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The genetics of fruit flavour preferences


Intensively bred fruit crops, including tomatoes and strawberries, are widely viewed as lacking flavour. The lack of breeder focus on the consumer is largely due to the genetic complexity of the flavour phenotype as well as a lack of a simple assay that can define consumer preferences. Rapid advances in genomics have opened up new opportunities to understand the chemistry and genetics of flavour. Here, we describe the underlying causes for the loss of flavour in fruits over time and delineate a blueprint for defining the chemistry of consumer liking, reducing that knowledge into a molecular roadmap for flavour improvement.

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The tomato work performed by the authors and described here was supported by grants from the US National Science Foundation as well as an endowment provided to the University of Florida by the Lyle Dickman family.

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The authors contributed equally to all aspects of the manuscript.

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The authors declare no competing interests.

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Correspondence to Harry J. Klee.



A plant variety that has been produced in cultivation by selective breeding for desirable characteristics.

Molecular breeding

A process broadly encompassing all aspects of molecular biology, including genetic engineering and genome editing, but more narrowly defined as the use of large-scale genomic data to define genetic differences between individuals in a breeding population. These polymorphisms are used to develop genetic markers that facilitate the rapid selection of cultivars with desired traits.

Genome-wide association studies

(GWAS). Association mapping of a phenotype in a population with whole-genome DNA polymorphisms.

Volatile organic compounds

Organic compounds that have a high vapour pressure at room temperature. High vapour pressure allows the chemical to partition into the gas phase. Volatile organic compounds are important contributors to flavour when they vapourize in the mouth and travel to the olfactory epithelium where they are recognized by specific sets of receptors.

Principal component analysis

A statistical method that is used to simplify a complex data set by transforming a series of correlated variables into a smaller number of uncorrelated variables called principal components.

Retronasal olfaction

The sensory modality responsible for flavour. Perception of volatiles generated within the mouth and transmitted to the olfactory epithelium.

Linkage drag

A negative effect on some aspect of quality or plant performance upon backcrossing a gene into a different cultivar. Typically refers to negative effects associated with genes physically linked to the gene of interest. A particular problem when introgressing a trait (such as disease resistance) from a different sexually compatible species.

Introgression lines

(ILs). A genetic line that contains a gene or region of a chromosome from one species in the genome of another. It is created by repeated backcrossing of an interspecific hybrid with one of its parents.

Heirloom varieties

Older varieties that have been maintained for some desirable attribute (for example, flavour, colour and shape). Although there is no legal definition of ‘heirloom’, it is generally considered to be inbred. Heirlooms usually lack the performance and disease resistance found in modern cultivars.

Quantitative trait locus

(QTL). A region of a chromosome that quantitatively influences a measured phenotype. That region, defined by polymorphic molecular markers, contains one or more physically linked genes causative of the phenotype.

Selection bottleneck

A substantial enrichment for a specific subset of genes with reduced allelic variation relative to the variation found in a species. Loss of diversity through intensive breeding with a small population.


Recurrent crossing to a parental variety in order to introduce specific genetic loci into an otherwise isogenic line.

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Further reading

Fig. 1: Synthesis pathways for tomato flavour volatiles.
Fig. 2: Identification of a locus controlling synthesis of phenylalanine-derived volatiles.
Fig. 3: Average changes in flavour-associated chemicals in modern tomato varieties.
Fig. 4: A roadmap for consumer-assisted genetic selection.