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Community Member


Jun 2, 2014

Best way to compute genetic crosses?

I have a large number of plants that I have been cross pollinating for the past 6 months. I would like to create some way of crossing two plants (i.e. selecting one individual and then another) and record if their cross was successful, the size of the resulting fruit, and the number of seeds from each fruit. There are two species that can hybridize and each plant can be male, female, or mixed gender. Furthermore, the order of crossing is significant.

Something similar to a multiplication table would be a good way of visualization but I need to be able to extract statistics on these three results given the stated criterion. What is the best method to do this?


Community Trekker


Jun 4, 2014

Re: Best way to compute genetic crosses?

Let me give it a try and you'll tell me what you are after. My example has 10 plants. Each plant has a unique ID and is characterized as either having female, male, or both kinds of flowers. I created this data in EXCEL and read it into JMP so I wouldn't have to do so much typing.

Step 1: Create Seedparent table from this data. which has columns Parent_Seed_ID and Rep_Status_Seed.

Step 2: Create Pollenparent table from this data. which has columns Parent_Pollen_ID and Rep_Status_Pollen.

Step3: Do a Cartesian join combining all four columns

Step4: Eliminating impossible combinations female x female and male x male

Step5: Eliminating impossible seed parents, i.e. male plants

Step6: Eliminating impossible pollen parents, i.e. female  plants

Step7: Close Seedparent file

Step8: Close Pollenparent file

From the Rep status columns you can create a unique classification variable for ANOVA with 4 levels FE_MA, FE_MX, MX_M, and MX_MX.

I have attached the script.