CHAPTER 1: Introduction to Coffee Plant and Genetics

The coffee beverage treasured by millions of people around the world results from roasted seeds of trees belonging to the botanical family Rubiaceae, genus Coffea. Coffee plants were discovered in Africa and eventually disseminated to countries throughout the world. Along this journey, a number of new cultivars have been created from selected varieties to fulfil the need for plants with higher productivity, resistance to diseases and superior cup quality, and over time, new wild varieties have been discovered as well. Currently, over 100 species within the genus Coffea are catalogued.^1–3  Despite this diversity, only two species are actually of great importance in the world market, C. arabica L. and C. canephora Pierre. Knowing the genetic origin of coffee varieties and cultivars within these two species is important to understand the main differences and similarities in their chemical composition and flavour.

Since its discovery, coffee has attracted the attention of explorers and botanists from all over the world, especially in the second half of the 19th century, when many new species were discovered. Because of the great variation in the types of coffee plants and seeds, botanists have failed to agree on a precise, single system to classify them or even to designate some plants as true members of the Coffea genus.⁴ 

Knowledge of the coffee plant and its characteristics is fundamental for understanding practical coffee growing topics, as well as topics related to interaction with the environment and its reactions to biotic and abiotic stresses.

In this chapter, we introduce the coffee plant, discuss its origin and genetic aspects of the two main species, and explain how they migrated from Africa to other continents, becoming the most commercially important coffee species in the world.

The coffee tree is part of the sub-kingdom of plants known scientifically as the Angiosperm, or Angiospermae, meaning that the plant reproduces by seeds enclosed in a box-like compartment, the ovary, at the base of the flower. It belongs to the botanical family Rubiaceae, which has some 500 genera and over 6000 species, subfamily Ixoroideae. The current classification of the Coffea genus results from recent fusions of several subgenera and genera.^4,5  According to Leroy⁶  and Bridson,⁷  two genera existed in this subfamily, Coffea L. and Psilanthus Hook.f. (an Australasian genus), with the Coffea genus being split into two subgenera, Coffea and Baracoffea. After morphological and molecular studies by Davis et al.⁸  and Maurin et al.,⁹  respectively, the group concluded that a sister relationship between both subgenera was actually highly unlikely and untenable.^10,11  Later, subgenus Coffea and genus Psilanthus were merged according to additional phylogeny analysis (using molecular and morphological data), leading to the current Coffea genus,¹²  which is by far the most economically important member of the Rubiaceae family.^4,13  The botanical classification of coffee is shown in Figure 1.1.

The various species of subgenus Coffea are largely present in the African continent, though they are mostly restricted to tropical zones when growing in the wild. There are 41 species from continental Africa (from Guinea to Tanzania and from Ethiopia to Mozambique), 59 from Madagascar and 4 from nearby islands (1 from Grand Comore and 3 from the Mascarenes Islands Mauritius and Réunion), each area having 100% endemicity for its species.^1,2,14  Considering the merge between subgenus Coffea and genus Psilanthus, located in Asia and in Australasia, currently there are at least 125 species in the genus Coffea.^1,5,10 

From all catalogued species under the genus Coffea, only three have commercial importance: Coffea arabica, Coffea canephora and, to a much lower degree, Coffea liberica, with the first being the most cultivated crop.⁴  C. arabica is a tetraploid species (2n = 4x = 44) originating from a natural hybridization between either C. canephora and C. eugenioides or ecotypes related to these two diploid (2n = 2x = 22) species.^17–19  It is the species with highest cup quality compared to other known species, but the plant is not as strong and resistant as C. canephora species. Triploid hybrids, originating from crosses between C. arabica and diploid species, have been reported. They tend to be robust plants but are almost completely sterile.^4,17  C. arabica is self-compatible (self-fertile nature), which so far has only been reported in two other coffee species: C. heterocalyx Stoff. and C. anthonyi Stoff. & F. Anthony, ined. Despite its inferior cup quality, C. canephora maintains heterozygosity due to its cross-pollinating (self-incompatible) nature.^4,9  Coffea liberica Hiern is a diploid species cultivated to a minor extent, mainly because of its sensitivity to diseases, especially Fusarium xylarioides. Its seeds tend to have a better cup quality compared to C. canephora species, but still inferior compared to C. arabica.²⁰  Despite the close phylogenetic relationship between C. liberica and C. canephora, these species differ substantially in their morphological characteristics. C. liberica could thus be of interest for interspecific breeding programs.²⁰ 

