust. Because coffee has long generation times, developing new cultivars is time consuming. Coffee is resistant to a wide variety of pests due to chemical defenses like that of the well-known chemical caffeine. In general, the plant can also exhibit hypersensitive tissue responses to pathogens like the rust fungus (Silva et al 2002). Coffee also demonstrates a defense response against rust. This response seems to be reduced during times of stress such as drought, nutrient deprivation, or heavy fruit load (Kushalappa and Eskes 1989).
2.1.2 Agricultural practices
Coffee is planted in tropical and subtropical regions, altitudes ranging from 0-1500 meters, in close rows. There is currently much debate about whether it is better to grow the plant in shade or sunlight, but most high-yield plantings are done in full sunlight, although some conclude from the data that some shade situations can indeed produce the highest yield (Perfecto et al 2007). The coffee plants are pruned to make it easier to harvest coffee seeds from them, as well as to aid in producing a maximum crop yield. Coffee plants are fertilized, and preventative fungicidal sprays are commonly used, based on rust epidemiological prediction models. There is a division between two types of coffee. Arabica coffee, Coffea arabica, produces the finest flavored beverage, but the plant is fully susceptible to coffee rust as well as other biotic and abiotic stresses. Robusta, Coffea canephora, is well named as it is resistant to rust and has different stress weaknesses, but the quality of beverage produced from Robusta beans is markedly lower than Arabica. For this reason, Robusta is frequently used to produce products like "instant" coffee (Vieira 2008).
Harvesting coffee is done primarily by hand because of the asynchronous ripening of fruit. Though some larger coffee plantations do use mechanized harvesting, this method results in a lower quality product due to a mixture of ripe and unripe coffee fruits. The coffee farmer processes the coffee fruits to separate the seeds from the pulp. This pulp removal is done by either wet or dry methods. The exported product is the green seed.
2.1.3 Agricultural distribution
Coffee is believed to have grown originally in highlands of Ethiopia (FAO, 1968), which was formerly known as the kingdom of Kaffa (Vieira 2008). Coffee was first cultivated in its native country, and later cultivated in Yemen (Rodrigues Jr. 1975). It is estimated that the majority of coffee comes from small individual plantations (Bacon 2005). The top five coffee -producing nations are Brazil, Vietnam, Colombia, Indonesia, and India. Roughly 4.4 million metric tons of coffee was produced by these five countries in 2006 (author's calculation from Vieira 2008). Approximately 70% of the world's coffee production comes from Arabica coffee (Mahe et al 2007). Assumingly, the reason this susceptible coffee is in the majority can be related to its higher value. At times, this percentage of production fluctuates. If rust disease outbreaks become severe, some farmers switch to C. canephora for its natural resistance to rust (Rodrigues et al. 1975).
2.2 The stressor
2.2.1 Biology of coffee rusts
Rust fungi (Basidiomycota, Urediniomycetes) in general are biotrophic fungi that attack plants causing minor to severe damage. Rusts can have single or multiple hosts and are serious parasites of numerous agricultural crops. Coffee rust, Hemileia vastatrix, is a single-host rust that attacks the leaves of coffee plants. This fungus has a complex life cycle, and not all of the factors affecting its epidemiology are well understood. Thus far, Coffea is the only known host genus. This rust fungus only germinates in the presence of liquid water, and not even 100% humidity is enough to cause it to germinate. Coffee rust grows in a temperature range of 15.5-28°C. The fungus is prolific, as most fungi are, and can produce hundreds of thousands of spores per lesion over a three to five month period. In the 1930's, it was first recognized that coffee rust existed in four distinct physiological races (Rodrigues Jr. et al. 1975). Coffee rusts now have over forty identified races, most of which are uncommon. The most significant race of coffee rust is race II, followed by races I, III, and XV (Rodrigues Jr. 1984). C. canephora is naturally resistant to the major races of coffee rust, while C. arabica is naturally susceptible.
2.2.2 Pathogenicity of coffee rusts
The coffee rust pathology cycle is atypical of rust fungi in that it does not rupture the epidermis of the leaves. The cycle follows this general pattern below as described by Voegele, Hahn, and Mendgen (2009). The pathology cycle of rust can be altered depending on a number of variables in both the environment and the coffee plant (Fig. 2).
