EXAMPLES to ORCHARD_MANAGEMENT 

Kang, K-S & Dag Lindgren, last edit DL 04-04-29

For training on the work book ORCHARD_MANAGEMENT?.xls

Setting

You are the responsible manager for a seed orchard of Pinus scotch var. whiskeys, and receive the questions listed below from your boss for consideration concerning the wisest seed orchard management. The seed orchard has 100 unrelated and non-inbred clones from the initial plus-tree selection, and pollen contamination is 40%. Contamination pollen contribute equally to all clones.

The breeding values of the orchard clones are known. The average breeding value of the initial plus-trees is set as 0 (this is just to get a reference point). The standard deviation of breeding values of clones is 1. The contaminating pollen has a breeding value which is usually less than zero (not as good as the initial plustrees), so the contamination inferiority (i.e., breeding value of contaminating pollen) is considered as –1.

 

Example 1

1-1.What are the predicted gain (G), status number (Ns) and gene diversity (GD) when seeds are harvested only from the best 10 clones without any genetic thinning?

1-2. What about genetic thinning with removing of 90% inferior clones? Thus, the 10 % best clones remains.

1-3. What genetic thinning will be required to get the same gene diversity as in Example 1-1, and what will the corresponding genetic gain be?

Solution

Use workbook: ORCHARD_MANAGEMENT? (simplest). Insert the red values given in the situation and example. For Harvest best clones, no thinning and Genetic thinning, genetic gain and gene diversity are as follows:

1-1 Harvest 10% best clones and no thinning: G = 0.665, Ns = 34.6 and GD = 0.986

1-2 Genetic thinning 90% inferior clones: G = 1.184, Ns = 15.6 and GD = 0.968

1-3 Balancing point:78% genetic thinning (22 clones remains after genetic thinning) get GD = 0.986 and G = 0.866.

 

Example 2

Now, you get the information of fertility variation (in terms of CV) among parents, which is estimated to 100%.

2-1) What are genetic gain, Ns and variance effective population size, Ne(v) if the seeds are collected from the best 50% clones without genetic thinning?

2-2) How about when the seeds are harvested from the remaining clones after genetic thinning of 50 % inferior clones?

2-3) If the seeds are collected from 20 best clones after the 50 % thinning?

 

Solution

Use workbook: ORCHARD_MANAGEMENT_? (advanced). Insert the all red values given.

2-1) Harvest 50 % best clones, no thinning: G = 0.196, Ns = 56.2 and Ne(v) = 112..4

2-2) Harvest all clones after 50 % genetic thinning: G = 0.433, Ns = 39.1 and Ne(v) = 78.1

2-3) Harvest 20% best clones after 50% genetic thinning: G = 0.730, Ns = 24.6 and Ne(v) = 49.3

 

Example 3

The seed orchard is genetically thinned down to 40 clones, a part of the seed orchard is completely replanted with 10 ten of the clones which remain in the seed orchard and 10 other clones. Seeds are harvested from the newplanted part before pollen production where has become important (thus the orchard pollen comes from the 40 clones around). Another problem which got the same answer is: there are 50 clones remaining in the seed orchard. There is a sexual assymmetry so 40 of the clones produce pollen and 20 seeds. The male fertility and female fertility are the same for all clones which has a reproductive output.  What is the value of  Ns? Speculate about under what condition the gain estimates given in the worksheet are relevant!

Solution

Use workbook: ORCHARD_MANAGEMENT?. Insert the relevant red values (e.g. Nf = 40, Nm=20 and Nfm=10). In advanced insert CV = 0.  

Ns =  54.1

50 clones contribute to the progeny

.....

Example 4

You have further information on the fertility variation. Fertility variation (CVm) of mother clones is 100 % and that (CVf) of father parents is 150 %. There is a negative correlation between maternal and paternal fertility (r = -0.2). What are the values of genetic gain and status number for the initial seed orchard and for the selective harvest of 50 % best clones? If the correlation coefficient is 0.2, what results do you get? Compare the results for both cases of correlation, why do you think things change?

Solution

Use workbook: ORCHARD_MANAGEMENT_? (more advanced). Insert all red values relevant for the situation.

  r = -0.2

Alternative 1 : G = -0.200, Ns = 99.8 and Ne(v) = 275.9

Alternative 2 : G = 0.196, Ns = 71.7 and Ne(v) = 198.4

  r = 0.2

Alternative 1 : G = -0.200, Ns = 84.6 and Ne(v) = 184.3

Alternative 2 : G = 0.196, Ns = 60.8 and Ne(v) = 132.6

The change in correlation has no effect on gain, but gene diversity get higher if there is a negative correlation. A negative correlation makes generally total fertility more equal and thus fertility variation lower and thus gene diversity higher.

Acknowledgements: We are grateful for helpful comments, in particular from Darius Danusevicius and Milan Lstiburek.