Managing Backup Sires

You can nominate the number of backup sires to report per mating under grouping and no grouping approaches. Results are shown in BackupSires.csv and as such can only be viewed after stopping the run. Backups are also known as “Replacement Sires” is some industries.

This is how it works: For each mating, the selected sire is replaced one-at-a-time by all other legal candidate males. For each of these the full solution is recalculated, including all targets that you have set up in the run (traits/inbreeding/markers/index).

Note

For Balance Strategies that involve Hard Constraints, it is possible that most or even all alternative males are rejected as backups because their use would result in breaking the hard constraint. If you find that too few backups are being offered in the reports, you can try changing Balance Strategy to one that uses a soft constraint.

Tip

Although backups are a logistically useful feature, it can lead to sub-optimal matings when backups are used. If possible, you should follow the ideal approach to backups as described below.

The percentage figures reported are on a linear scale of 100% for the best selected sire down to 0% for the worst legal replacement. This is done by swapping out the nominated sire with another, and testing the result with that replacement. This test uses the full prevailing objective function, including trait distribution items, etc. This is done separately for all possible backup males. The worst replacement is scaled to 0%, and the best (as nominated) is scaled to 100%. If a backup has a percentage figure of >100%, that shows that your run has not fully converged (the selected sire is not the best sire), and/or that by using that backup, you are breaking its MaxUse constraint, if allowed (see Use a male for backup even if it is at its MaxUse limit). MinUse constraints are not considered when Backup sires are evaluated. Use the percentage figures a bit like this:

• I have a 98% backup right here next to me, and a 99% backup two paddocks/barns away from me, I’ll use the 98% one.
• I have a 92% backup right here next to me, and a 99% backup two paddocks/barns away from me, I’ll make the extra effort and go get the 99% one.

Backup all matings of a sire as a block

To invoke this option, enable the “Backup all matings of a sire as a block” setting.

If enabled, then you will find that for all females in the same female Group that have been allocated to a given sire, the backup sires for these females will all be the same, and in the same order. This may be useful for paddock mating, where you want to keep the group of females intact when choosing a backup male.

If disabled (default), MateSel finds the most suitable backup males on a female-by-female basis.

Restricting backup sires to those that have not been selected

To invoke this option, enable the “Restrict backup sires to those that have not been selected” setting.

In the event that no unused sire is available in a sire group that is legal for the female concerned, the best sire that is already used will be chosen. Thus, for multiple backup sires requested, already-used sires may be included in the list, but they will be ranked at the end of the list - but still with the better ones nearer the front of the list. In effect this is done by subtracting 100 from their percentage values. Where no grouping-legal sire is available to fill a position, then no sire is nominated. When viewing BackupSires.csv, you will notice the Percent values for backups that have already been selected are negative. Also note that the worst unused sire has a percentage value of zero.

Use a male for backup even if it is at its MaxUse limit

To invoke this option, enable the “Use a male for backup even if it is at its MaxUse limit” setting.

You might choose to do this when the MaxUse value you specify is in fact quite flexible. Note that nomination as a backup male does not affect its Use (# of matings) value, so it is possible that a key male will be represented many times in the backup file – many more than its MaxUse number. You can always choose a backup male from further down the list. Backup sires breaking their MaxUse limit can show Percent values substantially greater than 100%.

The ideal approach to backups

Although the reported backups is a useful feature. It doesn’t give you an optimal result if used. When a backup sire is nominated for a given mating, the calculations involved are done in ignorance of which other matings will need a backup sire to be used – as the broken legs and failed libido that remove the primarily nominated sires from use have yet to take place. So, at this stage, the result will be unavoidably sub-optimal. For optimality, we want to know which matings need to have a backup sire actually used. To do this is easy, if it fits logistically:

1. Do the Matesel run without invoking backup sires.
2. At the stage when you are ready to use backup sires, add all the successful matings (those that do not require a backup sire) to the file CommittedMatings.txt.
3. Use the “Manual” Committed Matings MaxUse Calculation option. This option means that MaxUse for a sire covers these committed matings plus backup matings made at step 6 below. Use the “Automatic” option to set usage values for step 6 matings alone.
4. Remove the failed sires from candidacy (MaxUse=0 for these sires), if appropriate.
5. Add chosen backup sires to candidacy (MaxUse>0) if needed.
6. Re-Run MateSel. You should now get an optimal result for new backup sire allocations.
7. Repeat steps 2-6 above for later stages of failed matings detected, if and as required.

Using multi-sire joining for backup matings

Some operations use groups of bulls (or rams, etc) to carry out “clean-up matings” following a main mating round using natural and/or AI matings. This requires fewer mating paddocks, each containing multiple bulls and multiple cows, and might make for easier management.

However, genotyping is probably required for identifying parentage of the resulting progeny You might choose to do this by entering the main round matings as Committed Matings in CommittedMatings.txt and using Mixed Mating Groups (MMG) to set up the male and female groups for the backup matings. In this way, your backup mating decisions are conditioned on the main round matings you have already made. You can probably do this backup MateSel analysis immediately after you have completed the main round MateSel analysis.

This is not a perfect solution for a number of reasons – the prime one being that we do not know which females will not get pregnant to their main round matings, such that the MMG backup run has to cover all possibilities. There is not much we can do about that, except of course to remove any females that are known to be pregnant. Moreover, there will be many fewer progeny coming from the backup matings, compared to a normal MMG run, and any effects of this have not been tested. However, progeny that come from these backup matings should reflect the OCS policy (e.g. Target Degrees) used for the backup MMG run. Using this MMG backup approach, you can set up backup mating groups where the bulls and cows are appropriately matched, e.g. targeted at mating heifers with high calving ease EBV bulls, or targeted at different specific end uses. See Mixed Mating Groups for details.