The Perfect Milk Machine: How Big Data Transformed the Dairy Industry

Dairy scientists are the Gregor Mendels of the genomics age, developing new methods for understanding the link between genes and living things, all while quadrupling the average cow's milk production since your parents were born.

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Reuters.

While there are more than 8 million Holstein dairy cows in the United States, there is exactly one bull that has been scientifically calculated to be the very best in the land. He goes by the name of Badger-Bluff Fanny Freddie.

Already, Badger-Bluff Fanny Freddie has 346 daughters who are on the books and thousands more that will be added to his progeny count when they start producing milk. This is quite a career for a young animal: He was only born in 2004.

There is a reason, of course, that the semen that Badger-Bluff Fanny Freddie produces has become such a hot commodity in what one artificial-insemination company calls "today's fast paced cattle semen market." In January of 2009, before he had a single daughter producing milk, the United States Department of Agriculture took a look at his lineage and more than 50,000 markers on his genome and declared him the best bull in the land. And, three years and 346 milk- and data-providing daughters later, it turns out that they were right.

"When Freddie [as he is known] had no daughter records our equations predicted from his DNA that he would be the best bull," USDA research geneticist Paul VanRaden emailed me with a detectable hint of pride. "Now he is the best progeny tested bull (as predicted)."

Data-driven predictions are responsible for a massive transformation of America's dairy cows. While other industries are just catching on to this whole "big data" thing, the animal sciences -- and dairy breeding in particular -- have been using large amounts of data since long before VanRaden was calculating the outsized genetic impact of the most sought-after bulls with a pencil and paper in the 1980s.

Dairy breeding is perfect for quantitative analysis. Pedigree records have been assiduously kept; relatively easy artificial insemination has helped centralized genetic information in a small number of key bulls since the 1960s; there are a relatively small and easily measurable number of traits -- milk production, fat in the milk, protein in the milk, longevity, udder quality -- that breeders want to optimize; each cow works for three or four years, which means that farmers invest thousands of dollars into each animal, so it's worth it to get the best semen money can buy. The economics push breeders to use the genetics.

The bull market (heh) can be reduced to one key statistic, lifetime net merit, though there are many nuances that the single number cannot capture. Net merit denotes the likely additive value of a bull's genetics. The number is actually denominated in dollars because it is an estimate of how much a bull's genetic material will likely improve the revenue from a given cow. A very complicated equation weights all of the factors that go into dairy breeding and -- voila -- you come out with this single number. For example, a bull that could help a cow make an extra 1000 pounds of milk over her lifetime only gets an increase of $1 in net merit while a bull who will help that same cow produce a pound more protein will get $3.41 more in net merit. An increase of a single month of predicted productive life yields $35 more.

When you add it all up, Badger-Fluff Fanny Freddie has a net merit of $792. No other proven sire ranks above $750 and only seven bulls in the country rank above $700. One might assume that this is largely because the bull can help the cows make more milk, but it's not! While breeders used to select for greater milk production, that's no longer considered the most important trait. For example, the number three bull in America is named Ensenada Taboo Planet-Et. His predicted transmitting ability for milk production is +2323, more than 1100 pounds greater than Freddie. His offspring's milk will likely containmore protein and fat as well. But his daughters' productive life would be shorter and their pregnancy rate is lower. And these factors, as well as some traits related to the hypothetical daughters' size and udder quality, trump Planet's impressive production stats.

One reason for the change in breeding emphasis is that our cows already produce tremendous amounts of milk relative to their forbears. In 1942, when my father was born, the average dairy cow produced less than 5,000 pounds of milk in its lifetime. Now, the average cow produces over 21,000 pounds of milk. At the same time, the number of dairy cows has decreased from a high of 25 million around the end of World War II to fewer than nine million today. This is an indisputable environmental win as fewer cows create less methane, a potent greenhouse gas, and require less land.

At the same time, it turns out that cow genomes are more complex than we thought: as milk production amps up, fertility drops. There's an art to balancing all the traits that go into optimizing a herd.

While we may worry about the use of antibiotics to stimulate animal growth or the use of hormones to increase milk production by up to 25 percent, most of the increase in the pounds of milk an animal puts out over the pastoral days of yore come from the genetic changes that we've wrought within these animals. It doesn't matter how the cow is raised -- in an idyllic pasture or a feedlot -- either way, the animal of 2012 is not the animal of 1940 or 1980 or even 2000. A group of USDA and University of Minnesota scientists calculated that 22 percent of the genome of Holstein cattle has been altered by human selection over the last 40 years.

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