Genomics could revolutionize heifer selection methods

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There is a freight train of new management tools headed for U.S. dairy farms, and it’s aiming straight for the heifer breeding pen, says Pat Hoffman, professor of dairy science based at the University of Wisconsin’s Marshfield Research Station in Marshfield, Wis.

Dairy cow “Heifers are a new horizon for herd improvement with genomic testing,” says Hoffman. “Cows are already cows, so testing them doesn’t allow us to make informed management decisions about them the way we can with heifers.”

Dick Wallace, senior dairy technical service veterinarian with Zoetis Animal Genetics, says a first-calf heifer needs to perform as a productive member of the herd for more than one lactation to compensate for the cost of raising her.

The use of sexed semen and embryo transfer, along with improved reproductive programs, has left many dairies with far more heifers than they need to maintain their herd size. Couple that fact with today’s high feed prices, and it is easy to see why being selective about which heifers to raise could be beneficial to a herd’s bottom line and its genetic advancement.

Genomic decisions
“The decisions we need to make about every heifer are (a) whether she is needed in the herd, and (b) if she fits the genetic goals of the herd,” says Wallace. “If the answer to either question is ‘no,’ then genomics can help determine other routes for her than the breeding pen.”

Wallace works with herds on the application of CLARIFIDETM Dairy Genomics Test, a 6,909-marker (6K) panel that delivers genomic predictions for as many as 30 production, health and type traits, as well as nine composite indexes. He advises producers to test heifers as early in their lives as possible to make rapid decisions regarding their futures, suggesting that the results could send heifers down one of several paths. A herd plan might look something like:

1. Lowest 10 to 15 percent – sell for dairy or beef.
2. Next 20 to 40 percent – use as recipient animals for embryo transfer, allowing them to enter the milking herd but not transmit their genetics.
3. Next 20 to 40 percent – breed to sexed semen.
4. Top 5 to 10 percent – enroll in embryo transfer programs.

While those percentages will vary among herds, Wallace says the structure helps producers manage heifer inventories with confidence that they are continuously improving their herds. Another strategy some herds are employing is breeding a percentage of their low-end genomic animals to beef sires. “This approach captures some premium value for the calves, and removes the temptation to keep lowergenomic animals in the herd,” says Wallace.

Genetic insights
In addition to production decisions, genomic results also provide important genetic information that assists in making successful matings, including:

HAPLOTYPE IDENTIFICATION – Several haplotypes, which are sections of DNA inherited as a group, have been identified that negatively affect fertility. In Holsteins, they are HH1, HH2 and HH3. One has been identified in Brown Swiss (BH1) and one in Jerseys (JH1). These haplotypes are fairly common within their respective breeds, so culling based on their presence is not advised. But Hoffman says it is important to avoid breeding a female haplotype carrier to a haplotype-carrier bull, which would increase the likelihood of failed conception or early embryonic loss by about 25 percent. “Lost pregnancies are very expensive in heifers,” says Hoffman. “Using genomic information is an easy way to avoid a widespread problem in the industry.”

INBREEDING AVOIDANCE – Inbreeding is a silent scourge that can rob dairies of milk production potential, reproductive performance, and calf health and vigor. It also increases the risk potential for recessive genetic disorders. Genomic reports include the percent of homozygous genes an animal carries, meaning the animal received the same gene from both parents. Heifers identified as moderately to highly inbred can either be culled or carefully mated to diversify the genetic makeup of their offspring.

Jeff Ziegler, genomic program manager for Select Sires in Plain City, Ohio, acknowledges that genomics potentially could accelerate inbreeding. “Based on genomic data, we’re winnowing down the best of the best fairly quickly,” he says. “If we’re not careful, we could rapidly breed ourselves into a very narrow gene pool.”

To address this issue, Select Sires studied the diversity strategies of other genetics-based industries, including the seed corn industry. They recognized the importance of creating bloodlines that are not very closely related. Those bloodlines then can be crossed to reap the benefits of hybrid vigor.

