The Science of Tomato Flavors

Don’t judge a tomato by its appearance. You may salivate when thinking about the luscious large red tomatoes you just purchased in your grocery store, only to find out that they are extremely bland and lack flavor once you actually bite into them after preparing the salad you had been looking forward to all day. You are not alone. Many consumers complain about the growing blandness of fruits. Up until a few decades ago, it was rather challenging to understand the scientific basis of fruit flavors. Recent biochemical and molecular studies of fruits now provide a window into fruit flavors and allow us to understand the rise of blandness.

In a recent article, the scientists Harry Klee and Denise Tieman at the University of Florida summarize some of the most important recent research on the molecular biology of fruit flavors, with a special emphasis on tomatoes. Our perception of “flavor” primarily relies on two senses – taste and smell. Taste is perceived by taste receptors in our mouth, primarily located on the tongue and discriminates between sweet, sour, salty, bitter and savory. The sensation of smell (also referred to as “olfaction”), on the other hand, has a much broader catalog of perceptions. There are at least 400 different olfactory receptors present in the olfactory epithelium – the cells in the nasal passages which perceive smells – and the combined activation of various receptors can allow humans to distinguish up to 1 trillion smells. These receptors are activated by so-called volatile organic compounds or volatiles, a term which refers to organic molecules that are vaporize in the mouth when we are chewing the food and enter our nasal passages to activate the olfactory epithelium. The tremendous diversity of the olfactory receptors thus allows us to perceive a wide range of flavors. Anybody who eats food while having a cold and a stuffy nose will notice how bland food has become, even though the taste receptors on the tongue remain fully functional.

When it comes to tomato flavors, research has shown that consumers clearly prefer “sweetness”. One obvious determinant of sweetness is the presence of sugars such as glucose or fructose in tomatoes which are sensed by the taste receptors in the mouth. But it turns out that several volatiles are critical for the perception of “sweetness” even though they are not sugars but instead activate the smell receptors in the olfactory epithelium. 6-Methyl-5-hepten-2-one, 1-Nitro-2-phenylethane, Benzaldehyde and 2-Phenylethanol are examples of volatiles that enhance the positive flavor perceived by consumers, whereas volatiles such as Eugenol and Isobutyl acetate are perceived to contribute negatively towards flavor. Interestingly, the same volatiles can have no effect or even the opposite effect on flavor perception when present in other fruits. Therefore, it appears that for each fruit, the sweetness flavor is created by the basic taste receptors which sense sugar levels as well as a symphony of smell sensations activated by a unique pattern of volatiles. But just like instruments play defined yet interacting roles in an orchestra, the effect of volatiles on flavor depends on the presence of other volatiles.

This complexity of flavor perception explains why it is so difficult to define flavor. The story becomes even more complicated because individuals have different thresholds for olfactory receptor activation. Furthermore, even the volatiles linked with a positive flavor perception – either by enhancing flavor intensity or letting the consumer sense a greater “sweetness” then actually present based on sugar levels – may have varying effects when they reach higher levels. Thus, it is very difficult to breed the ideal tomato that will satisfy all consumers. But why is there this growing sense that fruits such as tomatoes are becoming blander? Have we simply not tried enough tomato cultivars? A cultivar is a plant variety that has been bred over time to create specific characteristics, and one could surmise that with hundreds or even thousands of tomato cultivars available, each of us might identify a distinct cultivar that we find most flavorful. The volatiles are generated by metabolic enzymes encoded by genes and differences between the flavor of distinct cultivars is likely a reflection of differences in gene expression for the enzymes that regulate sugar metabolism or volatiles generation.

The problem, according to Klee and Tieman, is that the customers of tomato breeders are tomato growers and not the consumers who garnish their salads or create tomato-based masalas. The goal of growers is to maximize shelf-life, appearance, disease-resistance, yield and uniformity. Breeders focus on genetically manipulating tomato strains to maximize these characteristics. The expression GMO (genetically modified organism) describes the use of modern genetic technology to modify individual genes in crops and often provokes a litany of attacks and criticisms by anti-GMO activists who fear potential risks of such genetic interventions. However, the genetic breeding and manipulation of cultivars has been occurring for centuries or even millennia using traditional low tech methods but these do not seem to provoke much criticism by anti-GMO activists. Even though there is a theoretical risk that modern genetic engineering tools could pose a health risk, there is no scientific evidence that this is actually the case. Instead, one could argue that targeted genetic intervention may be more precise using modern technologies than the low-tech genetic breeding manipulations that have led to the creation of numerous cultivars, many of whom carry the “organic, non-GMO” label.

Klee and Tieman argue that consumers prefer flavor, variety and nutrition instead of the traditional goals of growers. The genetic and biochemical analysis of tomato cultivars now offers us a unique insight into the molecular components of flavor and nutrition. Scientists can now analyze each cultivar that has been generated over the past centuries using the low-tech genetic manipulation of selective breeding and inform consumers as to their flavor footprint. Alternatively, one could also use modern genetic tools such as genome editing and specifically modify flavor components while maintaining disease-resistance and high nutritional value of crops such as tomatoes. The key to making informed, rational decisions is to provide consumers comprehensive information based on scientific evidence as to the nutritional value and flavor of fruits, as well as the actual risks of genetically modifying crops using traditional low tech methods such as selective breeding and grafting or newer methods which involve genome editing.


