Short vs Long-Term Inbreeding

MateSel offers two distinct methods for controlling inbreeding, which breeders should understand clearly as the difference is critical. You will see reference to Long-Term Inbreeding (Parental Coancestry) and Short-Term Inbreeding (Progeny Inbreeding). Also known as the “Two Inbreedings”:

• Short-Term inbreeding: The Progeny Inbreeding Histogram shows the distribution of inbreeding in your next generation progeny only (current matings) and hence we call this short-term inbreeding. It is affected by mate allocation for reduced relationship between the two individuals used in each mating. Progeny Inbreeding is also affected by selection, as some otherwise unselected individuals will be lowly related to at least some selected members of the opposite sex.
• Long-Term inbreeding: This aims to manage the inbreeding level in future descendants by selecting more individuals and less-related individuals as parents. Average Parental Coancestry is affected by selection but not by mate allocation.

Here are two illustrations that these two things are very different:

Consider aiming for the lowest possible Progeny Inbreeding when there is very high potential fecundity, such as in an IVF program. You might choose just one male plus one female as parents because they are totally unrelated, giving non-inbred progeny. Although you have done well for the short term, these parents’ ‘genes’ will meet each other in future generations, giving high inbreeding levels in the long term.

Consider aiming for the highest possible Progeny Inbreeding in a species such as pigs. For each female, you (or MateSel) will look for a full-sib male to mate with to get high progeny inbreeding. This means that many more males will be used than under normal circumstances. This makes for a high effective populations size, low Parental Mean Coancestry, and low inbreeding in the long term.

Tip

It is generally more important to lower Parental Coancestry (long-term inbreeding) than Progeny Inbreeding (short-term). For best results on the Frontier graph, keep the impact of Progeny Inbreeding (F) minimal. See MateSel’s guidance here for details on applying minimal emphasis on Progeny Inbreeding (F).