Enhancing Genomics with LimVision
By: Leighton Chachere
Each day the North American Limousin Foundation (NALF) works to improve the Limousin breed through programs and outreach efforts for Limousin breeders across the country. Last year, NALF embarked on a new breed improvement program through a collaboration with Neogen - LimVision.
LimVision allows Limousin breeders to genomically test their cow herd at a discounted research rate. The program sets out to increase genomic marker information on females and to increase accuracy of expected progeny differences (EPDs) in the NALF herdbook.
Since enrollment opened for the program in January 2020, NALF staff and board members have been heavily promoting the program and sharing the benefits of genomic testing, especially NALF Executive Director, Mark Anderson.
“The primary factor motivating members to genomically test their cattle is to improve EPD accuracy and accelerate EPD trait improvement on their cattle,” said Anderson. “This improves the quality of cattle offered by Limousin breeders to the commercial cattle industry throughout the nation.”
The first Texas Limousin breeder to enroll in the program was Gary Fuchs of Fuchs Limousin. Fuchs has been raising Limousin cattle in Cameron, Texas since 1978 and is a previous NALF board director. While he has seen the value of genomically enhancing his own EPDs, he is also encouraging other breeders to participate.
“It’s just common practice in a lot of breeds, and if we’re going to compete, then we need to know the most about our cattle to be in the market place correctly,” said Fuchs. “The first step to that was having my herd participate in the program and taking that first step to be there.”
Data is power in today’s world and data is exactly what genomic testing is helping breeders gain more of.
“The main reason we have breeders interested in the LimVision program is the genomics,” said Anderson.
Genomics is the study of the entire set of genes found in a living organism. For cattle testing, they identify each animal’s EPD accuracy utilizing marker subsets that are identified for each trait. Genomics give producers early insight to an animal's quality because of the progeny equivalents that are generated by genomic testing.
LimVision enrollment closes in December 2021 and specifically focuses on female data, as the majority of the breed’s sires have already been genomically enhanced. Genomically enhanced EPDs have been a benefit to bull sellers because it shows buyers that EPDs are more accurate for progeny equivalence. For cow factories though, the benefits can go even further.
“You think of the life of a cow - she may get 12 to 14 babies on the ground,” said Anderson. “Then you have to prove those out and get data on them to help bring up the accuracy on the EPDs and that’s why genomics has taken off.”
This ability benefits individual breeders and the breed as a whole, helping to identify unwanted genetics faster. Weight trait EPDs possess the progeny equivalency for having 20-25 calves on the ground once genomically enhanced. Carcass traits have progeny equivalency of 8-10 head. This lets a producer identify high quality cattle early in their life span in addition to sorting out inferior cattle.
“Once those cattle are enhanced, International Genetic Solutions (IGS) combines the genomic marker panel information with all the weight trait phenotype data you guys have turned in, for the weekly national cattle evaluation,” said Anderson. “So we get a good idea on the superior numbered cattle early in their life cycle, and you’ll find your cattle that maybe aren’t as desirable.”
Just having your cattle genomically enhanced doesn’t make them better though, Anderson explained; it’s simply the tool you use to help make better mating decisions for your herd. Once you have genomic testing done on your females, it becomes much easier to make breeding decisions based on real data.
One of the main reasons to participate in LimVision is the improved accuracy of projected matings - knowing exactly what you can expect from matings, helping breeders predict future profitability potential.
“I have confidence that what I’m going to see is a lot more accurate than what it was three or four years ago,” said Fuchs. “That’s when I make my matings, I get the EPDs right and marketable. Then, all I have to worry about is phenotype, and not what the EPDs are going to show.”
Confidence in EPD accuracy becomes an even greater benefit with tools available to run progeny projections for mating options considered. For Limousin breeders, this is available online through DigitalBeef.
“When your set of cows are done and you put a mating into DigitalBeef, you’ve probably got a set of projected EPDs that are going to be very close to the actual result of the mating before you even put the semen in the cow,” Anderson said. “This tool in DigitalBeef lets you try many potential sires on your cows to make genetic improvement even faster.”
