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

Wild relatives of tomato have often been used as a source of interesting traits, e.g. resistances, for the improvement of cultivated tomato. However, when you cross a wild and a cultivated tomato, not only the beneficial traits are transmitted to the offspring, also many undesirable traits are transferred. Actually, the more wild DNA is present, the higher the chance that the fitness of your offspring is hampered. To avoid this problem, it is possible to make so-called introgression line (IL) populations. These populations are based on a cross of two parents: (i) a wild donor species and (ii) an elite cultivated tomato line, followed by several rounds of backcrossing with the elite parent. By using molecular markers one can select for lines having only one or a few chromosomal introgressions from the wild donor in a cultivated background (Figure 2). All together, the lines of the IL population represent the entire genome of the wild donor. Since the introgression lines are mostly homozygous, they are stable and can be propagated by seed. By comparing the phenotype of an introgression line with that of the cultivated parent, one can easily attribute any change in phenotype to a specific chromosomal introgression(s) present in this IL, or more specifically to genes present in these introgressions. This makes introgression lines useful material to find which genes are responsible for plant phenotypes.

Open

Figure 2. An example of three introgression lines (ILs) (Click to enlarge)

In worksheet IL of the Excel file you see an example of an IL population based on a cross of the wild tomato relative Solanum chmielewskii and the elite tomato cultivar Moneyberg. A set of 1556 SNP markers was used to characterise this population. The markers and their physical position are depicted in columns 1 and 2: AA represents the genotype of Moneyberg, BB represents the genotype of S. chmielewskii. The names of the 49 introgression lines are shown in row 2. Column D and E show the marker scores for Moneyberg (AA, white) and S. chmiel. (BB, dark green), and each of the remaining columns reveals the genetic make-up of the ILs. When you zoom out the worksheet you will see all the introgressions (in green) in each of the individual lines. Homozygous introgressions are depicted in dark green, whereas heterozygous introgressions in light green. Missing values are drawn as NC. As you can see, some lines have a single homozygous introgression, others have a few and some have both homozygous and heterozygous introgressions. The name of the lines refers to the position of the main introgression of such a line. So, the main introgression in Line 1a is on the top of chromosome 1, the main introgression of line 6d is at the bottom of chromosome 6.

• Q1: Zoom the excel sheet out until you see all introgression lines on the screen. Now scroll down to see all the introgressions present in the population. Do we cover the entire genome of S. chmielewskii in this population? If no, which parts are missing?

• Q2: Please give your idea why we do not have introgression lines which contain introgressions from the wild species in these regions?

• Q3: Row 1 presents the fruit colour of each introgression line. (a) Which introgression regions are in common between all the pink lines? (b) Which region is unique for the pink lines and which markers form the borders of this region? (c) What do you conclude from this observation with respect to the gene for pink fruit colour? (d) What is the size of this region? (e) which proportion of CH1 does the QTL region for pink fruit colour represent?

• Q4: Worksheet CH1 genes lists all the 3441 genes present on chromosome 1 of tomato. How many genes are present in the introgression region for pink fruit colour? Any idea which gene might be responsible for pink fruit colour?