Inbreeding: Why is it important?

Inbreeding tells us about individuals and the likelihood that they can express the genetic diversity in the population. It also gives us an indication of whether to expect hidden genes to “pop up”. Inbreeding can lead to ill-thrift and poorer production and reproduction.

Inbreeding has 3 major consequences:

Animals that are inbred tend to perform more poorly than those that are not inbred or are outcrosses. Numerous scientific studies have shown a relationship between the level of inbreeding and the level of productivity, health and reproductive success in sheep, pigs, cattle and other species. On average, inbred animals grow more slowly, are more likely to have health problems or succumb to parasites or other infestations, and have lower reproductive rates, in terms of conception rate, litter size and progeny survival.

Hidden genes, or recessive genes, are more likely to show up in inbred animals. Often these recessive genes are lethal or cause serious problems. They are more likely to turn up in inbred animals because they can’t be “seen” in individuals that are carrying only one copy of the bad gene. If a sire carries a bad gene, his descendants several generations later may still carry it, and when these individuals interbreed the chances of progeny receiving two copies is much higher than if these individuals are bred to individuals where the bad gene is unknown. So as the average level of inbreeding rises, so too does the chance of these recessive genes pairing up to be expressed.

A population of inbred animals would tend to have low diversity and leave little room for selection. The only solution here is to buy-in animals from unrelated stock. Doing this successfully and at an affordable price depends upon having studs from which to source unrelated animals that are performing as well as your own. Buying-in is a good strategy in any case, but best done when superior genetics can be sourced rather than when there is an inbreeding problem to solve.

Avoiding inbreeding doesn’t have to be complicated

You can take a number of steps to avoid inbreeding:

1. Use more rather than fewer sires


2. Avoid using individual sires excessively


3. Monitor inbreeding levels each year


4. Plan matings to avoid inbreeding

X'Aim can help you do all of these and more.

By applying Optimal Contributions Theory, X'Aim helps you avoid developing a “bottleneck” in your gene pool, ensuring future diversity which not only helps for effective selection, but helps to avoid inbreeding. As you choose lower coancestry points on the frontier (see the posting on Genetic Tradeoff), you will be using more rather than fewer sires, and you will avoid using individual sires excessively.

X'Aim reports show the inbreeding level for each mating as well as the overall average.

What is possible depends upon the number of males and females that are available for breeding. Remember that having more sires available means you are more likely to achieve both lower coancestry and lower inbreeding.

What is Coancestry? Why is it important?

Coancestry describes how much individuals in a breeding program are related and impacts upon the effectiveness of the selection program.

Coancestry and why diversity is important

Coancestry describes how much “relatedness” there is in a breeding population. High coancestry means more individuals are more related to each other, while no or low coancestry means the individuals are not related at all or very much.

Coancestry is a population-level measure so the number of animals included in the data being analysed, and the depth of pedigree included, impact upon the estimate of coancestry.

The opposite of coancestry is diversity. High coancestry means low diversity, and low diversity means we have less ability to select better animals. All selection is based upon differentiating between better and poorer individuals where the difference is due to genetics. If we have high coancestry, there is less difference between individuals because they are more alike, in fact so alike that we can no longer see differences between them and can no longer select among them.

We need to manage coancestry so that we can ensure that we have genetic diversity for selection. We can do this by taking advantage of Optimal Contributions Theory, outlined in the fact-sheet entitled “The Genetic Trade-off”. X'Aim can help you select from a range of mating strategies so you can choose an appropriate balance between achieving high genetic gain and managing coancestry. These mating strategies help to attain results on or close to the "frontier", as illustrated below.

What level of coancestry is acceptable?

The level of coancestry (or position on the frontier relative to the bottom axis, left or right) you choose should reflect your policy on buying in un-related males, the number of breeding females you have (more females means lower coancestry), how quickly you turn your females and males over, and your time frame or future outlook (looking further into the future means keeping a closer eye on coancestry, while a shorter-term outlook would accept higher levels of coancestry). Each breeding population has unique values for coancestry (those on the graph above are only for illustration purposes).

We generally recommend a maximum level of coancestry of around 1% per year, so if your generation interval (the frequency of turning your stock over) is 3 years, you can accept up to 3% on this mating. If your generation interval is longer, say 5 years, then you can accept up to 5%. This is a general rule of thumb and you should discuss this aspect more with your genetic advisor or take a more conservative approach if you are unsure.

The Genetic Tradeoff

There is a trade-off between achieving maximum genetic gain and building up inbreeding too quickly. State-of-the-art scientific methods help to find the right balance between these two when selecting and mating your breeding animals.

Optimal Contributions Theory

Maximising genetic gain without considering the impact on future inbreeding will result in higher levels of coancestry (relatedness of individuals – see the article on Coancestry) and this will lead to undesirable levels of inbreeding (see the article on Inbreeding). There is an optimal balance between high genetic gain and low coancestry, achieved by using individuals in an optimal way. This is known as Optimal Contributions Theory.

Achieving the optimal contributions of individuals’ genes to the breeding program results in genetic gain that is more sustainable over time because it will not cause an excessive build-up of inbreeding in future.