Fig. 2. This diagram shows the pathology cycle emphasizing external factors that affect each stage of the cycle. This diagram is in the context of a single coffee tree. Solid lines indicate positive effects, dotted lines indicate an optimum effect, and dashed lines indicate a negative effect. Modified from Avelino, Willocquet, and Savary 'Effects of crop management patterns on coffee rust epidemics,' in Plant Pathology (2004).
Rust spores find their way to the surface of coffee leaves by way of wind or rain. The spores are then splashed upwards during rainstorms to the underside of the leaves above (Fig 3). The spores then germinate in the present of liquid water, and the germinating spore structure locates a stoma on the leaf undersurface. This is the point of entry for this pathogen. Once inside the leaf, the rust invades leaf cells, stealing resources locally from the leaf. It also seems that the fungus becomes a significant resource sink for the whole plant (Staples 2000). When mature, the rust grow out of the stomata of the leaf and produces primarily uredospores and occasionally teliospores. The undersides of the leaves form powdery-looking pustules that are orange or yellow (Adejumo 2005). The teliospores produce basidiospores, about which little is known. The uredospores become wind-born and distribute to the rest of the plant, plantation, or even further.
Fig. 3. Diagrammatic presentation of the way that rust spores are dispersed and positioned by rain. Modified from R. H. Fulton 'Chemical control of coffee leaf rust in Central America,' in Coffee Rust in the Americas (1984).
The rust disease usually starts at the bottom of the plant and travels upward. Younger leaves are generally more vulnerable than older, but this is reversed in some resistant cultivars. As expected, stressed coffee plants are more susceptible than unstressed. With an increase in coffee yield in amount of fruit per plant, there is an increase in susceptibility of the coffee plant to coffee rust (Kushalappa and Eskes 1989). Bright light, drought stress, and high temperatures also make coffee plants more susceptible to rust attack. Yield losses come in the form of smaller coffee fruits (and seeds) due to a loss of photosynthetic capacity and nutrients. The rust can also cause early leaf drop, and, in epidemic cases, severe defoliation, which can result in shoot and root dieback. This dieback can dramatically reduce yield for the following production year. The fact that the coffee rust lifecycle is shorter then the fruit production time of the coffee plant has significant implications. A heavy rust infection can significantly reduce the development of coffee fruits. Typically, rust has a greater effect on coffee tree foliage then it does on yield (Brown et al. 1995).
Coffee rust is currently found in every major coffee growing area in the world. It is very problematic in Africa, and somewhat less so in South America. Some suspect that this difference is due to moderate levels of a hyperparasitic fungus that helps in curbing the South American population of coffee rust by reducing the number of viable rust fungal spores (Vandermeer et al. 2009). During the early years of the history of coffee's cultivation, coffee rust was only found in a small portion of Africa. The rapid spread of coffee rust worldwide has been attributed primarily to wind (Nagarajan and Singh 1990) and to a lesser degree human activity. However, there are some cases where the geography and/or agricultural habits make humans the only culpable party (Becker-Raterink 1984). There is substantial evidence that wind is the means by which coffee rust spread to many of the coffee-growing areas of South America (Schieber 1975). The study of rust dispersal by wind and rain has lead to a number of predictive models that aid in preventative measures. Currently the primary means of reducing yield loss caused by rust fungus is preventative spraying of fungicides. Amounting of spraying is based on a wide variety of factors, but primarily rainfall and temperature (Avelino et al. 2004).
