When it comes to animal breeding, the term ‘linkage’ gets thrown around a bit, especially in conversations about breeding values and genetic evaluation. But let’s be honest, it can sometimes leave you wondering, ‘What actually is linkage, and why does it matter so much?’
If you’ve ever submitted data, only to find your animals don’t rank well or, worse, don’t get breeding values at all, you’ve likely run into the issue of poor linkage. It’s one of those behind-the-scenes factors that can quietly limit the value of your recording efforts if you’re not aware of it.
So, I thought I’d take a moment to break it down. In this article, I’ll unpack what linkage is, why it’s critical for making sense of your data and, most importantly, what you can do when your breeding program is starting with little or none of it.
Why linkage matters
Firstly, let’s zoom out. I looked up the formal definition of linkage, and this is what I found: Linkage: the action of linking or the state of being linked.
Not super helpful on its own, but drill down further and you get: Link: a relationship between two things, especially where one affects the other.
In the breeding world, that’s basically what we’re talking about. Linkage is the relationship between animals that are run in different environments but share some common genetics, and those shared genetics are the links. It’s these links that allow us to fairly compare animals across different flocks/herds, farms and even countries. Without them, we can’t confidently benchmark or trust the breeding values we’re looking at.
Think of linkage as a genetic bridge, created when animals in your flock or herd share a common sire with animals in other flocks or herds. That bridge helps to connect your data to the national evaluation system (for instance, Sheep Genetics or BREEDPLAN, here in Australia).
Once that bridge exists, the evaluation system can make fair comparisons between animals raised in different environments (imagine animals on different sides of the bridge). But without shared genetics (ie linkage), there’s no bridge, and your data can’t be reliably compared. This leads to lower EBV accuracy and reduced visibility of your animals in the national system.
For instance, you might have a ram that’s performing brilliantly in your operation: great growth, structure, lamb survival, etc, but his EBVs don’t reflect that. The reason? He isn’t genetically linked to animals in other flocks. Without that connection, the system can’t compare his data properly and has no way of knowing whether he’s good only in your environment and under your management, or whether his progeny will perform well elsewhere. The value is there, but without the genetic bridge, it’s hidden.
Causes of poor linkage
Just like any bridge, linkage doesn’t just appear, and it’s not built overnight. It’s something we need to keep in mind and build over time. If you’re new to performance recording, or you’ve had a break and are starting again, your flock or herd might not be well connected to the national evaluation system.
Poor linkage often comes down to a few key factors:
- One of the biggest factors is not having any shared sires with other flocks/herds. If your genetics aren’t used elsewhere, or you’re not using proven sires with wide industry use, there’s no genetic bridge to compare animals in different places.
- Another cause is the absence of DNA testing. Without genomic data, the system can’t detect deeper genetic relationships that might not be obvious from pedigree records alone.
- Finally, submitting minimal or isolated data causes issues. For example, only recording one trait, one group, or for one season, all limit the ability of the evaluation system to connect your animals to the broader population.
Overall, strong linkage takes deliberate effort. It’s essential if you want accurate, trusted breeding values that truly reflect the genetic merit of your animals.
Practical strategies to build linkage and value
Introduce connected sires
One of the most effective ways to build linkage is to bring in sires that are already genetically connected to other flocks (or herds). These ‘reference sires’ act as anchors, as their shared genetics form the bridge between your animals and the wider evaluation system.
Artificial insemination (AI) offers a great opportunity to access sires with high accuracy and broad usage. Sheep Genetics recommends that even if you use just one connected sire for every 10 rams, that’s often enough to significantly improve linkage.
Natural service sires can also be valuable if they come from flocks or herds with strong data and proven breeding values. Choosing sires with high accuracy for traits important to your breeding goals (like growth or muscle) ensures that their impact is not only genetic but also valuable in terms of benchmarking.
It’s also important to look at how widely a sire has been used across different environments and over multiple years, and how many progeny he has recorded across different flocks/herds. Sires with wide industry use give your flock or herd a common genetic thread with many others, allowing the evaluation system to compare data with confidence. Over time, repeating this strategy across generations compounds the benefit, giving your flock or herd long-term access to higher EBV accuracy and visibility in the national evaluation.
DNA testing with purpose
DNA testing is one of the most powerful tools to build linkage, but it works best when used strategically. Testing key animals like sires and retained replacements helps connect your animals to the broader evaluation system, especially if those animals share genetics with others in the database.
