Genomics: The Past, Present and Future 

In the past year, much has been said about genomics. In all, it's been a lot of information to take in so here's a brief recap of what genomics is and how it came about. The article also features a new genetic comparison of genomic-proven sires that now have milking daughters as well as a glimpse into the future of genomics.

Back to the Basics
Each cell within a bovine contains 30 chromosomes. The chromosomes contain strands of DNA. The DNA consists of different pairs of nucleotides or those little letters. The sequence of those 3 billion nucleotides contains all the instructions for the bovine body. The different sequences of nucleotides between animals in a population are what makes some animals better than others.

Genomic selection is the process of combining information from a large set of genetic markers (which cover the entire genome) with traditional genetic evaluations to select the best animals. What are the genetic markers? The genetic markers are SNPs (pronounced snips). These are the variations in a DNA sequence that occur when a single nucleotide is altered. How is the information from the genetic markers gathered? First, samples of blood, hair or semen are collected. From these samples, extract DNA. The DNA is placed on a chip that examines over 50,000 SNPs evenly distributed across bovine chromosomes.

The United States Department of Agriculture (USDA) conducted research to determine about 38,000 of those 50,000 SNPs on a bovine's DNA are informative for calculating genomic evaluations. The USDA did this by analyzing the DNA from the sperm of thousands of bulls that had semen collected throughout the past 40 years. The associations observed between the SNPs and the known genetic abilities of these highly reliable, progeny-proven sires made it possible to identify SNPs that impact the genetic traits the industry measures.

Now, genomics has made a large impact on the dairy genetics industry because geneticists are able to analyze the DNA from a baby calf and better determine the animal's genetic ability.

In a previous issue of Horizons, Dr. Kent Weigel of the University of Wisconsin-Madison explained the improvement in reliability with genomics, "Genomic research shows that, for a young Holstein bull or heifer, we can combine the animal's parent average with genomic information to get a ‘genomic PTA' with a reliability of 60 to 70 percent. This is vastly better than the reliability of merely its parent average which is typically only 30 to 40 percent."

How Dependable Are Genomic Rankings?
Do not doubt the ability of the 50K SNP chip to, on average, correctly predict the genetic merit of sires. On the one year anniversary of when genomic predictions were publicly released, milking daughters are telling us these predictions are correct.

Today, there are over 6,200 bulls reported with genomic predictions. The marketplace has well over 250 active status genomic-proven sires being promoted and marketed by artificial insemination (A.I.) companies.

Just a quick 12 months ago, Genex activated 34 genomic-proven sires. (The industry, as a whole, activated approximately 350.) Those original 34 Genex sires have progressed exceptionally well. Thirteen now average 70 milking daughters. The January 2009 Lifetime Net Merit (LNM) average for the 13 was +$588. Now with a total of 910 milking daughters, they average +$444. Before comparing these numbers, the base change and LNM formula change must be accounted for. Because of the base change and LNM formula change all sires across the industry decreased by an average $114 for LNM. Therefore, here's the math $588 - $444 - $114 = $30! That's right, the genomic prediction of this group of sires was only off by $30 LNM.

We can analyze PTA Type and Udder Composite as well. In both cases, the differences were minimal. The difference in PTAT as the genomic sires gained classified daughters was a decrease of 0.29. The difference for Udder Composite was a 0.18 decrease. Whether it is production traits or conformation traits, genomic predictions are very close to actual daughter performance levels.

The real question may be - in the old system would these 13 sires have been activated based on daughter information. To answer that, 10 out of the 13 are still on the active list today and another one would be except he died. That adds to 11 out of 13 sires (or 85 percent accuracy).

The sub group of 13 sires mentioned above has stood up to the test, but the phenomenal results come from all 273 Genex bulls that were genomic tested and now have milking daughters. These 273 bulls have 20,052 daughters or 73 on average per sire. According to the table below, which shows the difference between these sire's genomic- and daughter-proven evaluations, these 20,000 daughters speak volumes about the confidence one can have in genomics. LNM had only a $31 difference. Protein had no difference!

Table 1. Comparison of genomic proofs (1-2009) to daughter proofs (1-2010) for 273 Genex sires taking into account the genetic base change.

The early type information is very convincing as well. Genex owns 135 bulls that now have on average 35 classified daughters. In January 2009, these genomic sires had a +1.53 average PTAT. Once daughters were evaluated by a professional Holstein classifier, the sires averaged +1.40 (adjusted for base change). That is only a small difference of 0.13!

These comparisons prove we can confidently remove the terms "young sires" and "proven sires" from our vocabulary. Today all A.I. sires are proven sires - some are just proven by genomics and some by daughters.

What Does the Future Hold?
The genomic testing currently conducted with the 50K SNP chip revolutionized the selection of bulls for A.I. and had significant impact among registered breeders in the breeding and merchandising of females. Now, take the genomics thought process one step further as the future availability of a more cost efficient SNP chip or mini chip will open doors of opportunity to every dairy producer for the everyday management of females.

The cheaper mini chip will utilize about 3,000 SNPs and return a fairly reliable estimate of the animal's genetic levels for LNM and most yield, conformation and health traits routinely summarized by the USDA and breed associations.

The mini chip could have several potential applications. A dairy producer will have the ability to determine the optimum type of semen to use on that heifer. For instance, some dairy producers may use the SNP chip to identify the top 30 percent of heifers to breed to GenChoice™ sexed semen and thus yield more heifers from the highest genetic females.

Other future applications with the mini chip include official parentage verification, but the potential also exists to conduct parentage discovery. Thinking bigger and farther into the future, there may very well be the capability to group cows according to nutritional needs or provide individualized veterinary care based on the animal's genotype.

Illumina, Inc. recently announced the development of a 500K chip. The better the industry can describe the genetic characteristics of cows and bulls, the more information available to determine how management and environment interact with genetics.

Never will genetic testing be smarter than Mother Nature, or replace good common-sense decision making, but future genomic technologies that are cost efficient to the dairy industry will give farmers the powerful tools to better feed the world. The potential of genomics is enormous, and we are just beginning to make use of that potential.