You could achieve sustainable genetic gain by taking a conservative approach that keeps coancestry at bay, but this level of genetic gain is often less than desirable.

If you calculate the highest genetic gain that is possible and the corresponding level of coancestry, then the lowest possible coancestry with the corresponding level of genetic gain, as well as a number of points in-between the two, you can connect up the points and you have the “frontier of genetic gain and coancestry”.

This represents the best that your breeding population can do this year, given the constraints you have put on sire uses and the number of females being mated. Each point on the frontier is a mating list that you could implement, not a theoretical position. This, however, is not a trivial calculation to do by hand.

In X'Aim, we have chosen 3 points on this frontier to provide a range of possibilities for Index, coancestry, and inbreeding. We refer to each point as a "mating strategy" which you can implement when requesting a new mating analysis. We've also retained and named the original balanced mating strategy that doesn't require a genetic selection Index:

• Balanced Diversity - Equal emphasis is placed on long (coancestry) and short-term inbreeding (progeny inbreeding), but no emphasis is placed on genetic Index. This is the only strategy available when Index is not available for all your available animals.

• Balanced + Gain - This strategy is similar to Balanced Diversity but with a small emphasis on genetic Index (gain). This is an ideal strategy if maintaining diversity and avoiding inbreeding is most important but some improvement in genetic Index is desired.

• Middle Road - All of long and short-term inbreeding and genetic Index have equal emphasis. This strategy is ideal if all 3 are equally important and neither of diversity or genetic Index are more important than the other. This strategy will still result in good genetic gain on Index but will not be as aggressive as the Performer strategy below.

• Performer - Choose this strategy when your main focus is to make rapid genetic gain on Index. X'Aim will still try to keep long and short-term inbreeding as minimal as possible, but you should expect both of these to result in higher values than any of the other strategies.

Why is the Performer strategy not the highest point? In theory, we could be just slightly higher in Index, but this would come at the cost of considerably increased coancestry, which isn't worth the small increase in Index. This illustrates particularly well the Genetic Tradeoff we are trying to illustrate here. Striking the right balance between genetic gain, inbreeding and coancestry is at the heart of a good mating strategy.

Genetic selection now with X'Aim

New features have been added to X'Aim to provide genetic selection tools. These include:

• the ability to import genetic selection Indexes for animals
• view Indexes on the list of animals and in animal details
  
• 3 new mating strategies to balance genetic gain on Index, inbreeding and coancestry
• mating lists with predicted Index for the progeny of each mating (as well as inbreeding)
• export Index and comments as well as all other data

A quick genetics primer

Genetic improvement is the result of selecting superior animals to replace inferior animals through the use of breeding. The determination of what is "better" or "best" depends upon many things such as:

• what traits, or combination of traits, is more profitable?
• what traits or characteristics make animals healthier?
• what traits or characteristics are more appealing?
• what kind of animal does the environment support?
• what kinds of animal products does the market demand?

This determination is usually made by livestock or animal owners and breeders, and sometimes by a national or cooperative body representing the industry. The more formal terminology is "setting the breeding objective" and entire books are written on the subject.

What is important here is that the breeding objective, once formulated and applied, is represented by a single figure called an Index. This number can be used to rank animals, with better animals having higher numbers, and poorer animals having lower numbers.

Often the Index is in $ terms, and can be interpreted as such. For example, if there are two animals, one with an index of 100 and another with an index of 110, then the second animal is 10 index points better than the first. If this is a $Index, then the second animal's progeny are each $5 better than the first animal's progeny. Why half? Because if the Index is based upon Estimated Breeding Values (EBVs), then 1/2 is passed on to progeny. If the Index were based on EPDs (Expected Progeny Differences) then all of the Index would be transmitted to progeny. In short, EPD = 1/2 EBV (if the trait is the same one)!

This property of $Indexes can be useful for determining the economic value of the genetic merit of an animal for commercial production. If each animal had produced 100 progeny, then the second animal should have produced $500 more than the first one. The following table illustrates this example with 2 bulls. The second bull is 10 EBV index points better than the first. The figures in the columns beginning with "$" show the additional $ earned from Bull B over Bull A. Note that this only compares these 2 bulls; Bull A could be an excellent bull and already much better than average (you could do this comparison with the breed average Index value also!).

Why the differences? In our example, the second animal might be genetically superior for carcase traits, or grow faster, or his daughters may lactate better or produce more lambs (if he were a ram). There are lots of reasons why the genetics of an animal may result in superior performance and therefore profitability, so it isn't hard to see why genetic selection works.

In the Example population in X'Aim we've created a number of generations of selection using the new mating strategies with Index. Check out the new table of reports with summaries of the mating list easily comparable from report to report. The "Performer" strategy should result in the most genetic gain. Try it yourself to see how you can have different amounts of genetic gain on Index, progeny inbreeding and coancestry.

Being on the "Elite" plan gives you full access to genetic selection tools including Index. If you're not yet on an "Elite" plan you can still check out the new features including Index on the Quick Tour page on our website.