2.3 History of coffee plant resistances
2.3.1 First appearance
The following summary of the history of resistance in C. arabica to rust comes primarily from the thorough work of Rodrigues, Bettencourt, and Rijo (1975). The need for breeding resistance to coffee rust in C. arabica plants became obvious when an epidemic of rust broke out in the coffee plantations in Ceylon (now Sri Lanka) in the late 1860's. The rust completely destroyed the coffee industry there in less than fifteen years. Ceylon went from being the world's largest coffee producer to not producing coffee at all. Resistance to coffee rust was first discovered in C. arabica in 1911 in an estate in India. This single plant produced what was referred to as the Kent cultivar. This partially resistant cultivar was effective in combating rust for a little less than twenty years in India. Until the 1950's, there was little information about resistance in C. arabica. At that time, expeditions to collect germplasm and study coffee rust in the field were conducted. In 1955, the American and Portuguese governments agree to fund and equip Centro de Investigacao das Ferrugens do Cafeeiro (CIFC) for the purpose of studying coffee rust. As of 1975, there were yet to be any purely C. arabica coffee plants that are fully resistant to all races of coffee rusts. It was also documented that other species of the Coffea genus exhibited high levels of resistance to coffee rust. In some localities, the epidemics of rust caused growers to seek out other coffee plants that were resistant to rust. The most significant alternative is C. canephora, which, unlike C. arabica, naturally possessed either complete resistance or complete susceptibility to coffee rust within the same stand. To a lesser extent, there are also partially resistant/partially susceptible individuals. This variability is explained by the allogamous properties of C. canephora. Because of the introduction of new coffee types into older plantations, a number of natural hybrids with C. arabica have been formed. Hybrids between C. arabica and other coffee species (Lashermes 2009) produce triploids, and most of said hybrids are useless for producing useful cultivars themselves due to extreme genetic variability (Eskes 1982). The most well known naturally formed tetraploid hybrid is Hibrido de Timor (referred to as HdT) discovered in Portugal around 1927 (Rodrigues Jr. 1984). HdT had its cultivation origins in the 1940's in Timor. HdT has been shown to be resistant to at least 30 races of rust, but suffers from high variability in yield and morphology (Rodrigues Jr. 1984).
2.3.2 Development of resistance
C. arabica as a modern cultivated plant originates from two narrow populations referred to as typical and bourbon. There is some evidence that the C. arabica originated as a species from a cross between C. eugenloides and C. canephora (Lashermes and Anthony 2007), as is illustrated in Fig. 4 A. Because of this narrow genetic base, C. arabica is susceptible to a number of coffee pests and pathogens, including coffee rust. The Brazilian Instituto Agronomico de Campinas (IAC) in cooperation with CFIC began breeding coffee plants for resistance in the 1950's. Since that time, coffee plant breeding for resistance has taken place simultaneously in Angola and Colombia (Rodrigues et al. 1975). Currently the resistance for which breeding is being done is of a vertical nature, though there is evidence that horizontal resistance does exist in coffee (Rodrigues et al. 1975). Work towards a rust resistant cultivar of C. arabica has been primarily focused on breeding in desirable resistance genes from other coffee species. This poses some difficulties because of the uniqueness of C. arabica chromosomal status (Fig. 4 B).
Fig. 4. A and B showing chromosomal transmissions that are most influential to work with C. arabica. Modified from P. Lashermes and F. Anthony 'Coffee,' in Genome Mapping and Molecular Breeding in Plants, vol. 6 (1984).
2.3.3 Current status
Currently molecular markers are being used to isolate, identify, and screen for resistance genes (Mahe et al 2008). It is hoped that rapid identification of resistant plants will be possible through the identifying and labeling of resistance genes. There are no fewer than nine known dominant genes in coffee plants that are responsible for resistance to rust fungi (Rodrigues et al. 1975). These genes are labeled SH1 through SH9. Following the gene-for-gene concept, it seems as though rust species possess virulence genes that parallel the resistance genes. These parallel virulence genes are referred by V1, V2, and so forth. Different combinations of virulence genes, or lack thereof, are presumably responsible for the existence of rust race varieties (Rodrigues Jr. 1984). One study indicates that there is a correlation between the production of chitinases and induced coffee rust resistance (Guerra-Guimaraes et al. 2009). A study made by a similar research team concluded that resistance to rust also involves peroxidases (Silva et al. 2008). With plant breeding alone, it is estimated that developing a new resistant, stable cultivar of coffee takes 30 years (Carneiro 1999). The length of time is partially due to the long generation times of the coffee plant (4-5 years) and the number of backcrosses required to breed out the negative traits that were introduced when plants are hybridized with a more resistant species. Modern techniques, such as gene insertion and embryogenesis, have been used to shorten the time required for the development of new cultivars of coffee (Vieira 2008).
