What We Look For When Selecting Our Herd Genetics

One of the questions you often ask us is: “What makes Clover Creek milk and cheese so good?” The answer begins well before the milk ever reaches the cheese vat. It starts with the genetics of our cows.

Each year, we make deliberate breeding decisions. Our goal is to improve the quality of the milk in your glass. We also aim to enhance the cheese on your plate. This week, we wanted to share three of the traits we focus on. We will show you how each one connects directly to what you taste.

 Why Breeding Decisions Matter to You

All of our milk comes from our own cows right here on the farm. We don’t buy milk from other farms. Our choices about our animals have a direct impact. This impact is visible in your glass of milk and your wedge of cheese. Better cows mean better milk. Better milk means better cheese.

Here are the three things we’ve been focusing on most.

1. A2A2 Protein — Better Digestibility

You may have heard of A2 milk before. Several of you have told us that our milk is easier on your stomach than other milks you’ve tried. That’s not a coincidence. It’s something we’ve been actively working toward through selective breeding.

Here are the science basics: cow’s milk can contain two main types of beta-casein protein. These are A1A1, A1A2, or A2A2. Research suggests that A2 protein is gentler on the digestive system for many people. The A1 protein can be harder for you to break down. It may cause some discomfort. This discomfort leads people to think they’re lactose intolerant when they actually may not be.

If you remember your Punnett squares from biology class, this is where it gets interesting. A1 is the dominant gene. A2 is recessive. This means a cow needs two copies of the A2 gene to produce purely A2 milk.

Simplified Punnett Square — Beta-Casein Genetics

	A2 (father)	A2 (father)
A2 (mother)	A2A2 ✓	A2A2 ✓
A2 (mother)	A2A2 ✓	A2A2 ✓

When both parents carry only A2 genes, the offspring will be 100% A2A2. This is the goal we’re working toward for our whole herd.

We’ve been selecting A2A2 bulls for breeding for 20 years now. We are proud to say that approximately 90% of our herd has reached A2A2 status. The other 10% are A1A2. We’re working to bring that to 100% A2A2.

We’ve heard from many of you that you can enjoy our milk without the discomfort you experience with store-bought milk. That feedback keeps us pushing toward a fully A2A2 herd.

A Note on Raw Milk & Digestibility

Here’s something that surprised even us when we dug into the research. Raw milk — milk that hasn’t been pasteurized or homogenized — appears to be more digestible. This occurs regardless of whether it’s A1 or A2 protein.

The reason has to do with heat. When milk is pasteurized, the high temperatures denature the proteins. These temperatures essentially “unfold” and alter them. The process also destroys some of the naturally occurring enzymes that help your body process it. In raw milk, these proteins and enzymes remain intact. They are in their natural state. Many people find this easier to digest.

A2A2 genetics provides one advantage. In addition, our milk is sold raw. Together, these benefits help customers who have had trouble with pasteurized milk.

2. Kappa-Casein BB — Better Cheese

As our cheesemaking has grown, we’ve started looking at genetics through a cheesemaker’s lens, too. That led us to a milk protein most people have never heard of: kappa-casein.

Kappa-casein is a protein. It plays a crucial role in how milk coagulates. This means it is essential for transforming liquid milk into the firm curd that becomes cheese. Without strong coagulation, you get a soft and weak curd. This curd yields less cheese and is harder to work with in the aging cave.

The kappa-casein gene comes in three options — A, B, and E. And just like A2A2, we’re selecting for bulls that carry the BB genotype. Cows with BB kappa-casein produce milk with higher protein content. This results in better cheesemaking properties. It means more cheese per gallon, more consistent results, and a better final product for you.

This is a newer focus for us, and one we’re excited about. Every wheel of Clover Creek cheese you buy results from such decisions. It represents years of patient and deliberate breeding.

3. Pasture-Adapted Breeds — Built for the Grass

The third pillar of our breeding program is less about a single gene. It focuses more on the whole animal. We want cows that not only survive but thrive on pasture. This philosophy has led us to look beyond the typical American dairy breeds. We are exploring genetics from New Zealand, Australia, and continental Europe.

Most U.S.dairy farmers have been selected for one thing: lots of milk from cows kept inside and grain-fed. That’s not what we do here. Our animals live outside on grass. We need a cow that can efficiently convert pasture to milk and muscle. She must stay healthy and sound on her feet. Moreover, she should maintain a healthy body weight through the seasons without requiring corn and soy to keep her producing.

The “dual-purpose” angle matters a great deal to us. Bull calves and older cows are part of the reality of a working herd. With genetics selected for dual-purpose use, those animals grow well on grass and yield high-quality beef. That’s a direct connection between our breeding decisions and grass-fed beef.

There’s a flavor dimension here, too. European dual-purpose breeds are well known among cheesemakers for the richness and complexity of their milk. Higher butterfat and more protein contribute to the depth of flavor. A different fatty acid profile also enhances the taste you experience in our aged wheels. French Comté and Swiss Gruyère are some of the most celebrated cheeses in the world. They are made from the milk of these same breeds. We’re drawing on that tradition, right here in central Pennsylvania.

We don’t just breed for a number on a paper. We are breeding an animal that fits the land and our system. This animal produces milk and beef that reflect the quality of the grass she’s standing on.

The Bigger Picture

When you buy milk or cheese from Clover Creek you’re buying into a system of decisions that stretches back years. The wedge of aged cheddar you pick up at the farmers market reflects our choices when selecting a bull. It shows how we manage our pastures. It also demonstrates the time we’ve invested in understanding what makes our milk exceptional.

A2A2 genetics for digestibility. Kappa-casein BB for better cheese. Pasture-adapted, dual-purpose breeds that thrive on grass and contribute to our beef program. These aren’t marketing talking points. They are the practical, intentional decisions of a family farm. The farm takes the relationship between our land, our herd, and our customers seriously.

We’re grateful for every one of you who asks questions like “what makes your milk different?” — it’s exactly that curiosity that keeps us pushing to do better. If you want to learn more, visit us. We’d love to have you on our farm to see the herd for yourself.