Pedigree file upload and data file export

X'Aim is designed to make your job of tracking your animals easier, and to facilitate that we have created both a pedigree file upload facility and a data export facility.

To upload your pedigree file, it's a simple matter of navigating to the "Import" tab from your "Animal List" page. An X'Aim hint will guide you through the details of importing. A flexible data file format means you can define how fields such as "sex" are read - maybe you use "male" and "female" or maybe you have a code like "M" and "F" or "1" and "2". Specify what fields are in which columns and what types of identifiers are used (like M and F or 1 and 2), and upload your pedigree, large or small! This can save considerable time if you already have your pedigree in electronic format.

At X'Aim we don't want to tie you in to using our software product. We also recognise the need to download data to other software for various purposes. For this reason we've created a one-click data export so that you can easily get at your data. The file is exported as comma-separated, making it ready to use in spreadsheets or databases, or your favourite text editor. You'll find the export facility on the "Export" tab on your Animal List page.

Sign up now for your free X'Aim account: http://www.xaim.com.au

Add comments to animals

Now you can keep track of observations about individual animals using the new "comments" field on the individual animal details view on your X'Aim animal listing page. View details about individuals by clicking on their ident/tag. This brings up a new window showing animal details and tabs where you can view the pedigree and the progeny of that individual.

On the first view of the animal's details is a new field called "Comments". When you hover your mouse over the word "Comment" an edit-icon will appear to the left. Clicking on the edit-icon lets you add comments to the animal. Save or cancel your edits when you're done. It's that easy!

Keeping comments on animals can help store important information about individuals. For example, you might find a ewe that is an exceptionally good mother and want to make note of it for next year, or for when you look up her lambs. Maybe they are also good mothers!

Use X'Aim to help keep track of your animals, their pedigrees, and now important information about individuals.

New pedigree viewing feature in X'Aim

The X'Aim on-line animal tracking and mating software tool now lets you view the details of an individual animal, simply by clicking on its ident or name tag on the animal listing page. A smaller window with the following three tabs will appear:

• Animal Details
• Pedigree
• Progeny

Animal Details contains information about the animal, including birthdate, sire, dam and inbreeding coefficient.

The Pedigree tab shows a 3-generation pedigree tree for the animal. Each parent in the pedigree tree can be clicked to change the view of the pedigree to be for that new animal/parent. This makes surfing up the pedigree quick and easy. When a parent is a common ancestor in the pedigree, leading to inbreeding of the animal in question, it is highlighted to draw attention to the source of inbreeding.

The Progeny tab lists all progeny for the animal, each progeny being "clickable" to change the focus of the view to be for that new animal. This changes the pedigree and details views as well. This allows surfing "down" a pedigree in addition to surfing up the pedigree using the pedigree tab.

For a quick view of the pedigree tree, see http://www.xaim.com.au/tour.html

X'Aim is for everybody

X'Aim, as an animal tracking and inbreeding avoidance on-line software tool is for everybody that would like to keep track of their animals, whether they have many animals or just a few, whether they are livestock, pets or conservation species.

All you need to know about your animals is their sire and dam, and that each identifier (or tag) is unique; that is that no other animal has the same number or name. If you do have more than one animal called "Mary", just name them Mary1 and Mary2 to distinguish between them (now they're unique).

By having each animal with a sire and a dam, you have enough to build up your pedigree history. X'Aim does this automatically for you, adding sires and dams to your animal listing. Check out the easy animal adding and editing and other features of X'Aim at: http://www.xaim.co.nz/tour.html, or watch a quick video tour of X'Aim: http://www.xaim.co.nz/video.html.

The pedigree is essential for estimating inbreeding of each animal. X'Aim does this for you showing each animal's inbreeding coefficient on the animal listing page. When you're ready for mating you can get X'Aim to generate a mating list that has recommended matings to avoid inbreeding. It also sets up the matings to reduce future inbreeding by maintaining a larger gene pool. This is why it is important to consider all the matings at once, not just one at a time.

X'Aim is available now. Sign up for free! In New Zealand: http://www.xaim.co.nz or at http://www.xaim.com.au for the rest of the World.

X'Aim is Live!

X'Prime Pty Ltd was proud to launch its latest product X'Aim in July at the New Zealand National Fieldays at Mystery Creek which featured "The Business of Breeding".

X'Aim has a free basic version and because we want to share our excitement with everyone we are giving out free automatic upgrades for 6 months to the "Plus" level (offer expires July 31, 2006).

X'Aim lets you record your animals and their pedigree and calculates the inbreeding of each animal. It also incorporates state-of-the-art mate selection so that you can select matings to minimise inbreeding and coancestry.

There is no obligation and no requirement for credit card details to sign up, and you can download your data at any time at no cost. Because the software is on-line, there is no need for complicated downloads, you simply use your web browser.

Our web site: http://www.xaim.co.nz has more information, including coming features and product levels and pricing options, and a place where you can sign up.

We hope you find our software interesting and useful and would love feedback to help give direction for further development of the product.

We will be using this blog to keep you up-to-date with the latest information about X'Aim and will also be sharing interesting hints and tips on animal breeding and related topics.