Klee, H. J & Denise M. Tieman (2018). The genetics of fruit flavour preferencesNature Reviews Genetics, (published online March 2018)

Note: An earlier version of this article was first published on the 3Quarksdaily blog.


To Branch, Or Not To Branch – Plant Hormones Help Turn A Stem Into A Bush

When we hear the expression “stem cells”, we tend to think of cells from animals or patients that are used to treat diseases or promote regeneration. However, stem cells are also present in plants. The growing tips of plants are called meristems and they are reservoirs of plant stem cells. A meristem is formed at the base of each leaf and can remain dormant as a small bud or be activated and give rise to a whole new branch. Gardeners know that pruning leaves can activate the buds and help transform a single stem plant into a multi-branched bush, but the exact mechanisms that govern branch formation are not fully understood.


The recent paper “Strigolactone Can Promote or Inhibit Shoot Branching by Triggering Rapid Depletion of the Auxin Efflux Protein PIN1 from the Plasma Membrane” published in PLOS Biology by Naoki Shinohara and colleagues has uncovered an important novel pathway that regulates the formation of branches in plants. The researchers based their work on an existing model which states that the plant growth hormone auxin is a central regulator of branch formation. Auxin levels are highest in activated buds because this is where auxin is produced. Auxin then flows to the roots, where auxin levels are low (“auxin sinks“). The removal of auxin from the activated bud allows for further auxin production and thus creates a continuous auxin flow pattern. This is thought to establish a positive feedback loop for the activated bud, which then ultimately results in the formation of branch emanating from the activated bud. This model is called the “auxin transport canalization” and is explained in an excellent accompanying article “Transforming a Stem into a Bush” by Amy Coombs, also published in PLOS Biology.

Once an activated bud initiates the positive auxin feedback loop, it also becomes necessary to inhibit the branch formation from other buds. If all the buds in a plant started making branches at once, the plant’s resources would probably become depleted very quickly, possibly resulting in the chaotic formation of too many suboptimal branches. There is a clearly a need for a system that allows some activated buds to go on to make branches, while putting the brake on other buds so that they bide their time. The details of such a fine-tuned balance of selected activation and inhibition have been a bit of a mystery, but the work by Shinohara and colleagues is a major step forward in unraveling this puzzle.

The researchers show that the plant hormone strigolactone removes the auxin export protein PIN1 from the cell surface and increases its degradation. Therefore, a plant without strigolactone would have more PIN1, sustain greater auxin flux and thus increase branching. Genetically engineered plants that do not produce strigolactone did indeed show more branch formation. When the researchers added back synthetic strigolactone (called GR24), they were able to suppress the excessive branch formation. However, the researchers also obtained a somewhat counter-intuitive result: When they gave GR24 to plants with defective auxin transport, low doses of GR24 actually helped branch formation and only higher doses suppressed branch formation. The problem with these results is that the synthetic strigolactone also severely impacted the general growth of the plants (not just branch formation) in the auxin transport mutants, and it is difficult to interpret whether the subtle differences between low and high doses were just generalized effects due to reduced overall plant health or whether they were truly related to aberrant branching.

The oddly opposite results obtained with low dose and high dose GR24 treatment are probably going to raise some controversy, and as Amy Coombs pointed out, not all scientists agree with the auxin transport canalization theory of branch formation in plants. This is not the first study to propose an interaction between strigolactone and auxin as regulators of plant branch formation, but it is one of the most comprehensive papers in this area. It includes a mathematical model of the interaction between these two regulators, tests the model with experiments and identifies a novel cellular mechanism for how strigolactone reduces PIN1. These results do suggest that plants have a very finely-tuned system involving at least two hormones, auxin and strigolactone, that act together to promote branch formation in some buds, while suppressing bud formation in others. As a stem cell biologist who works with mammalian stem cells, I am quite intrigued by this fascinating interplay between activating and suppressing hormones in plants that permit a self-organized branch formation. In mammals, we still do not fully understand how during development, some embryonic stem cells commit to one lineage and form organs such as a heart, while also preventing other stem cells in the developing embryo to form a second or third heart in other areas. It is quite likely that developing mammalian embryonic stem cells also depend on positive feedback loops and inhibitory systems, similar to what the researchers found in the plants. Many major discoveries in cell biology and molecular biology are first made in plants and we then discover similar principles of regulation in animals and humans.


Image credit: Panel from Figure 5 of the PLOS Biology (2013) paper by Shinohara N., et al, Green indicates the PIN protein and magenta shows the autofluorescence of chloroplasts

Shinohara, N., Taylor, C., & Leyser, O. (2013). Strigolactone Can Promote or Inhibit Shoot Branching by Triggering Rapid Depletion of the Auxin Efflux Protein PIN1 from the Plasma Membrane PLoS Biology, 11 (1) DOI: 10.1371/journal.pbio.1001474