2.3.4 Future directions
The future goal is to create a resistant coffee cultivar that has good resistance to biotic and abiotic stress, good cup quality, and high yield. However, it is frequently true that only one or two of these traits can be easily combined in one plant. The Brazilian coffee research agency Centro de Investigaacao das Ferrugens do Caffeeiro (CIFC) is perhaps one of the most important entities working on solving this and other similar problems. It seems that the future of resistance creation will be more biotechnology-based and geared toward designing the perfect coffee plant through gene insertion, embryo rescue, and various other approaches (Satana et al. 2007). It is the author's opinion that this is too optimistic of a view, and present observations indicate that many in the western world (the major consumers of coffee) have strong reservations about anything that is not "natural."
3. Resistance Testing and Screening
3.1 Resistance techniques used
Searching for coffee resistance is initially accomplished through DNA marker assays of coffee plants. Plants that possess resistant genes are subjected to further testing involving a leaf disc test, where a leaf sample is inoculated with rust spores, and success of spores is indicative of resistance. Because of a degree of unreliability of information acquired from greenhouse testing, field trials are necessary for determining the extent of resistance (Kushalappa and Eskes 1989). The level of resistance a coffee plant has to coffee rust is generally proportional to the number of rust lesions that form per leaf after inoculation with rust fungus. Using a one to ten scale, with complete resistance to rust being ten, coffee plants with zero lesions per leaf would be a ten, while leaves with an average of one to two lesions per leaf would be a one. It is also possible to do a holistic rating of the coffee plants. Plants with no defoliation due to rust would be a one, while plants with extreme (near complete) defoliation would be a ten. The latter approach has the advantage of detecting tolerance, but the disadvantage of not taking into account loss of the photosynthetic resources due to the resource sink created by the rust fungus. Besides the two previous hypothetical categories, methods of resistance level have been measured by coffee leaf reaction to rust spores. Small aberrations of the leaf undersurface form when the coffee plant effectively resists the coffee rust fungus, and this result is called R (for resistant). When a large uredosporic rust pustule forms, the leaf is considered susceptible (S). There are at least two intermediate reactions referred as moderately resistant and moderately susceptible (MR and MS respectively) (Rodrigues et al. 1975).
3.2 Comparison with another crop
Another crop that often suffers from rust attack is wheat (Triticum). Wheat stripe rust, Puccinia striiformis, is a serious pest of wheat in the majority of wheat-growing areas in the world (Line 2002). It is difficult to make comparison with wheat as it is not a woody plant, and it is annual rather than perennial. In addition, rust fungi in wheat attack a number of wild grasses, whereas the species that attacks coffee has no known secondary host. Wheat infected by rust can readily die, but coffee rust infections have not been recorded as killing coffee trees. Breeding for resistance in wheat is often done within the species (Line 2002), whereas the parentage of coffee creates a need to look outside the primary species for viable resistance genes (Lashermes et al. 2009). Despite these differences, there are some informative similarities. Both rusts are readily transported by the wind, and both are heavily influence by rainfall. Leaves are the primary target of both, and there are numerous races of the two different rusts.
3.3 Available germplasm
Because much of the current resistance in coffee plants comes from a relatively narrow base, there is no small concern at the rapid disappearance of the geographical home of C. arabica (Hein and Getzweiler 2006). This makes it difficult to collect new and diverse germplasm that could significantly aid the search for better resistance. Several other Coffea species germplasms are maintained with the hope that their resistance genes can be transferred to C. arabica. C. dewevrei is maintained for its resistance to drought and poor soils, C. racemosa is considered important for its capacity to endure high temperatures and drought, and C. stenophylla is regarded as important source of genetic material because of its resistance to the coffee leaf miner, Leucoptera coffeella (Vieira 2008).
Coffee is an important crop economically, and a number of tropical countries rely on it as a major portion of their economies. It is true that coffee is not a food plant, and for that reason it is perhaps not as high a priority as some food crops like rice, wheat, or corn. However, because over twenty million smallholders, as well as some countries, rely on coffee for livelihood, it is worth pursuing the development of resistance in coffee plants.