Specific Scenarios

Species that produce multiple offspring

If I’m using reproductive technologies OR females have multiple progeny per mating, should I enter duplicate entries into CommittedMatings.txt?

It depends.

If we assume that a past Committed Mating will make the same level of long-term contribution as a New Mating, then a Committed Mating should have an influence on the analysis that is similar to that of a New Mating. Accordingly, if the average New Mating produces 10 piglets, that implies that a CM should represent the same. This means that a CM should be entered just once for whatever number of progeny from that mating are in the pipeline.

This situation would be the same for a scenario in which reproductive boosting is used for all females in a species that normally has a litter size of one, or a few (eg cattle and sheep): If, due to reproductive boosting, every female is expected to raise say 8 progeny, then only make a single entry in CommittedMatings.txt for each mating. However, if only some females are reproductively boosted, then you should enter each such mating (say) 8 times in CommittedMatings.txt (using duplicate lines), to reflect the level of contribution for these matings compared to normal matings, which get a single entry.

Some progeny from Committed Matings might be culled, reducing contribution from that mating, and yet the surviving progeny will have an increase in likely contribution because they have passed a selection stage. Overall, this is not perfect use of available information, as we might predict different future contributions from different Committed Matings, but we have to have a balance between technical accuracy and simple operability. The stage to remove a mating from CommittedMatings.txt is then a judgement for the user – probably at a stage when most or all of that mating’s offspring have either been culled, or made available as selection candidates. In practice, for simple operations, this may be a fixed-timed event, such that all matings from a given selection round are removed from CommittedMatings.txt at the selection round when any unculled offspring are expected to be available as candidates. Of course, where a mating produces no offspring, or all its offspring are culled, that mating can be removed when this information is available.

For scenarios with many Committed Matings but few New Matings to be made

With few weekly New Matings to be made, and a long list of Committed Matings, we might have somewhat unusual outcomes:

• Very little range in Progeny Index and Parental Coancestry seen on the Frontier graph. This is because the many Committed Matings are fixed, and the few New Matings have limited power to change these values. You may have little impact on mean parental coancestry/index at each analysis, but they add up in their impact over time.
• At low Target Degrees, targeting high Progeny Index, you will probably have just a few high-index sires selected, the same as without using Committed Matings. However, you might also find just a few sires selected at high Target Degrees, targeting low Parental Coancestry, quite unlike the situation without using Committed Matings. This is expected – when evaluating New Matings, the importance of the number of sires and their relationship to each other can be greatly diminished under Committed Matings. What is most important is the relationship of candidate males to the animals in the Committed Matings list. So Matesel will aim largely at those few sires that are most lowly related to the Committed Matings parents. [A warning: eg. missing pedigree information on some males will push them to the front of the queue, most especially in the current scenario, as they will be seen as unrelated.] This can lead to operational difficulties: If for example just three males are used in one week, then in the next week they will be in the Committed Matings list, and will be less likely to be selected for the next week. Such fluctuation in sire use may be unpopular in the operations team. In this case, consider using Spread sire use more evenly over weeks in pigs and other species as described below.

Spread sire use more evenly over weeks in pigs and other species

This can also be relevant to other species such as poultry, or even beef and sheep under female reproductive boosting programs.

Without attention to this issue, the number of matings allocated to a male over a number of weeks can be quite erratic. For example, 10 matings in week 1, followed by 1 mating in week two, then 12 matings in Week 3 … that is frustrating for operators.

To keep selection and use of males more consistent over their usable lifetime, then, once selected and used in a given ~week, a male can have its AbsMinUse value set to an appropriate value or values in future weeks in order to even out its use over time. This helps logistics, with a technical compromise that is probably rather be small.

You could use MinUse (where 0 uses is permitted) rather than AbsMinuse, and cull the male as of the week that it is allocated 0 matings. Or possibly a combination: Eg. for last week’s allocation being >=8, use MustUse = 6, else use MinUse = 6. You might want to modify your database scripts to automate the creation of such settings in your datafiles.

Of course, such manipulations can reduce technical performance. However, any compromises made will be accommodated in mating results at future mating rounds.