Genomics can help meet future challenges

genome

It has accelerated genetic progress, and could help livestock industries in future

Livestock producers are under increasing pressure to produce more protein with fewer resources, and face scrutiny from consumers over issues such as water and land use, climate change and antimicrobial resistance.

To meet these challenges, genetic advancements, particularly the use of genomics, can play a significant role in creating a robust future for Ontario livestock producers, according to a recent White Paper released by the Livestock Research Innovation Corporation (LRIC).

Why it matters: Genomics can help livestock industries meet the challenges of the future, but there is still a lot of work to be done.

Genomics studies the entire genome, or all of the genes that an animal has and how these genes interact with each other, what they do, and how they influence growth and development.

In a webinar hosted June 8 by LRIC on genomics, Dr. Stephen Miller, deputy director of the Animal Genetics and Breeding Unit in Armidale, Australia and a former University of Guelph professor in beef cattle genetics, provided an overview of how genomics has advanced gains in animal breeding, and what direction it could take in the future.

Miller says prior to sequencing the genomes of animals, genetic progress was slow. Through the use of molecular genetics (identifying individual genes of interest), he says scientists were able to discover some genes that affected certain traits in livestock, but "it wasn't hugely successful."

But the use of genomics has been "transformative," he says.

For example, once the cattle genome was fully identified in 2009, the dairy industry has seen phenomenal improvements in the Lifetime Profit Index (LPI), which is an expression of genetic merit. Prior to 2009, estimated breeding values were used and calculated using animal performance measures along with pedigree relationships amongst animals, the LRIC paper states. Although genetic progress increased year over year, the introduction of genomic selection in addition to performance and pedigree measures gave it "a big boost."

Miller says the LPI gain per year on average prior to 2009 was about 46 points, and when genomic selection was implemented, "it's now over 100 points, which is a little more than doubling of genetic gain.

"Really what the technology is doing is it's allowing you to come up with an accurate genetic prediction based on the genotype (the genetic makeup of an animal)."

He says the benefit is that the industry can genotype young bulls without having to wait until it has thousands of daughters in milk and he's several years old to determine his genetic worth. "It really shortens the generation interval and increases the accuracy on young animals."

Now that genomic analysis has been around for a little more than a decade, the cost of performing the analysis has decreased, making it a more affordable component of animal breeding programs, according to LRIC. It notes that when the human genome was sequenced in 2001, the cost was $100 million, but the cost today would be under $1,000.

While genomics has accelerated genetic progress and will continue to be an important tool in selecting animals with key performance traits, "it's not magic" and there is still a lot of work that has to be done in this field, says Miller.

Miller says using genomics to identify a trait you want to change is only part of the process — a reference set of thousands of animals is still needed to measure the trait against the genotype. While individual genes can be identified, understanding how the gene influences a trait requires measurements on many, many animals to increase selection accuracy.

The biggest stumbling block for geneticists is understanding the relationship between the phenotype (the performance of an animal) and its genotype.

LRIC says environmental factors such as feeding, housing and health can significantly impact animal performance. The genotype determines an animal's genetic potential, but this potential can be greatly limited if the environment the animal is in is not optimal.

Although certain traits such as growth are relatively easy to measure, traits of interest such as health are far more dynamic, says Miller. That's why using genomics as a tool along with large reference sets of animals and proper management will be key to making progress in this area.

But that doesn't mean progress can't be made in the future.

"If you can dream it in terms of what you want to change, you can change it. It's simply a matter of measuring it, genotyping it, and making selections. And then you repeat…measure genotype, select and repeat," he says. "The method and the recipe is there."

Miller says he thinks genomics can provide a key solution to the challenges facing livestock producers in the future.

"It's really up to the industry to determine where want to take this and what challenges they want to tackle."

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