The Perfect Dairy Sire

The Atlantic:

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.

Wow, 22 percent?  I would like to see a chart of the top producers' family trees.  That has to be a tangled mess.