Variation in the Number of Beans per Coffee Cherry: Botanical Bases and Estimates for Coffea arabica in Colombia

Introduction

The coffee cherry, the fruit of the genus Coffea, is a drupe that under normal conditions contains two seeds: the coffee beans. Botanically, Coffea is a dicotyledonous plant: its embryo has two cotyledons, and each seed that we roast and grind corresponds to the hard endosperm surrounding that embryo. However, in farm practice and post-harvest processing, variations are observed: cherries with a single bean (caracolillo or peaberry) and, much more rarely, cherries with three beans.

This document explains, based on botanical and embryological principles, why the coffee cherry usually behaves as a “dicotyledon” (two beans) and under what conditions monocotyledon-like (one bean) and tricotyledon-like (three beans) forms appear, including a percentage-based estimation for Coffea arabica in the Colombian context.

1. Basic botany of Coffea and the role of cotyledons

Commercial coffee species (mainly Coffea arabica and Coffea canephora) belong to the group of dicotyledonous angiosperms. The seed embryo has two cotyledons; however, in green coffee these cotyledons are surrounded by a highly developed endosperm and occupy only a small portion of the seed.

The green coffee bean that is commercialized is essentially endosperm rich in cell wall polysaccharides (mannans, galactomannans, arabinogalactans), sucrose, lipids, and phenolic compounds (including chlorogenic acids).

The coffee fruit is a drupe composed of an exocarp (skin, red, yellow, or other colors depending on the variety), mesocarp (pulp), endocarp (parchment), and inside it, one or more seeds surrounded by the silver skin (spermoderm) and the endosperm. In the vast majority of fruits, the ovary produces two viable ovules, and the final result is two fully developed seeds within the cherry.

2. Normal fruit development: dicotyledonous cherry (two beans)

During flowering, Coffea flowers are hermaphroditic and present an inferior ovary that is typically divided into two locules. In each locule, one ovule is formed; after pollination and double fertilization, both ovules can be fertilized and give rise to two embryos, each with its own endosperm. This structure leads to the formation of two seeds per cherry.

Fruit development proceeds through several stages: fertilization and fruit set, rapid pericarp growth, and finally the endosperm filling and maturation phase. Between approximately 60 and 150 days after flowering, the endosperm of each seed expands, accumulates reserve compounds, and partially lignifies. The two seeds develop pressed face-to-face, which explains the plano–convex shape of normal beans and the central groove observed in green coffee.

Under adequate agronomic conditions, the vast majority of Coffea arabica cherries in Colombia follow this pattern: two seeds per fruit, each with a dicotyledonous embryo. When, from a farm perspective, cherries are described as “dicotyledon,” this actually refers to this pattern of two developed seeds within the drupe.

3. Monocotyledon-like cherries: caracolillos or peaberries (one bean)

In a smaller percentage of cherries, only a single seed develops. This phenomenon is known on farms as caracolillo and in international literature as peaberry. In these cases, the fruit remains a drupe, but only one of the potential ovules develops a functional embryo and endosperm. As a result, the internal space of the cherry is occupied by a single seed, which adopts a more rounded or ellipsoidal shape, lacking the flat contact surface typical of a paired bean.

From an embryological standpoint, the most common origin of peaberries is the abortion of one ovule (before fertilization) or the failure of embryo and/or endosperm development in one of the two potential seeds. In other words, the flower had the structural capacity to produce two seeds, but only one reached full development. The resulting seed is not monocotyledonous in the strict sense (the embryo still has two cotyledons), but rather a single dicotyledonous seed occupying the entire volume of the drupe.

Several factors can increase the probability of peaberry formation:

• Environmental stress during flowering and fruit set (high temperatures, drought, water imbalance).

• Pollination problems (low pollen viability, adverse conditions for fertilization).

• Genetic factors specific to certain genotypes or hybrids with greater instability in ovule and embryo formation.

• Anomalies in early cell division of the ovule or endosperm tissue.

Studies on Coffea arabica and other species indicate that peaberries represent, on average, between 5% and 7% of total harvested beans, with occasional reports reaching values close to 10% or higher under stress conditions or poor management. This aligns with post-harvest experience on many Colombian farms, where peaberry percentages typically remain within single-digit ranges.

