This exercises aim to help you a. better understand how GS can be applied in a breeding program and b. get guided practice applying GS. Consider the following:

Also imagine that the breeding cycle has been repeated two times. We have the marker data and the phenotypic data from these two cycles of selection. In the data, population A corresponds to the DHs generated in breeding cycle 1 and population B corresponds to the DHs generated in breeding cycle 2.

load("Breeding Population Data.RData")

Imagine you are in charge of performing the 3rd cycle of selection.

How will you perform GS in cycle 3?

What will be the training set? Will you select prior to phenotyping, why or why not?

Estimate the accuracy of GS before phenotyping.

What will you use for model training? What will you use as a validation set?