To find the progeny calculator on the DigitalBeef website, breeders can simply click on “tools” on the work menu then find “prog calc” in the red tab. Once clicked on, this prompts to start with bulls or females first. For bulls, breeders can search by registration numbers, and for females, by registration numbers or by pulling up their entire list of cows.
“I use the progeny calculator a lot,” said Fuchs. “When I’m looking for a herd bull and get the registration number on the bulls I’m looking at, I run the EPDs and see what the progeny sired by that bull across my whole cow herd would look like.”
With genomically enhanced EPDs, running numbers through the progeny calculator only increases the accuracy of the results found.
“I love it,” said Fuchs. “I use it on almost everything I do. I’ll use it when I’m looking at semen next year.”
DigitalBeef also provides a sire search option that Anderson says is extremely helpful when searching for semen and preferred EPD numbers. Once on the site, breeders can use the EPD tab to search each trait for minimum and maximum numbers on potential sires. The tool also gives options to select for Purebred, LimFlex, homozygous black, homozygous polled and more. Once preferred characteristics are selected, the site provides an entire list of sires that fit that criteria, and even highlight in yellow, those that have been genomically enhanced.
With the benefit of projected mating accuracy and encouraging breeders to focus on numbers while selecting matings, one goal of the LimVision program is to improve breed EPDs. Some of the EPD characteristics the breed is hopeful to improve include scrotal circumference, birthweight, docility, stayability and marbling.
“In our world of carcass marketing now, we’ve got to be aware of marbling,” said Fuchs. “Whether we like it or not, we like to be a yield grade breed but the world likes marbling right now.”
LimVision captures unbiased, complete performance and reproductive information for more reliable genetic predictions for Limousin breeders. With this comes a few requirements for program participants, though.
First, participants must be enrolled in the LIMS Whole Heard program database and have a NALF registration number to qualify. According to Anderson, most breed associations have some form of whole herd reporting and it greatly benefits breeders trying to sell commercial bulls.
Another requirement for program participants is that they must submit DNA samples on 90% or greater of their mature cow herd.
“The reason they want 90% is because they don’t just want your top cows,” Anderson said. “They want everything from the top to the bottom, and that helps train the marker panels, it makes it that much more accurate.”
Lastly, DNA samples must be submitted via All-Flex Tissue Sampling Unit or Blood Card on the electronic LIM Vision Cowherd Project. According to Fuchs, both are viable and easy options on collecting data, though he highly recommends the tissue sample collector.
“I collect them out of the ear and it’s like a very small tag punch, like the size of a pen head,” said Fuchs. “You poke out of a calf's ear and it goes into a tube of solution that preserves it and that is the easy way now.”
The largest benefit of enrolling in LimVision now, before enrollment closes, is the reduced price of getting your cow herd genomically enhanced. Typically, genomic testing costs $55 per animal, but through this program, breeders receive a discounted rate of $24 per head, which is the research rate.
On top of the discount, if breeders turn in a body condition score and mature weights on their cows, NALF will give them an additional $3 off per head, dropping the rate to $21 per animal. The additional benefit to enrolling now is, even after the program ends, breeders can still get new females tested at the discounted rate in years to come.
“You’ve got to have a little pain upfront,” said Anderson. “But you’re getting the discounted research rate and that qualifies you to get those replacement heifers updated every year so it helps reduce the impact of the initial cost and enables producers to genomically enhance their cow factories at a discounted rate.”
Overall, there are many benefits to enrolling in the LimVision program and according to Anderson, the market place is starting to demand genomic testing in cattle.
“When you go to these sales, a lot of people are wanting to see if those cattle are genomically enhanced,” said Anderson. “To see those higher accuracy numbers represented on that EPD set on a bull or that dam, or heifer prospect coming.”
The hope is to have as many breeders enrolled as possible to move the Limousin breed forward and to improve the breed one test at a time. Summing up the value and importance of the program, Fuchs encourages all Limousin breeders to enroll.
“It’s important for us to use the tools that are available to us to make our breed more marketable,” said Fuchs.
Enrollment for LimVision ends in December 2021, and a limited number of research 50K genotypes and rebate funds are available for the project. For more information, or to enroll your herd, please contact Mark Anderson at firstname.lastname@example.org.