Windmill Farms 15 Year Breed Preservation Initiative

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Breed preservation steps involve a multifaceted approach focusing on maintaining genetic diversity and health within the breed. Key strategies include understanding and monitoring coefficient of inbreeding (COI), kinship, genetic diversity testing of offspring, avoiding incestuous pairings, and assessing gene pool quality. Other important steps include using pedigree analysis, conserving sire and dam-line diversity, and utilize outcross pairings,  also known as outbreeding, referring to the breeding of individuals within the same breed that are not closely related, typically with no common ancestors for several generations.  

Here is how I systematically approach finding and preserving them: 

1. Identify the "Underrepresented" Alleles
When looking at the VGL data, pay close attention to alleles or haplotypes with an occurrence frequency below 5%.

The Goal: These alleles are at high risk of being lost due to Genetic Drift (random chance) or Selection (breeders focusing on specific "popular" traits).

The Risk: If these rare variants disappear, the breed's Effective Population Size () effectively shrinks, even if the total number of living dogs remains high. 

2. Calculate the Preservation Priority
To determine how "critical" a specific dog is to your breed's diversity, you can use a simple mental framework:

Frequency in Population  
Presence in Your Dog
Action

3. Combat the "Popular Sire" Effect
The most common way rare alleles are lost is when the majority of a breed's population begins to descend from a single highly-awarded male.

The Displacement: As the popular sire's alleles move toward 80-90% frequency, the rare alleles you found in the VGL data are pushed toward 0% and eventually extinguished.

The Strategy: Use dogs carrying these rare alleles in your breeding program, even if they aren't "perfect" specimens, to ensure those genetic "options" remain available for future generations. 

4. Watch for DLA Haplotypes
VGL often provides data on the Dog Leukocyte Antigen (DLA). These are the genes responsible for the immune system. 

Diversity is Safety: Research suggests that high diversity in DLA haplotypes correlates with better autoimmune health and resistance to pathogens.

The Key: If you find a rare DLA haplotype in your dog, that dog is an invaluable asset for the long-term health of the breed's immune system. 

Important Note on "Rare" vs. "Damaging"
Be sure to distinguish between neutral diversity (like coat color or non-coding markers) and deleterious mutations. A rare allele isn't inherently "good" if it's linked to a known genetic disorder; however, most VGL diversity markers are neutral and serve as excellent proxies for the overall health of the genome.

Practicing assortative mating, avoiding back to back repeat breedings, ensuring sibling contribution, monitoring fitness indicators, and attempting founder balancing.