Examples on breeding cycler

Last edit Dag L 04-04-30

These examples are for breeding cycler. The suggestion on how to gear the programme to solve exercise BC1 is given, the solutions are given after the text, you should mark the text below the heading "Solutions" and change the text colour to black.
 

Exercise 1

Hi,
I am going to optimise our breeding program for Dream Forest Inc. My boss thinks that it is a good idea to start with optimising it assuming that (1) the program is completely balanced, i.e. each parent get exactly two kids (each parent takes part in two crosses, i.e. double-pair mating among founders, like the Swedish breeding program), (2) the idea for long-term breeding is cycling by double-pair mating and to select one individual within each full-sib family as a parent in next breeding cycle. The budget allocated to the project is 10$ per year and member of the breeding population (founder = cross).

My boss wants me to find out which of the following three alternatives for selection of one genotype per full-sib family (cross) is the best to achieve the highest Group Merit Gain per year (GMG/T): (1) phenotypic selection of individuals, (2) clonal test, (3) progeny test (see illustration of the alternatives in sheet "Selection alternatives"), i.e. my choice may be phenotypic selection, versus more accurate breeding value estimates by clonal test or progeny test. My boss does not believe in any harm of rise in coancestry (he thinks that is taken care of by balanced within family selection), thus, the weighting factor for group coancestry can be set to 0. The choices open are number of individuals to be tested (family size in phenotypic selection (alternative 1), ortet number and number of ramets per ortet in clonal test (alternative 2), and number of female parents and seedlings per family in progeny test (alternative 3)).

My boss suggests the following assumptions: one experimental plant costs 1$ for all alternatives, no initiation or other costs (=0$), cycling (recombination phase including crossings) costs 30$ per founder and takes 3 years. Within-family variance components are the following: additive variance is 1, dominance variance is 0.25 and environmental variance is 3.75. The additive standard deviation of the final forest value (within a full sib) is 10% of the forest value. Time before establishment of the selection experiment is 1 year for phenotypic selection (production of seedlings), 4 years for clonal test (basically, production of ortets) and 6 for progeny test (basically, production of female parents). Time after measuring the trial (from selection of individuals to production of their seeds) is 2 for all the alternatives.

I have heard that you are working with a new spreadsheet which may give the answers. Can you please suggest which of the following three alternatives for selection forward of one individual per full sib family (per cross) would be the best as regards group merit gain per unit of time?
 

Tips on how to solve the Exercise 1 by using the EXCEL BREEDINGCYCLE tool.

1) Set the variance components in Box 1 (yellow cells): keep additive variance fixed at 1 and set the dominance and environmental variance (observe % ratio between dominance and additive variance and changes of heritability in the breeding population in the box to the right), set the other parameters in Box 1 (as indicated in the assignment).

2) Set the cost and time for recombination in Box 2 and your budget restriction in Box 3 (the programme will automatically calculate for how long you have to grow the selection trial) as well as cost and time components for each of the alternatives in Box 4. Go back to Box 2 and chose the *selection alternative* (cell C18) you will test.

3) Now you shall find maximum group merit gain per year (GMG/T) for the three alternatives by setting various family size (alt. 1), ortet and ramet number (alt. 2) and number of female parents and progeny (alt. 3). You may reach your goal by using the following two methods:

a) SLOW method: use the downmost box (box to assist): for alt. 1, vary family size in Box 4 until you will get the maximum GMG/T (after each input of family size, press the macro button in the dawn most box to copy the values needed), for alt. 2, try to find the combination of number of ramets per ortet and number of ortets which would give the highest GMG/T (e.g. if number of ortets=4 the highest GMG/T was reached with, say, 12 ramets per ortet; if number of ortets=8 the highest GMG/T w

as reached with 8 ramets per ortet; and so on until you will find the maximum). Again, after each input, press the macro button in the dawnmost box, to copy the data. Proceed in this way with alt. 3. The ADVANTAGE of this method is that you will be able to compare on how GMG/T varies with test age and number of genotypes and plants in the test.

b) FAST method: use SOLVER to find the family number and size which would give the maximum GMG/T (go to TOOLS+SOLVER). The solver shall be run separately for each of the alternatives. Set up of the solver box is the following: Target cell (i.e. cell to maximise) is GMG/T; the cells to be changed (experimented with) are family size (alt.1), family size (i.e. ortet number) and number of ramets per ortet (alt.2), and family size (number of female parents) and number of seedlings per family (alt.3). NOTE: when SOLVER finds the maximum value and asks you how to present the result, DO NOT click on KEEP SOLVER SOLUTION, as it will overwrite the formulas. Rather we would suggest to write dawn the parameters on the paper (GMG/T, family size and time until selections made (selection trial grows) or GMG/T only).
 

