Finding the gene that makes tomatoes pink

Attachment: Finding the gene that makes tomatoes pink.xlsx (please download the file, don't use the preview) 


Most of the tomato fruits sold in Europe have red ripe fruits (Figure 1A). Fruits with pink pigmentation (Figure 1B) are the most commonly consumed tomatoes in Asia. The red colour of tomato fruits is determined by a combination of two pigments: (i) the carotenoid lycopene, which has a pink colour and an unknown pigment of yellow colour (Figure 1C). The peel of pink tomatoes is lacking the yellow pigment and, therefore fruits looked more pink compared to the red tomatoes (Figure 1A, B). The pink mutation has already been described in 1925 and the underlying mutation was called y (yellow). Old classical genetic studies revealed that the pink colour is determined by a mutation in a single recessive gene on chromosome 1, but for many years the nature of this gene and the biochemical basis for the yellow pigment was unknown. Dutch breeders want to enter the enormous Asian tomato market with their varieties. However, it is absolutely required to have a pink fruit colour in order to be successful. Therefore, they would like to start breeding programs in which they would select for pink fruited tomato cultivars. In principle, this selection can be done by simply screening for fruit colour. However this approach takes a long time because breeders have to wait for a few month till fruit will ripe.

Figure 1 (click to enlarge). Phenotype of red and pink tomato fruits. A. Red fruits and red peel; B. Pink fruits and pink peel; C. Schematic representation of how tomato fruit colour is determined by pigment combinations.

Modern breeding makes use of molecular markers to select for traits of interest at an early stage. A molecular marker is created using DNA differences (polymorphisms) which are linked (very closely located) with the actual gene that causes the phenotype (e.g. fruit colour). There are two major advantages of molecular markers in breeding: (1) A marker that is tightly linked to a phenotype that appears in fully mature plants, like fruit colour, allows you to predict and select for this phenotype at the seedling stage already and grow mature plants from the selected seedlings only and (2) a genetic marker, once established, can replace the use of difficult phenotyping procedures. The success of a molecular marker depends on how close the molecular marker is located in the genome to the actual gene that causes the phenotype: the further away the marker is from the gene (genetically), the higher the chance of recombinations between the marker and the gene, which may lead to errors in phenotype prediction. Therefore, a DNA polymorphisms found in the causal gene underlying your phenotype of interest is the best possible genetic marker. Thus the main aim of this assignment is to find the gene that causes either red or pink pigmentation of tomato fruit.


Part 1:  The use of an introgression line population to determine the physical position of the y locus for pink fruit colour

Part 2:  The use of biochemical information to find the metabolic basis for pink fruit colour

Part 3:  Combining the information to find the causal gene for pink fruit colour