Owing to the richness of coffee species and varieties, and to the popularity of the coffee beverage, when referring to the main coffee species, some confusion has been observed regarding nomenclature, and the authors found it useful to clarify some misconceptions. For example, ‘Coffea canephora’ has been described as ‘Coffea robusta’, when ‘robusta’ is actually mostly reported as being a variety or subvariety of the Coffea canephora species. In the same way, the word ‘robusta’ has been popularly used for commercial and other purposes as a synonym of ‘Kouilouensis’ (also called ‘Kouillon’ or ‘Conilon’), which is a different variety of Coffea canephora, widely cultivated in Brazil and with different chemical and sensory characteristics. Another misunderstanding sometimes occurs with the term ‘Coffea dewevrei’, which has been used to refer to a separate species in some instances, and, in other instances, as a synonym for Coffea liberica. In fact, ‘liberica’ and ‘dewevrei’ (the latter also called ‘excelsa’ coffee) are different varieties within the Coffea liberica species. In addition, coffee varieties (wild genotypes) have been confused with cultivar names (plants selected by humans for cultivation).⁴  As science advances and studies go deeper into unveiling the genetic, chemical and sensorial differences among coffee species and varieties/cultivars, knowledge of coffee genetics and nomenclature becomes ever more important for interpretation and dissemination of correct information in scientific reports.

Coffea species have colonized many types of forests throughout a wide elevational distribution in the African continent. Up to 70% of species in Coffea subgenus are present in humid and evergreen forests, and at least 13% are adapted to seasonally dry forests in continental Africa. The other 17% of the species are adapted to various other types of forest, including humid evergreen forests, gallery forests, seasonally dry (evergreen to deciduous) forests, savannah woodlands and shrublands.^14,21 

In Madagascar, 67% of the species grow only in humid evergreen forests, 17% grow only in seasonally dry forests and the remaining species grow in both types of forests.^1,21,22 

Coffee trees are naturally found from sea level up to 2500 m, but no species grow throughout this entire range.²²  Species presenting the broadest elevational range of growth are: C. eugenioides (300–2200 m); C. brevipes (80–1450 m); C. canephora (50–500 m); C. liberica (80–1800 m); C. mongensis (400–200 m); C. munfindiensis (950–2300 m); C. salvatrix (400–1850 m); C. dubardii Jum., C. homollei J.-F. Leroy and C. perrieri (50–1200 m).^1,22  The largest number of endemic species in Africa is present between 200 and 1000 m above sea level, including C. canephora and C. liberica sub sp Dewevrei.²²  This broad range is mainly caused by variations in latitude. For example, in Uganda, an equatorial country where the minimum temperatures are warm and relatively stable, C. canephora grows above 1000 m. The altitude range for C. arabica optimum growth is 1200–1950 m, with average growth occurring at 1575 m. It is worth noting that this elevation range is observed both on the continent and on islands, though the number of species that grow over 1000 m above sea level is higher in continental Africa than in Madagascar.^21,22  Figure 1.2 presents the average elevational distribution and type of forest colonized in Africa by important species of subgenus Coffea. The broadest elevational range species presented above are not in the pyramid. Throughout the rest of the world the presence or absence of species is largely defined by minimal temperatures, which is in most cases determined by elevation and latitude.^21,22 

The natural evolutionary history of coffee probably occurred between 150 000 and 350 000 years ago in the African continent.²¹  Biogeographic analysis had indicated that the centre of origin of subgenus Coffea was in Kenya.²¹  However, new DNA analysis and floristic records suggest that Lower Guinea in west equatorial Africa could be the centre of origin and speciation of Coffea subgenus Coffea as well as the richest sub-centre of endemism in the Guineo-Congolese region. Diversity in subgenus Coffea has, therefore, been underestimated for a long time.^21,23  This region likely played the role of refuge for coffee trees during the last arid maximum (18 000 years before Pangea: B.P.) and previous arid phases. In Central Africa, a chain of small refuges has been located near the Atlantic Ocean: in west and south Cameroon, in the Crystal and Chaillu Mountains in Gabon and in the Mayombe Mountains in Congo. These areas, rich in coffee species, are known to be hotspots of biodiversity.^1,11,14  Figure 1.3 shows the original distribution of the current genus Coffea L., including subgenus Coffea in Africa and the additional Australasian Psilanthus spp.¹² 