Solution to Exercise 1 (change colour of the font to see the solution)

Phenotypic selection (alternative 1)
Given the budget of 10 $ per founder and year, the highest group merit gain per year (GMG/T) of 0.3419 may be achieved by testing 156 seedlings per family and selecting 1 seedling per family in 12.6 years after establishment of the selection trial.

Clonal test (alternative 2)
Given the budget of 10 $ per founder and year, the highest group merit gain per year (GMG/T) of 0.3722 may be achieved by testing 43 ortets with 6 ramets each and selecting 1 ortet (clone) per family in 19.8 years after establishment of the selection trial.

Progeny test (alternative 3)
Given the budget of 10 $ per founder and year, the highest group merit gain per year (GMG/T) of 0.2654 may be achieved by testing 16 female parents with 17 seedlings each and selecting 1 female parent per family in 19.2 years after establishment of the selection trial.

Conclusion (letter to the boss):

My dear boss,
Under the given genetic parameters and cost as well as time scenario, I would recommend to carry out the clonal test by testing 43 ortets with 6 ramets each for each of the 50 full-sib families and to make the final selection of 1 individual per full-sib family in 19.8 years after establishment of the selection trial. Now, I expect you to rise my salary as much as I have raised the annula group merit gain of your forest ...

Results in summary
 

Exercise 2

Hi,
I am going to optimise our breeding program for Dream Forest Inc. My boss thinks that it is a good idea to start with optimising it by assuming that (1) the program is completely balanced, i.e. each parent get exactly two kids (each parent takes part in two crosses, i.e. double-pair mating among founders), (2) the idea for long-term breeding is cycling by double-pair mating and to select one individual within each full-sib family as a parent in next breeding cycle. The budget allocated to the project is 10$ per year and member of the breeding population (founder = cross).

My boss wants me to find out which of the following three alternatives for selection of one genotype per full-sib family (cross) is the best to achieve the highest Group Merit Gain per year (GMG/T): (1) phenotypic selection of individuals, (2) clonal test, (3) progeny test (see illustration of the alternatives in sheet "Selection alternatives"). My boss believes that group coancestry should be penalised as inbreeding, thus, the weighting factor for group coancestry shall be set to 100 (note that this is different from the previous task, and thus the differences in the results indicates what difference it makes if the increase in group coancestry is neglected). All calculations (except diversity loss) are within family. The task is to optimise the program so it returns maximum progress in Group Merit per year. The chooses open are propagation method, how long selection trial grows, number of individuals to be tested.

The boss suggests the following assumptions: An experimental plant costs 1$, no initiation or other costs (e.g. for cloning cost, but ramets and progeny have the ordinary per plant cost associated to them), cycling (that means the recombination phase including crossings) costs 30$ and takes 3 years. Additive variance is 1, dominance variance 0.25 and environmental 3.75. The standard deviation of the final forest value (within a full sib) is 10% of the forest value. Time before selection experiment is set up is 1 year for phenotypic selection, 4 years for clonal and 6 years for parental selection. Time after can be set to 0 for all alternatives. Specify lacking parameters (if any) needed for the worksheet.

I have heard that you work with a new spreadsheet which may give the answers. Can you please suggest something about the exact design close to optimal based on that spreadsheet?
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Solution to Exercise 2 (change colour of the font to see the solution)

Phenotypic selection (alternative 1)
Given the budget of 10 $ per founder and year, the highest group merit gain per year (GMG/T) of 0.3159 may be achieved by testing 169 seedlings per family and selecting 1 seedling per family in 13.9 years after establishment of the selection trial.

Clonal test (alternative 2)
Given the budget of 10 $ per founder and year, the highest group merit gain per year (GMG/T) of 0.3569 may be achieved by testing 46 ortets with 5 ramets each and selecting 1 ortet (clone) per family in 17 years after establishment of the selection trial.

Progeny test (alternative 3)
Given the budget of 10 $ per founder and year, the highest group merit gain per year (GMG/T) of 0.2495 may be achieved by testing 17 female parents with 18 seedlings each and selecting 1 female parent per family in 22.6 years after establishment of the selection trial.

Conclusion
Under the given genetic parameters and cost as well as time scenario, I would recommend to carry out the clonal test by testing 46 ortets with 5 ramets each for each of the 50 full-sib families and to make the final selection of 1 individual per full-sib family in 17 years after establishment of the selection trial.