Managing Inbreeding within the Suffolk Breed

Shane Conway Signet Breeding Services, January 2013

What is inbreeding?

Inbreeding is the practice of mating two genetically related animals. To a degree this is inevitable within any long-term selection programme involving a closed population.

Breeders will sometimes deliberately inbreed specific bloodlines to fix certain characteristics in the flock, increasing the frequency of favourable genes – or more rarely to expose recessive genes.

Inbreeding may have a place in a breeding strategy as in some instances it will bring a number of favourable genes together. However, it will also tend to increasethe number of recessive or deleterious genes being expressed – leading to a reduction in fitness and productivity; this is referred to as “inbreeding depression”.

The challenge to avoid inbreeding

To make fast genetic progress in any particular attribute a small number of rams and ewes that excel in that attribute tend to be mated together. If this approach is taken to an extreme, it can quickly result in an increase in the level of inbreeding within the flock.

Modern livestock breeding programmes can be susceptible to increases in inbreeding due to the widespread use of AI & ET, fast generation turnover, selective use of specific family lines and the tendency for a relatively small number of different sire families to dominate within certain breeds. Increases in inbreeding are observed in both recording and non-recording flocks.

Breeders need to strike a balance to optimise rates of genetic gain, whilst controlling increases in levels of inbreeding.

Calculating Levels of Inbreeding

The level of inbreeding is calculated as the probability of two alleles being identical by descent. This value is called the "inbreeding coefficient".

Typical inbreeding percentages are as follows, assuming no previous inbreeding between any parents

  • Father/daughter, mother/son or brother/sister → 25%
  • Grandfather/granddaughter or grandmother/grandson → 12.5%
  • Half-brother/half-sister → 12.5%
  • Uncle/niece or aunt/nephew → 12.5%
  • Great-grandfather/great-granddaughter or great-grandmother/great-grandson → 6.25%

Should breeders completely avoid inbreeding?

Complete avoidance of inbreeding is almost impossible and a balance has to be struck between the genetic superiority of a specific ram and the level of inbreeding he creates in the future flock. Low levels of inbreeding (<6.25%) are often considered an acceptable compromise. Levels higher than that should be avoided.

The best solution to the inbreeding challenge is to measure the level of inbreeding between individuals and make recommendations based on this information.

What can the Suffolk breed do?

There are two things the Suffolk breed can do.

1). Calculate and publish the inbreeding co-efficient of every animal in the database.

This would enable:-

  • Inbreeding to be monitored at a breed level
  • Inbreeding to be monitored and reported at a flock level

2). Consider providing web based software to breeders that enables them to work out inbreeding co-efficients between specific individuals.

This would enable Suffolk breeders to work out how closely related future matings are likely to be and manage the inbreeding risk accordingly

Summary

Breeders shouldn’t stop making good use of the reproductive and genetic tools available to them – but they can take steps to minimise increases in inbreeding now and in the future.

Appendix 1. Inbreeding in Suffolk Sheep

Signet has looked at the rates of inbreeding within the Suffolk breed.

This work was based on calculations undertaken by SAC based on SuffolkRun 2 2012.Signet extracted data for male lambs only (to avoid any female recipient ewe bias). The chart below shows the level of inbreeding in Suffolk lambs born since 2007 – and their parents in each given year.

While rates of inbreeding within the breed appear relatively low, they have increased in the last 2 years – in part due to the use of sires with slightly higher levels of inbreeding.

The chart shows a change in the rates of inbreeding, but care should be taken in determining the significance of this difference.

Signet has chatted to Marco Winters, DairyCo Geneticist about this subject over the summer and Marco made the following quick observations.

  • Inbreeding coefficients are highly dependent on depth of pedigree, and therefore the level can sometime be under estimated. Direction and speed of change may therefore be more relevant to the sheep industry.
  • The 2% inbreeding co-efficient seen here (assuming it is calculated on deep pedigrees >5 generations) is perfectly acceptable. Anything less than 6% is nothing to worry about in the medium term.
  • Speed of change is many respects is more important; 1% over 5 years would be fairly rapid. In the case of Suffolk’s the change is about 0.5% over 5 years (very similar to the dairy industry 0.1% per annum), which is not unexpected and perfectly manageable
  • Whilst these rates of inbreeding are not a major concern at the moment - at this rate you do want to monitor it and talk to breeders about this issue.

Appendix 2.

Breakdown of the Inbreeding Co-Efficients for the 2011 Suffolk Lamb Crop

This table shows the breakdown of inbreeding co-efficients for the Suffolk population. While the vast majority have very low levels of inbreeding – it is interesting to note that about 6% of the population already have inbreeding co-efficients above the 7% threshold usually set as a sensible upper limit for inbreeding.

Inbreeding Co-Efficient (2011 crop) / Number of Records / Proportion of population
0 / 354 / 2.64%
under 1 / 8543 / 63.82%
under 2 / 1782 / 13.31%
under 3 / 825 / 6.16%
under 4 / 592 / 4.42%
under 5 / 337 / 2.52%
under 6 / 188 / 1.40%
under 7 / 186 / 1.39%
under 8 / 113 / 0.84%
under 9 / 90 / 0.67%
under 10 / 46 / 0.34%
under 11 / 29 / 0.22%
under 12 / 20 / 0.15%
12 to 25 / 174 / 1.30%
over 25 / 107 / 0.80%

Appendix 3.

Inbreeding and influence

This chart shows the inbreeding co-efficient of sires used to produce the 2011 lamb crop plotted against progeny number. The chart shows a number of sires with inbreeding co-efficients over 7% being used to produce lambs.

This isn’t a problem providing they are being used as an outcross – but it is indicative of a gradual increase in inbreeding levels in the population.