The C. arabica species has its primary centre of diversity in the southwestern Ethiopian highlands (in altitudes between 1000 and 2000 metres), the Boma Plateau of Sudan and Mount Marsabit of Kenya.^19,24  Its strict natural localization is due to the way that C. arabica speciation processes have occurred, as explained above. On the other hand, C. canephora has colonized various regions in Central Africa, stretching from West Africa through Cameroon, Central African Republic, Congo, the Democratic Republic of Congo, Uganda and northern Tanzania down to northern Angola.^25,26  In general, C. liberica habitats are localized to the same regions where C. canephora grow.^21,22 

The history of coffee cultivation is incompletely documented with regard to the domestication of the coffee plant in Africa and its dispersion throughout the world by humans (Figure 1.4).²⁷  Welman²⁸  reported in 1961 that the cultivation of C. arabica varieties began when wild coffee was introduced from Ethiopia to Yemen as early as 575 ad or ac (Anno Domini, or After Christ), although other authors have reported possible cultivation even before that.²⁹  However, such data have been based on myths and legends, not scientific texts. Based on historical and scientific data, C. arabica diverged into two genetic bases, which have been described as two distinct botanical varieties: Coffea arabica var. arabica (usually called Coffea arabica var. Typica Cramer) and Coffea arabica var. Bourbon (B. Rodr.) Choussy.¹⁷  These have subsequently led to most of the commercial C. arabica cultivars grown worldwide.¹⁹  Bourbon-derived cultivars are characterized by a more compact and upright growth habit, higher yield and better cup quality (sensorial quality) than Typica-derived cultivars.²⁴ 

Historical data indicate that the Typica variety originated from a single plant that was taken from Yemen to India.^30–32  Subsequent generations from this plant were taken to the island of Java in 1690 and then Amsterdam in 1706 or 1710, where plants were cultivated in the botanical gardens.^19,27  From Amsterdam, coffee was introduced to the Americas when seedlings were taken to Suriname in 1718. From there, an arabica coffee tree was introduced in the West Indies (Martinique) in 1720 or 1723.³³  In 1727, seeds were taken to the state of Pará in northern Brazil, apparently from French Guiana. Seeds from Suriname also became the parent of numerous self-progenies, which were further disseminated around the Americas (Jamaica, Puerto Rico, Haiti, Cuba, Central America, the Guianas, etc.).^27,34,35 

The Bourbon variety originated with the re-introduction of coffee trees to Bourbon Island (now Réunion, one of the Mascarenes Islands) with plants from Mocha, a city on the Yemeni coast (1715–1718). From there, Bourbon plants were possibly taken to Mauritius Island and later to various coffee growing origins worldwide.^18,19 

The spread of C. canephora from Central Africa throughout the world is more recent. It was initially taken to Indonesia in the 20th century as a solution to the coffee leaf rust that was attacking coffee plantations since it had presented resistance to this disease.³⁰  There are many varieties of C. canephora in Africa. However, only two have been commercially disseminated throughout the world: C. canephora from Guinea, and C. canephora from Congo.²⁶  C. canephora cultivars such as Laurenti (originated in the Belgian Congo), Apoã and Guarani (produced by the Agronomic Institute of Campinas, IAC) are less important economically.^25,26 

All of the places that grow C. canephora species, as well as hybrids with C. arabica, report its introduction due to the presence of coffee leaf rust and the need for breeding programs. Additionally, C. canephora thrives in warmer regions where C. arabica varieties are not well adapted.^25,26 

Currently, coffee is cultivated in the belt between the two tropics, being widely found in the tropical regions of South America (Brazil and Colombia), Asia, Oceania, Africa, Central America and Mexico.³⁶  C. arabica species prefer annual average temperatures between 18 °C and 22 °C and tend to grow in highlands. The closer this species gets to the equator, the higher the altitude needed for optimum growth. Therefore, the optimum altitude for growth and production to achieve a quality beverage will vary according to the country or growing region. C. canephora is more suitable for intertropical lowlands and can withstand higher temperatures than C. arabica.²² 

This section covers the anatomy of the coffee plant, including the root system and aerial parts of the plant, and provides an overview of the flowering process and coffee fruit development.

