Animal Breeding / Biotechnology / Cattle / Dairying / Genetics

Dairy scientists of the genomics age: How big data transformed the dairy industry

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Holstein-Friesian cow, Biggle cow book, Philadelphia, W Atkinson Co., 1898 (photo on Flickr by Biodiversity Heritage Library).

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.

‘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. . . .

‘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. . . .

‘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.

‘In a sense that’s very real, information itself has transformed these animals. The information did not accomplish this feat on its own, of course. All of this technological and scientific change is occurring within the social context of American capitalism. Over the last few decades, the number of dairies has collapsed and the size of herds has increased. These larger operations are factory farms that are built to squeeze inefficiencies out of the system to generate profits. They benefit from economies of scale that allow them to bring in genomic specialists and use more expensive bull semen.

‘No matter how you apportion the praise or blame, the net effect is the same. Thousands of years of qualitative breeding on family-run farms begat cows producing a few thousand pounds of milk in their lifetimes; a mere 70 years of quantitative breeding optimized to suit corporate imperatives quadrupled what all previous civilization had accomplished. And the crazy thing is, we’re at the cusp of a new era in which genomic data starts to compress the cycle of trait improvement, accelerating our path towards the perfect milk-production machine, also known as the Holstein dairy cow. . . .

‘With that in mind, allow me to suggest, then, that the dairy farmers of America, and the geneticists who work with them, are the Mendels of the genomic age. That makes the dairy cow the pea plant of this exciting new time in biology. Last week in the Proceedings of the National Academy of Science[s], two of the most successful bulls of all time had their genomes published.

This is a landmark in dairy herd genomics, but it’s most significant as a sign that while genomics remains mostly a curiosity for humans, it’s already coming of age when it comes to cattle. It’s telling that the cutting-edge genomics company Illumina has precisely one applied market: animal science. They make a chip that measures 50,000 markers on the cow genome for attributes that control the economically important functions of those animals.

‘. . . The unique dataset and success of dairy breeders now has other scientists sniffing around their findings. Leonid Kruglyak, a genomics professor at Princeton, told me that “a lot of the statistical techniques and methodology” that connect phenotype and genotype were developed by animal breeders. In a sense, they are like codebreakers. If you know the rules of encoding. it’s not difficult to put information in one end and have it pop out the other as a code. But if you’re starting with the code, that’s a brutally difficult problem. And it’s the one that diary geneticists have been working on. . . .’

Read the whole article at the AtlanticThe Perfect Milk Machine: How Big Data Transformed the Dairy Industry, 1 May 2012.

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