Lost Tomato Flavors Regained.

biopicThis is a guest post by Arif Ashraf. 

Arif Ashraf is PhD student at Iwate University, Japan and Graduate Student Ambassador of ASPB. His research interest is understanding the hormonal interplay in primary root development of Arabidopsis. He blogs about plant science at

Lost Tomato Flavor

Tomatoes show up in a lot of our daily food items, from salad to pizza and more. From their South American origin, tomatoes have become popular worldwide due to their nutritious value and flavor. According to scientists, however, modern commercial tomato varieties are inferior with respect to flavor compared to heirloom, open-pollinated varieties. Thanks to a January 2017 report in Science Magazine from Tieman et al., better tomatoes both for producers and consumers may be possible.

Figure 1: Heirloom tomatoes (Source: Recipe Geek)

The popular scientific question is: Why do modern tomato varieties stink? This question was answered in another Science Magazine paper published in 20121.

Traditional breeders focused on large-scale production and convenience. During that selection process, breeders picked up one variety and bred it with many other varieties, because it gives a uniform, luscious, scarlet when ripe. The iconic red tomato phenotype makes it easier for farmers to pick ripe tomatoes. According to Tieman et al., modern tomato (Solanum Lycopersicum) varieties are bred with a loss of the uniform ripening (u) gene variety. Light green fruit phenotypes at first least to a harvest of uniformly ripened tomatoes. The U gene encodes a Golden 2-like (GLK) transcription factor (a protein involved in switching other genes on or off), SIGLK2, which determines how much chlorophyll accumulates and its distribution in developing fruit – tomatoes start out life green. In tomato, two GLKs – SIGLK1 and SIGLK2 – are expressed in leaves, but SIGLK2 is exclusively expressed in tomato fruits. Expressing either GLK in the fruit through genetic engineering increased fruit chlorophyll content whereas SIGLK2 suppression showed the u flavorless red tomato phenotype. GLK overexpression enhanced fruit photosynthetic components’ gene expression and chloroplast development (where photosynthesis takes place), leading to elevated sugars and carotenoids in ripe fruit. SIGLK2 influences photosynthesis in developing fruit, contributing to mature fruit characteristics and suggesting that selection of u mutant inadvertently compromised ripe fruit quality in exchange of desirable production traits1 . This example is the story of how we lost interesting tomato flavor specific loci (genes) through the generation of breeding practice.

Reviving Tomato Flavors

Food flavor is the combination of taste and olfaction. In the case of tomato, sugars and acids activate taste receptors, and several volatile compounds activate our olfactory receptors. Flavor-associated volatiles are present at low picomolar (one 10 billionth of a mole) to nanomolar (one billionth of a mole) concentrations in fruits are why it is extremely tough to quantify them. Continuous ignorance for profiling volatile and immense emphasis on yield accelerates the process of losing these desired flavor traits during the breeding. In the January 2017 Science paper, Tieman et al. took both chemical and genetic approaches together to find specific volatile compounds and responsible loci2. They identified the most important chemical contributions based on consumers’ preference, and tried to understand what has been lost from modern varieties and the mechanism of why those chemicals were lost.

Figure 2: Cover of Science Magazine about lost flavor of tomatoes

Tieman et al. examined 398 varieties of tomatoes including modern, heirloom, and wild accessions. The idea of including wild varieties was to help the scientists understand if         flavor-related volatiles remained unaltered through breeding programs. Firstly, they identified chemicals most preferable to consumers. Then they divided examined tomato varieties into two groups – modern and ancient cultivars – to identify any lost chemicals in modern varieties. They found 13 volatiles were significantly reduced in modern tomato varieties compared to their ancient counterparts.

Next, Tieman et al. focused on the genetic basis of lost flavor chemicals. Through changes in DNA, like the mutation of U (u described above), we have already demonstrated the power of single base mutations and how this single base-pair change got incorporated through breeding. The major differences among varieties lay in single base mutations, also known as Single Nucleotide Polymorphism (SNP). Due to advances in modern sequencing technologies, we can easily sequence genomes of different accessions to find SNPs and compare them. Through these comparisons, it helps scientists find some loci with unique SNPs compared to other accessions. This kind of study is popular for deciphering phenotypes dependent on multiple genes or studying natural variations/accessions are known as Genome-Wide Association Study (GWAS).