Coffee plants are perennial, and the establishment of an adequate root system is fundamental to the health of the tree and its subsequent production throughout its lifetime. The root system (Figure 1.5) plays several key roles for the plant. Though often overlooked, it serves the basic function of fixing the plant in the soil or substrate. Perhaps the most widely known role is providing water to the plant. Apart from being a major constituent of plants, water acts as a solvent that serves to transport gases, minerals and other solutes from cell to cell and organ to organ; is a reactant in important processes such as photosynthesis; and maintains turgor, which is essential for cell enlargement and growth.³⁷  The root system also serves as a reserve for carbohydrates, and produces and accumulates key phytohormones such as auxins, abscisic acid and cytokines.^38,39 

It is impossible to succinctly define the root structure pattern of coffee plants since, as with all plants, it is patterned postembryonically, adapting its structure to optimize resources and respond to biotic and abiotic signals.⁴⁰  Many factors may affect the pattern of the root system and the size of the roots, including species and cultivar; physiological factors such as fruit load; vigour of the aerial part of the plant; plant reserves; pest and disease attacks; plant spacing; prunings; the chemical, physical and biological conditions of the soil; and the soil water content, among others.^39,41–44 

The aerial and root systems of the plant are directly related. Any alteration in the aerial part of the plant, such as pruning, excess fruit loads, pest attacks and diseases can lead to depletion of the root system, potentially causing root death, especially of roots with smaller diameters.^41,45  Similarly, the root system may, depending on conditions, either provide assimilates to the aerial parts of the plant, or it may act as a relatively important sink, such as during dry seasons, draining assimilates from non-fruiting and sometimes fruiting branches.⁴¹ 

Despite this variance, there are common features such as the presence of tap roots, axial roots, lateral roots, feeder roots and root hairs. In coffee, as in other dicotyledonous plants, the first root axis arises from the radicle and is called the tap root.⁴⁶  Though long lived, tap roots in coffee are generally not prominent, usually terminating at a depth no greater than 0.5 m.^39,44,47  Plants may also contain more than one tap root.^44,48  If the tap root becomes bent or twisted upon planting, this may result in a twisted or contorted condition, which may negatively affect the plant throughout its lifetime.^39,48  Because of this, many growers have adopted the practice of cutting the bottom few centimetres of the tap root before transplanting in an effort to avoid a twisted tap root. This results in removing the apical dominance of the tap root and triggers more lateral ramification.³⁹ 

Ramifications from the tap root can be divided into two types, depending on the direction of their growth. Axial roots grow vertically below the plant, generally reaching depths of around 2–3 m. Lateral superficial roots, on the other hand, grow parallel to the soil surface and usually reach depths no greater than 2 m. Lateral roots tend to concentrate under the plant skirt, but can extend outward, often interweaving with neighbouring tree roots in densely planted fields. Feeder roots of various lengths are distributed on the axial and lateral roots. The root hairs that grow on these feeders are the main providers of mineral nutrition for the plant.⁴⁸ 

Above the ground, coffee plants exhibit a dimorphic branching behaviour (Figure 1.6), in which orthotropic (vertical) stems produce plagiotropic (horizontal) branches, which in turn produce more plagiotropic branches and coffee fruit.^{30,42,44,45,49} 

The principal plant stem, or trunk, is orthotropic. There can be one or several main orthotropic stems per plant, depending on the desired plant stand. Orthotropic stems always grow vertically, or perpendicular to the soil. The apical meristem gives rise to two types of vegetative buds: serial buds and head of series buds. Serial buds on orthotropic stems form other orthotropic stems, called suckers. Head of series buds on orthotropic stems produce primary plagiotropic shoots, or branches. Each head of series bud is capable of producing only a single branch. Therefore, should the branches die (from frost, hail, over-shading, drought or other factors), it is necessary to stump the tree back, inciting the growth of new orthotropic stems, which will have new head of series buds capable of forming more primary plagiotropic branches.

