21/01/2026
Inbreeding vs Line Breeding – Part 6
Bottlenecks, Blind Spots, and What We Actually Know
By Tim from Linessa Farms
If you’ve followed this series from the beginning, you may have noticed something uncomfortable by now:
Most genetic narrowing does not happen because someone intentionally set out to line breed aggressively.
It happens quietly.
It happens unintentionally.
And it often happens under good intentions.
That’s what this final article is about.
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How most farms bottleneck without realizing it
You don’t need close matings to create inbreeding pressure.
It happens when
– the same ram is used too long
– replacement females all trace back to the same few animals
– outside genetics stop coming in
– selection focuses on a narrow set of visible traits
– culling pressure drops
No one calls this line breeding.
But biologically, it still increases genetic uniformity.
That’s why many people are already “under the umbrella” of inbreeding without ever putting their finger on it.
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COI, pedigree, and the illusion of precision
Inbreeding coefficients (COI) are often treated like a safety score.
But COI only estimates probability, not outcome.
It does not tell us
– which genes became homozygous
– whether those genes matter
– how they interact with environment
– or what management is compensating for
COI is also only as reliable as the records behind it.
If pedigree assumptions are wrong, or someone “fudged” records, the math can be clean and the answer meaningless.
COI is a risk indicator, not a verdict.
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Why some traits fade quietly
One pattern has repeated throughout this series:
– simple traits respond quickly
– complex traits degrade quietly
Traits like color, horn status, and body style stabilize fast.
Traits like
– fertility
– parasite resistance
– robustness
– longevity
– feed efficiency
are polygenic (multiple genes involved) and environment-dependent.
They don’t fail dramatically.
They lose margin.
And that loss often isn’t noticed until
– stress increases
– management slips
– animals move to a new environment
Nothing suddenly “went wrong.”
The system just ran out of room.
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Phenotype tells the truth — just not the whole one
Phenotype reflects gene expression under a specific set of conditions.
Two animals can carry the same genes and express them very differently depending on
– environment
– nutrition
– stress
– disease pressure
– management
That’s why animals can perform exceptionally well in one system and struggle in another without anything “changing genetically.”
Phenotype tells us what worked here, now, under this system.
It does not guarantee transferability.
Consistency is not the same thing as resilience.
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What responsible line breeding actually does
Responsible line breeding does not create universally superior animals.
It creates animals that fit a specific system very well — sometimes at the cost of flexibility outside that system.
Done well, it requires
– understanding which traits are simple vs complex
– constant, honest selection
– tracking fertility and longevity
– accepting culls when outcomes aren’t right
– recognizing that performance is system-specific
Done casually, it narrows genetics faster than people realize.
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The real risk most people miss
The biggest risk in breeding isn’t inbreeding itself.
It’s mistaking consistency for margin.
Uniform animals can look stable right up until the moment pressure changes.
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What I hope this series actually did
This series was never about telling anyone what they should do. Without trying to sound gruff, I could honestly care less if people choose to line breed or not. This is an education piece; that’s it. If you felt this was bashing your methods or promoting others, that’s just you projecting.
It was about
– cleaning up language
– removing false certainty
– separating probability from promise
– explaining why biology resists shortcuts
If this made breeding feel a little less tidy — and a little more honest — that’s a win.
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What’s next?
I’ll be following this series with a short companion video using a simple parking garage analogy to visually explain genes, alleles, homozygosity, and why environment changes outcomes. This is the visual I use when teaching human genetics. It still applies and I think many of you who are visual learners will find it helpful. Look for that post in a few days.
Not to convince anyone — just to make the structure easier to see.
Because once the structure makes sense, the arguments mostly disappear.
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Breeding isn’t about fixing genetics.
It’s about managing risk, margin, and reality.
Thanks to everyone who helped put these articles together! You are appreciated. I will be posting these articles together on our website as soon as I de-format them from Facebook to PDF.