4. Tricotyledon-like cherries: fruits with three beans

Cherries containing three beans are much rarer than peaberries. Botanically, their origin may be associated with several uncommon situations:

• Trilocular ovaries instead of the typical bilocular structure, allowing the formation of three locules with corresponding ovules.

• Polyembryony, in which a single ovule generates more than one embryo that share the internal space of the fruit.

• Anomalies in early embryonic segmentation that produce structures with more than two cotyledons or more than one recognizable embryonic unit.

In farm practice, when cherries with three beans are found, the beans are usually smaller and irregular in shape. To date, there is no robust statistical basis quantifying their exact frequency in Colombia; however, they are considered an extraordinarily rare botanical curiosity, well below 1% of cherries and likely on the order of tenths of a percent in most lots.

5. Role of the endosperm and bean structure

In all cases (two-bean cherries, peaberries, or three-bean cherries), the endosperm is the tissue that determines industrial quality. As the seed matures, the endosperm accumulates reserves (polysaccharides, sugars, lipids), and its cell wall strengthens, defining the hardness of the green bean, its density, and its behavior during roasting.

In cherries with two beans, the space is shared, and each endosperm develops in contact with the other, generating the flat face and characteristic groove of normal beans. In peaberries, the single endosperm expands without internal “competition,” adopting a more rounded shape. Recent studies have shown differences in the expression of genes related to cell wall formation and endosperm development in peaberries compared to normal beans, suggesting subtle anatomical and physical differences that may influence heat transfer during roasting.

In tricotyledon-like cherries, the presence of three small, asymmetrical seeds limits the space available for each endosperm, resulting in beans that are less uniform in size and shape. This can complicate roasting, and in general these beans are not separated as high-value microlots but are treated as curiosities or mixed with other minor morphological defects.

6. Agronomic and commercial implications

From the producer’s perspective, the presence of peaberries and tricotyledon-like cherries is part of the natural variability of the crop. However, when the percentage of anomalous beans (peaberries, floaters, immature, malformed beans) increases significantly, it may indicate agronomic problems such as water stress, inadequate nutritional management, insufficient or excessive shade, or pollination failures.

In the industry, peaberries can be separated by size and density classification, and many roasters market them as special lots due to their rarity and subtle differences in roasting behavior and sensory profile. In contrast, cherries with three beans currently have no specific market; their low frequency and association with irregular shapes make them more of a botanical curiosity than a commercial category.

7. Estimated distribution of cherry types in Coffea arabica (Colombian context)

Based on scientific literature on peaberry occurrence, studies on bean quality under different planting densities and management systems, and industry and post-harvest reports, a reasonable estimate can be proposed for the distribution of cherry types in Coffea arabica under average growing conditions in Colombia. These ranges may vary between farms depending on variety, altitude, climate, and agronomic management.

• Dicotyledonous cherry (two normal beans): approximately 90–94% of cherries.

• Monocotyledon-like cherry (peaberry / caracolillo, one bean): approximately 5–8% of cherries, consistent with internationally reported ranges of 5–7%, with higher values under stress scenarios.

• Tricotyledon-like cherry (three beans): extremely rare cases, likely below 0.5% of cherries in most commercial lots.

In a well-managed Coffea arabica lot in Colombia, a practical numerical approximation for educational and planning purposes could be, for example: 92% cherries with two beans, 7% cherries with one bean (peaberry), and 0.3% cherries with three beans—understanding that these values are referential and do not replace direct measurements on each farm.

8. Comparative table of cherry types by number of beans

Conclusion

By biological design, the coffee cherry is structured to develop two dicotyledonous seeds, but field realities introduce variation. Cherries with a single bean (peaberries) and cherries with three beans are visible expressions of embryological processes that deviated from the norm, whether due to genetic, environmental, or pollination-related factors. Understanding these variations helps producers and roasters better interpret physical coffee quality, make more informed selection and classification decisions, and build sensory and technical narratives that reflect the true biological complexity of the coffee plant.