Plagiotropic branches are the lateral branches, with primary plagiotropic branches originating from the orthotropic stems, and secondary and tertiary plagiotropic branches originating from other plagiotropic branches of respective orders. As with orthotropic stems, plagiotropic branches have serial buds and head of series buds. Serial buds, contained in the leaf axils, may form either fruit or more plagiotropic branches. Head of series buds only form other plagiotropic branches. Since plagiotropic branches cannot generate orthotropic stems, cuttings that will be used for plantings must originate from orthotropic stems in order to generate a normal, vertically growing tree.

The development and growth of the plant is dependent on species, variety and the environmental conditions in which the plant is situated. With C. arabica, within one year the plant typically develops six to ten levels of plagiotropic branches. After two years the orthotropic stem is usually 1.2–2 m in height, and the first flowers appear. After three years, the plant reaches maturity and usually begins to yield commercial crops.^30,48 

The foliar surface of adult coffee trees varies according to species, state of health, irradiance levels and many other factors.^48,50  In the principal commercial varieties, C. arabica and C. canephora, leaves are generally thin, shiny and waxed, elliptical in form and conspicuously veined. They typically grow in pairs that are opposite to each other on the branch. Between these two species, the main difference is that Coffea arabica leaves are smaller, with a glossy dark upper surface, while Coffea canephora leaves are often lighter in colour, less waxy, larger and slightly undulating (Figure 1.7).³⁰ 

Leaf colour varies between species and variety. For example, younger leaves of C. arabica are either light green or bronze, depending on whether the plant is of Bourbon or Typica variety in origin, respectively (Figure 1.8). The bronze colour of Typica plants fades with age.⁴⁸  Leaf coloration is generally lighter on the abaxial (lower) leaf surface compared to the adaxial (upper) leaf surface, resulting from different cutin compositions (Figure 1.9).³⁹ 

Leaves contain domatia, small cavities found in the lower epidermis. Although there is not a consensus regarding their exact function, it is possible that they play a positive role by harbouring mutually beneficial predators such as mites.^51,52  They can be used to distinguish Coffea species by comparing their size, shape, placement and the presence or absence of stomata on the outermost cell layer of the domatia.

Stomata are apertures in the epidermis, facilitating the gas exchange of the plant with the external medium. Stomatal density is a function of both the number of stomata and the size of the epidermal cells, and it varies between species and even between leaves on the same plant. Stomata are typically composed of two stomatal cells, or ‘guard cells’, with an aperture between them called the ostiole. Through this pore, the internal atmosphere within the intercellular spaces communicates with the exterior. Like other epidermal cells, stomatal cells are lined with a cuticle, which spreads down into the ostiole and lines the external wall of the substomatal chamber.

The cuticle is a waxy substance that covers the leaf and is largely impervious to liquids and gases. It is made mainly of cutin, a fatty substance that becomes oxidized and polymerized on the outer cell surface through a process known as cuticularization.⁵³  The cuticle protects the leaf against abiotic damage and provides a barrier to water evaporation. In fact, it has been estimated that only about 5% of the water lost from leaves escapes through the cuticle. Almost all of the water lost from leaves is lost by diffusion of water through the stomata.⁵⁴ 

The lifecycle of coffee leaves varies between species. C. arabica, under greenhouse (phytotron) conditions, reaches full leaf expansion after 30–35 days and maximum dry weight after 50–60 days.^54,55  The lifecycle can be divided into four stages: quiescent buds, in which the apical meristem and paired leaf primordia are covered by two firm stipules (leaf-like appendages); the emergence of the bud, where the leaves emerge by pushing apart the stipules, although they remain tightly associated to each other; lamina expansion and mechanical strengthening of the leaf; and finally senescence.^30,56 

While in equatorial regions, such as Colombia, the coffee flowering and fruit cycle may occur at various times throughout the year, in non-equatorial regions, which represent the majority of worldwide coffee production, coffee plants follow a single annual cycle of growth and fruiting.⁴² 

Coffee plant flowering consists of two distinct processes: flower bud initiation and flower opening, or anthesis (Figure 1.10). Flower bud initiation occurs when the serial buds of plagiotropic branches are induced to differentiate into flower buds. Buds grow to 4–6 mm and then enter a dormancy period, which in most growing regions coincides with a dry season.^48,57 

