Part 6 Linkage analysis

To find linkage between SNPs and whitefly resistance a segregating population of 324 plants was analyzed. To find the most linked marker (and automatically the localization of the markers and the resistance trait on the genome) all 324 F2 plants were genotyped with a large number of SNPs. The most linked marker(s) can later be used in Marker Assisted Breeding.

Also, the 324 plants were fenotyped and their resistance level was determined with a clip-on cage test. Five clip-on cages were used per plant, after three days the number of living whiteflies were counted and removed and ten days later the number of eggs was counted. Additionally the number of type IV trichomes was counted per cm² leaf.

As an example the results of 24 plants are given below.

Open

The Excel file: 'linkage analysis whitefly calculation.xlsx' can be used to calculate adult survival and oviposition rate for 24 plants and 24 SNPs.  Please download the file, don't use the preview. The experimental data are given under each individual leaf disc. For finding the best linked marker use the sort option in Excel.

We use only 24 plants but actually it should be done with all 324 F2 plants. But then software solutions are needed.

Questions Linkage analysis

6.1          Calculate adult survival and oviposition rate of each plant.

6.2          Is there a relationship between the occurrence of trichome Type IV and resistance?

In the excel file (linkage analysis whitefly no answers) these 24 plants have been scored with 24 SNP markers.

6.3          Which of these SNP markers is linked to adult survival?

6.4          Is this SNP only linked to adult survival (AS)?

6.5          One of the plants is completely like one of the parents, how is this possible?

6.6          What can be the reason that SNP patterns of two plants are identical?

6.7          What is the reason that two SNPs segregate identical (identical means that they have the same scores for the 24 plants)?