The commercial result of those efforts is a Holstein sire genetic development program from Select Sires called StrataGENTM. For several years, Select Sires has been mating and sorting bulls — both daughter-proven sires and young sires — specifically designed to fit one of five distinct bloodlines. Herds then can apply the information to a three- to five-line rotation over multiple generations using a simple, color-coded system.

Ziegler emphasizes that while some of the bulls used to develop the StrataGEN breeding lines possess fairly unique genetic profiles, all of them still are high-ranking sires. “We didn’t sacrifice performance for genetic diversity,” says Ziegler, noting that every bull in the program has been or will be proven through Select Sires’ progeny test program, with specific emphasis on milk production, moderate body size, fertility, and the ability to maintain body condition score.

PARENTAGE CORRECTION – Genomic results also will flag animals whose genetic makeup does not correspond with the animals identified as the sire and dam on their submission form. Usually, the correct sire can be found in the USDA genomic database, as can the dam if she has been genomic-tested.

“We currently are logging 17 to 20 percent sire identification errors with CLARIFIDE,” says Wallace. “With multiple people performing breeding and recording information on dairies, it is a fairly common issue, despite everyone’s best efforts on the farm.” By correcting parentage information, more accurate matings can be performed, and inbreeding can be avoided.


Practical application

Hoffman has observed slow, steady adoption of genomic testing of heifers in the near-term, but at the same time cautions that no technology stands on its own. “The information from genomics is powerful, but it must be accompanied by the fundamentals of successful replacement-rearing,” he says. “We still need to be hitting health and growth targets for our heifers, and get them pregnant in a timely fashion. If we don’t, we lose some or all of the added value that genomic selection affords.”

The direct financial outlay for genomics testing is no small consideration, with the cost per animal ranging from about $45 to $60. However, Wallace points out that there are both short- and long-term payoffs to maximize the investment. He says the cost of feeding a heifer today is approximately $90 per month, compared to $50 to $60 just a few years ago. “Herds usually can cull enough heifers to immediately cash-flow the test,” he says.

Of course, the long-term goal of genomics is to advance the genetic potential for milk production, conformation and fertility in the herds that apply them. “For herds that already are doing a great job with milk production, milk quality, breeding, heifer management and feedstuff production, I think genomics is the next tool to bump them to even higher levels of performance,” says Wallace. “The information should be the vehicle to help them continuously achieve the goal of milking better cows.”

Next month: Profiles of herds and how they are applying genomic information.

Sidebar:

Genomic sampling made easy

Collecting samples for genomic testing can become a routine on-farm procedure. University of Wisconsin professor Pat Hoffman and Zoetis technical services veterinarian Dick Wallace both suggest sampling and testing heifer calves as early as possible, so that timely management decisions can be made based on the results.


Genomic tests require blood, hair follicle or tissue samples from individual animals. (Twins require hair follicle or tissue samples). Samples are submitted to one of the current providers of genomic testing, which include the Holstein, Jersey and Brown Swiss associations, and Zoetis Animal Genetics. Each submission should include the animal’s identification number, birth date, and a bar code. Identifying the animal’s sire and dam on the submission form is not required, but improves accuracy of the results.


Combining sampling with other procedures that already are performed in the first few days of calves’ lives can make the process more efficient. Following are suggestions for streamlining the sample collection process:

• Collect blood samples when screening for IgG/total protein levels. After drawing blood for IgG screening, apply a spot for every animal to individual FTA® cards. The cards can be stored at room temperature until the dairy has accumulated a batch that then can be submitted for testing.

• Collect hair follicle samples when processing newborns. When feeding colostrum, tagging, dipping navels or administering vaccines, pull a pencil-width hair sample from the ear or tail switch. Be sure to collect the hair bulbs from beneath the skin. Place in samplecollection pouches from the test provider, seal and label for each animal. These samples, too, can be stored at room temperature for batch processing.

• Combine ear-tagging with sample collection. Zoetis will soon be introducing a new skin-punch tool that collects a tissue sample while administering RFID tags. The tiny notch of skin punched out to install the tag is automatically gathered in a vial with preservative that can then be sealed, identified for each animal, and processed in batches.


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