The dry period is necessary to break the dormancy of the floral buds. An extended dry season affects phytohormone levels in the plant. It also leads to low internal water potential which increases the unusually low hydraulic conductivity of the coffee roots, predisposing the trees to rapid rehydration following the first rains.⁴² 

During the first 3–4 days after a water stimulus, meiosis occurs and there is an increase in the levels of endogenous, active, gibberellic acid in the flower buds.⁴²  Inflorescences of both C. arabica and C. canephora are of the glomerular type, and flowers on C. canephora plants are generally more abundant and larger. The flowers are ephemeral, generally only lasting for two days. Several blossoming events can occur in each flowering season, and the greater their number and longer the spaces between them, the less uniform the coffee fruit will be upon the harvest.

The fruit of the coffee plant is typically described as a drupe: a fleshy, indehiscent fruit with a pericarp that is clearly differentiated into an exocarp, mesocarp and endocarp (Figure 1.11).^58,59  These layers surround the coffee seed, which comprises an embryo, endosperm and perisperm. How these layers develop, and their interaction during development and later post-harvest, will ultimately determine the quality and flavour profile of the coffee beverage. This development, as well as the anatomical components of a mature coffee fruit, are discussed in this section.

The time from flowering to the completion of fruit maturation varies greatly between species and is dependent on factors such as genotype, climate and cultivation practices. In general, the maturation times for several species are around 80–90 days for C. racemosa, 220 days for C. arabica, 300 days for C. canephora and 360 days for C. dewevrei and C. liberica.⁶⁰ 

Despite these differences in maturation times, key steps in fruit development among commercial species appear to be identical and can be divided into five stages.^45,59  The first stage generally occurs for the first six to ten weeks after flowering in C. arabica, although fruits may enter into a latent state for up to 60 days after pollination.⁶¹  This stage is one of limited fruit growth and is commonly referred to as the ‘pinhead’ stage (Figure 1.12).^42,45,48  The growth that occurs in this stage is mainly through cell division, not cell expansion.

The second stage, generally lasting from 6 to 16 weeks after flowering in arabica, is the rapid swelling stage, characterized by a rapid increase in volume and dry weight, mostly due to pericarp growth. Unlike the first stage, this second stage is dominated by rapid cell expansion. Fruit locules swell to full size through the growth of the transient perisperm, which will later be consumed by the endosperm as it fills the locules in future stages.^59,61  Endocarps, which will line the locules, begin to lignify. The size to which the locules swell depends greatly on the water status of the plants during this period; fruits that expand during wet weather become larger than fruits that expand in hot, dry weather.⁴² 

After this rapid growth, the fruit enters the third stage, which is one of suspended and slow growth and lasts for only two weeks. In this stage, though the final fruit size is obtained, the amount of dry matter is still low.⁴⁵ 

In the fourth stage, the endosperm fills in the locules, consuming all but a small amount of the perisperm that had previously occupied this space.⁵⁹  The remnants of the perisperm will become the silverskin that comes off as chaff when the coffee is eventually roasted. In arabica, this stage generally occurs between 17 and 28 weeks after flowering.⁴⁵ 

The final stage of development is the ripe stage. Changes in this stage occur mostly in the pericarp, in particular an increase in the dry weight, the breakdown of the mesocarp leading to a softening of the fruit and the change in colour of the exocarp from green to red, yellow or in some cases pink or orange, depending on the flavonoid compounds associated with the genotype.

Knowledge of the anatomical aspects of the coffee fruit is relevant to determine how interactions between the anatomical components impact coffee quality, as well as to accurately study how quality can be maximized both during fruit development and in removing and drying the bean. The mature coffee fruit consists of a pericarp, comprising the outer layers of the coffee fruit (exocarp, mesocarp and endocarp) and the seed, comprising the embryo, endosperm and silverskin (Figure 1.13).^47,58 