By GWAS, two important loci (gene locations) have been identified on chromosomes 9 and 11 of the tomato genome. These loci were previously known to be important during domestication and modern varieties contain a combination of versions of these genes (alleles in scientific parlance) resulting in less sugar content. For example, the gene on that particular position of chromosome 9 is known as Lin5 and encodes extracellular invertase. In Lin5, a single base mutation causes a change in one of its constituent parts, an amino acid residue at position 336 from Asn (Asparagine) to Asp (Aspartic acid). The transgenic plant over-expressing the ancient version containing the aspratic acid at position 336 of the enzyme produces more sugar. However, there is a negative correlation between fruit size and sugar content. Bigger fruit, less sugar. As a result, during domestication, farmers were concerned about fruit weight and picked up varieties containing larger fruits. By going for bigger fruit, they unintentionally lost the high-sugar alleles.

The Tale of Two Volatiles

Several loci responsible for volatiles such as geranyl acetone and 6-methyl-5-hepten-2-one (MHO) were found. These two volatile compounds are known as apocarotenoids and are usually products of carotenoid oxidation. For instance, geranyl acetone is produced due to oxidation of phytoene, phytofluene, carotene, and neurosporene. This volatile has no color, an attractive smell, and is safe for human health. It has been used in creams, soaps, and a flavoring agent in food. Carotenoids are known as color pigments and volatiles come from an oxidation event of carotenoids. So, a high amount of volatiles may cause a less attractive color tomato. In the case of geranyl acetone, precursor carotenes are present in a smaller amount in the plant and doesn’t affect the color of ripening tomato. At the same time, its smell is popular with consumers.

The other mentioned volatile, 6-methyl-5-hepten-2-one (MHO), is generated by oxidation cleavage of lycopene. First, lycopene has a major contribution in pigmentation of ripening fruit. Due to its intense color, lycopene is used as coloring agent in food. Generally animal systems lack the capability of producing carotenoids. But, these compounds have antioxidant capacity and are precursors of Vitamin A. That’s why we get carotenoids from dietary sources. Tomato varieties containing more lycopene gives a nice red color. So, farmers love to pic those varities during selection process. At the same time, increased amount of lycopene ensures more oxidation and elevated level of 6-methyl-5-hepten-2-one (MHO) prodcution. It has already been found in apple that 6-methyl-5-hepten-2-one (MHO) is linked to moldy, musty and an off-odour3 . In the 2017 Science paper, the authors have identified the responsible loci for 6-methyl-5-hepten-2-one (MHO) and geranyl acetone and showed that modern varieties contain more 6-methyl-5-hepten-2-one (MHO), but less geranyl acetone, resulting in a less tasty tomato.

Better Tomatoes Ahead

This article provides a comprehensive insight about our modern tomato varieties and how we lost high sugar and desirable volatile genes in the quest of larger and deep-red colored ripe tomatoes. Precise identification of loci and chemical composition provide guidelines for creating better tomatoes. With recent genome editing techniques such as CRISPR/Cas9, it’s possible to modify an exact position in the genome to get back our desired high sugar or volatile genes and develop tomato varieties that are sweet, flavorful, and high yielding.


  1. Uniform ripening Encodes a Golden 2-like Transcription Factor Regulating Tomato Fruit Chloroplast Development
  2. A chemical genetic roadmap to improved tomato flavor
  3. Mouldy, Mutzu, Earthy off-odour compounds in “Golden Delicious” apple fruit skin


One thought on “Lost Tomato Flavors Regained.

  1. Interesting about the negative correlation between size and sugar content. I guess this also explains why the sweetest cherry tomato varieties are far sweeter than any slicer varieties. Thanks.


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