Even small numbers of well-chosen animals can significantly strengthen your linkage. For example, DNA testing a sire that’s also used in another flock or herd enables the system to make confident comparisons between both environments. It also uncovers hidden genetic relationships that may not have been captured in traditional pedigrees.
When used over time, DNA builds a genomic picture of your flock or herd’s structure, allowing the evaluation to estimate breeding values more accurately, even for traits with low heritability.
The key is to be deliberate. Don’t waste resources testing every animal or at random. Instead, test those that will influence future generations or will be used for benchmarking. This approach to DNA testing not only improves the visibility of your animals in the national database but also allows your breeding values to gain strength and accuracy, even in the early years of recording.
Focus on within-flock/within-herd values
When linkage is still developing, don’t underestimate the power of good within-flock/herd selection. While breeding values may be low in accuracy early on, your own adjusted weights, structural assessments and raw performance data are still valuable for guiding breeding decisions. Keep detailed records of weights, growth rates, lambing outcomes and visual traits, especially if you’re selecting replacements or sale rams.
In commercial operations, feedback from kill sheets or client performance can also be useful for identifying consistent sire lines and high-performing ewes.
This internal data becomes more powerful as linkage strengthens over time. Early on, it helps you make sound genetic decisions even if national benchmarks aren’t yet fully developed for your flock or herd. Ultimately, within-flock/herd selection keeps your breeding program progressing while you work toward building broader linkage and full confidence in the national genetic evaluation.
Target key traits first
When beginning to record and build linkage, it makes sense to focus on traits where your raw data has the most impact.
Traits like weaning weight, post-weaning growth and eye muscle depth are moderately to highly heritable and relatively straightforward to measure. Because of their genetic simplicity and ease of collection, they’re also more likely to generate useful EBVs even when linkage is still developing.
In contrast, traits like reproduction, eating quality or worm resistance are lower in heritability and often require large datasets or genomic support to estimate with confidence.
So, early on, lean into the traits where progress is more visible and the data you collect has more weight. That doesn’t mean ignoring the more challenging traits, but rather being cautious in how you interpret their breeding values while the accuracy is still developing. As your linkage and dataset grow, accuracy will improve across all traits. Focusing on the key, high-impact areas first can build momentum, both in genetic gain and in confidence in your data system.
Collaborate to build linkage
Linkage doesn’t have to be built alone. In fact, collaboration can fast-track the process. Working with neighbouring breeders or within a producer group allows you to use shared sires intentionally and benchmark your animals more quickly. By selecting a common AI sire or swapping sires with trusted breeders, you instantly create genetic connections that strengthen the evaluation for everyone involved.
Producer groups or breed society trials are ideal for this. Even small-scale collaborations, such as two producers agreeing to use a shared sire and compare results, can make a difference. Data from multiple environments provides more context and confidence in genetic evaluations, which boosts breeding value accuracy and usefulness. You can also benchmark traits and performance across farms, allowing for honest feedback and improvement.
Programs like sire evaluations, young sire programs or resource flocks/herds are designed with linkage in mind. And the bonus of these initiatives is that you’re not just building linkage; you’re building community and shared learning, which benefits your breeding business beyond the data.
Keep perspective
Building linkage and seeing strong breeding values isn’t something that happens overnight. It can take several years of consistent recording, smart sire choices and ongoing DNA testing to see the full benefit of linkage. But that investment pays off in the form of accurate, reliable breeding values that reflect your animals’ true genetic merit. The key is to stay consistent and not get discouraged if your breeding value accuracy looks low early on. Remember, even the most well-established flocks and herds started somewhere. Every shared sire, every DNA test, every year of good data recording is a step forward.
Linkage is cumulative, meaning the more connections you build, the stronger your evaluations become. Celebrate the wins along the way, whether it’s better lamb survival, improved growth rates or positive customer feedback on your rams. Over time, these small wins compound to provide you with a flock or herd that’s not only genetically stronger, but also recognised and benchmarked at an industry level. Stay the course and it’ll be worth it in the long run.
Linkage is the foundation of meaningful genetic evaluation. Without it, your best-performing animals risk going unrecognised. So, take a strategic approach, lean into collaboration and don’t lose sight of your breeding goals. With consistency and purpose, you’ll build a program that not only makes progress within your own gates but also helps lay down a strong genetic bridge, one that connects your animals to the broader industry. And once that bridge is built, your animals can be fairly compared, accurately benchmarked and recognised for the true value they bring.
If you have any unanswered questions about linkage, let me know where I can dive deeper into the topic!
Join the conversation on The Hub
Take a moment to head over to the neXtgen Agri Hub to share your thoughts and questions about linkage.
Further reading