Exocarp – The exocarp or epicarp, commonly called the skin or peel, is the outermost tissue of the coffee fruit. It is composed of a single layer of compact, polygonal parenchyma cells.^47,58  The exocarp is green for most of the fruit’s development. Toward the end of maturation, chlorophyll pigments disappear, and after a transient yellow phase, the exocarp cells accumulate anthocyanin, bringing on a red coloration that can range from pink to burgundy. In the case of yellow fruit, leucoanthocyanin replaces anthocyanin, allowing exposure of the yellow pigment luteolin.⁶² 

Mesocarp – The mesocarp, also called the mucilage or ‘pulp’, is the fleshy part of the fruit between the parchment and the skin. In some literature, it is referred to as the ‘true pulp’,⁵⁹  and in other literature it is divided into an inner mesocarp, called mucilage, and an outer mesocarp, which is called the pulp per se.⁶³  However, popularly speaking, the part called pulp is the exocarp, the part of the mesocarp that is removed during the pulping process.

It is formed by parenchyma cells and vascular bundles and in general accounts for around 29% of the mass of the dry fruit.⁶⁴  Increases in altitude lead to higher concentrations of dry matter in the mucilage.⁵⁸  The mesocarp is hard in unripe coffee fruit. As the coffee matures, pectinolytic enzymes break down pectin chains, resulting in a hydrogel that is insoluble and rich in sugars and pectins. This difference is fundamental in the pulping process as it allows for the separation of unripe and ripe fruit.

Endocarp – The endocarp, more commonly called the parchment, is composed of sclerenchyma cells and completely envelops the seed. It is mostly composed of cellulosic material.⁶⁵  The endocarp is formed by 5–6 layers of intercrossing fibres, which give it extraordinary strength.⁴⁷  While it serves to protect the seed from mechanical damage, it is a barrier to both the transfer of chemical compounds from the pericarp to the endosperm, and the removal of water from the coffee seed during drying. It also acts as an impediment to germination, perhaps through mechanical resistance.⁶⁶  Nonetheless, the parchment is usually not removed since it is recommended to store coffee in parchment (or dried fruit pods), and the hulling process to remove the parchment can damage seeds, negatively impacting germination.³⁹ 

Seed – Coffee seeds are generally elliptical and plane-convex in shape, with a longitudinal furrow on the plane surface. They comprise the silverskin, endosperm and embryo.

The silverskin, also called the perisperm or spermoderm, is the outermost layer of the seed and is composed of sclerenchyma cells. It is thought to serve in the accumulation and transport of biochemical compounds from the pericarp to the endosperm, although exactly which compounds are transferred and how this occurs is not well known.^59,61  As the fruit matures, the perisperm is consumed by the growing endosperm, and transforms into a thin pellicle that may become partially detached upon drying in C. arabica. This difference in adherence, as well as the colour of the silverskin after the coffee has dried, are used to determine the presence of immature coffee beans in several classification protocols.^67,68  In C. canephora the silverskin is adherent and brown.

The endosperm is the principal reserve tissue for initial plant growth after germination. It is a living tissue that is formed by the fusion of one spermatic nucleus and two polar nuclei, resulting in a triploid (3n) tissue.^47,65  Initially a liquid milky-coloured tissue with thin cell walls, as the coffee fruit develops, its cell walls thicken due to the deposition of complex polysaccharides. These thick and partially lignified cell walls do not present intercellular spaces, but are crossed by many plasmodesmata, which establish connections between these cells and play a key role in the transport of water and other substances.⁶⁹  The external part of the endosperm is composed of small polygonal cells that are rich in oils, and it is sometimes called the ‘hard endosperm.’ The internal part of the endosperm, sometimes referred to as the ‘soft endosperm’, is composed of larger rectangular cells with slightly thinner cell walls.^47,59 

The embryo is small (3–4 mm long in C. arabica), composed of a hypocotyl attached to two cotyledons, and localized close to the convex surface of the seed (Figure 1.14).^39,47,48  It contains few storage reserves and is therefore dependent upon the endosperm for nutrients during its initial growth.

The authors acknowledge the financial support and scholarship from the Coordination for the Improvement of Higher Education Personnel (CAPES); National Research Council (CNPq), Brazil; Carlos Chagas Filho Foundation for Research Support in the State of Rio de Janeiro (FAPERJ), Brazil; and Dr Aymbiré Fonseca, Pedro Malta Campos and Thompson Owen from Sweet Maria's Coffee for generously providing photos for this chapter.