2.3 Exchange, performed classically. Casus.

A research group wants to determine the influence of different Brassica nigra genes (BB) on the flowering time in Brassica juncea. B. juncea is a hybrid (AABB) of B. nigra (diploid, BB) and B. rapa (diploid, AA). A or B refers to one copy of a genome. The research group phenotyped a selection of 2000 B. juncea plants for flowering times. These B. juncea plants were generated from the same B. rapa (AA) parent, but different B. nigra (BB) parents. The research group has invited representatives of different sequencing companies to discuss the possibilities for identification of B. nigra genes that correlate with flowering time. All companies like to be hired.

The students from group 4 and 5 represent the research group. The students from group 1, 2 and 3 represent three different companies that want to be hired. Group 1 represents an Illumina platform, Group 2 represents a PacBio platform, and Group 3 represents a Bio Nano optical mapping platform.

If a single company knows a way to solve the problem it will earn 50.000 Euros. If two companies work together they will each earn 30.000 Euros. If they share the order between the three of them, they will each earn 20.000 Euros. It is therefore attractive for a company to see if they can perform the task alone. However, they must be able to deliver a good result, either alone or shared. If they fail they will not earn any money, but still pay the costs they made.

Discuss the information that is needed to answer the research question, and which company or combination of companies can provide the necessary information. Think of aspects like phasing, chromosome assembly, and genetic markers. Remember that whole genome sequencing of 2000 plants is not feasible.