Genomics, Phenomics Research Paves the Way for Improved Animal Health and Productivity

By Laura McGinnis, Sharon Durham, Ann Perry, Jan Suszkiw, Alfredo Flores and Don Comis, Agricultural Research Service Information Staff. The Agricultural Research Service’s genomics and phenomics research is laying the foundation for future livestock production improvements.
calendar icon 17 August 2008
clock icon 7 minute read

Understanding how inherited characteristics relate to specific genomes will eventually allow researchers to develop tools that can be used to guide animal breeding, selection, and management decisions. Throughout the United States, ongoing ARS research projects are changing the way industry members breed, raise, and produce our nation’s most valuable agricultural animals.

Identifying DNA Markers and Traits

Immunologist Hyun Lillehoj holds a chicken gene chip that contains up to 10,000 chicken genes.

ARS scientists at Clay Center, Nebraska, and Miles City, Montana, joined an international consortium in sequencing the bovine genome in 2002. Today, ARS scientists throughout the country are using this information to improve beef cattle management and production.

Some ARS researchers are using genomic research to improve animal health. This is particularly useful in situations with infected but asymptomatic cattle, says Mohammad Koohmaraie, former director of the Roman L. Hruska U.S. Meat Animal Research Center (USMARC) at Clay Center. For example, cattle can carry diseases like bovine respiratory disease (BRD) without having symptoms. This complicates attempts to assess their genetic resistance. Having ways to identify asymptomatic cattle or those at higher risk of illness would allow scientists to more accurately gauge how genes affect resistance.

To improve their assessments, USMARC researchers led by geneticist Larry Kuehn are working with scientists at the ARS National Animal Disease Center in Ames, Iowa, to develop large collections of cattle phenotypes, or observable traits. These include traits such as general immune-system functionality, body temperature, respiratory rate, and feeding behavior. The phenotypes will be drawn from populations representing prominent breeds in the U.S. beef industry.

The SNP50 BeadChip. Each chip has the capability of testing just under 80 million DNA-coated glass beads, allowing ARS researchers to test 60,000 locations at once, with a substantial amount of intended redundancy to ensure accuracy.

“By examining a larger group of traits, we can more accurately classify animals into categories according to their potential disease risk or resilience,” Koohmaraie says. This will enable researchers to identify traits that are most indicative of potential BRD risk and determine how those traits relate to genetic resistance to it.

One tool that could help scientists in this and other projects is the Illumina Bovine SNP50 BeadChip—a glass slide containing thousands of DNA markers called “single nucleotide polymorphisms,” or SNPs, which are used to find relationships between DNA markers and traits of economic importance.

The BeadChip has research applications for both beef and dairy cattle. Design was led by ARS researchers at Beltsville, Maryland, in collaboration with scientists at Clay Center, the University of Missouri, and the University of Alberta in Canada. The chip is being used at all those locations and many others—a total of at least 23 locations in 11 countries.

A single chip generates about 53,000 genotypes for each of 12 individual animals. DNA samples from the animals are applied to the BeadChip, chemically labeled, and scanned to produce genotypes. Statistical analyses of genotypes can identify relationships between DNA markers and economically relevant production traits.

“Genomic tools like the 50K SNP chip will provide the greatest opportunity to transfer our genomic discoveries in a usable form to the industry,” Koohmaraie says.

Beef Cattle: Fat and Feed Efficiency

Geneticist Curt Van Tassell and biological technician Alecia Bertles select bull semen samples for DNA extraction and testing using the SNP50 BeadChip technology.

One project using the BeadChip technology is a USMARC investigation into the influence of genetics on feed efficiency. Research leader Cal Ferrell, geneticist Mark Allan, and their colleagues are identifying phenotypes that relate to postweaning feed efficiency and lifetime productivity in beef cattle.

“One objective of the study is to determine the genetic variation in feed efficiency among individuals and breeds, using quantitative and genomic technologies,” Ferrell says. The researchers are also using the genotypes generated from the chip to find relationships between DNA markers and phenotypes that can be used to enhance genetic selection in beef cattle.

“These studies could lead to development of genomic tools that could enhance the accuracy of breeding and management decisions,” Allan says. “Genetic markers provide opportunities to improve selection for traits that are difficult to measure in an industry setting.”

ARS scientists are also using genomic research to improve beef cattle production at the Fort Keogh Livestock and Range Research Laboratory in Miles City, Montana. There, they have identified genetically significant areas called “quantitative trait loci” (QTLs) related to production traits such as beef quality and composition, feed efficiency, and reproductive success.

“Our work has led us to loci with significant effects on beef quality and composition, which have potential implications for human health,” says geneticist Mike MacNeil. MacNeil, geneticist Lee Alexander, and physiologist Tom Geary have collaborated with USMARC geneticist Warren Snelling to analyze whole-genome scans of 328 cattle bred by crossing Wagyu and Limousin parents. Wagyu is a Japanese breed with substantially more marbling than the more muscular French breed, Limousin.

In all, the team has identified seven QTLs related to tenderness, palatability, and fat composition. They found a region on chromosome 2 that influences the concentration of monounsaturated fat—believed to be healthier than saturated fat—in beef. With further research, in collaboration with USMARC chemist Tim Smith, they hope to develop genetic markers associated with the variation in this trait. That could ultimately lead to identification of the gene or genes responsible and allow for marker-assisted selection in other cattle breeds to alter the fatty acid content of the meat.

Cream of the Crop: Breeding Better Dairy Cattle

Geneticist Tad Sonstegard prepares to load a flow cell into a genome analyzer to generate a billion bases of DNA sequence for SNP discovery in cattle.

ARS scientists at Beltsville played a vital role in designing the BeadChip and are using it in genomics-based studies on dairy cattle. Beltsville geneticist Curt Van Tassell is leading development of a new genomic method to identify bulls that produce daughters with optimum milk production, calving ease, and other traits.

“Progeny testing,” the method now used to determine a bull’s genetic merit, is time-consuming and costly. At ARS’s Bovine Functional Genomics Research Unit, Van Tassell, with ARS geneticists Tad Sonstegard and George Wiggans, is working to whittle down the cost of progeny testing to about $500 a bull.

Their approach is called “genome-enhanced improvement.” It combines computer-aided statistical analysis with more than four decades’ worth of records on dairy performance and conformation to help locate desirable genes.

Collaborating with the Beltsville team are professors Jerry Taylor and Robert Schnabel with the University of Missouri-Columbia; and Illumina, the San Diego firm that manufactures the BeadChip.

The researchers plan to examine a total of 53,000 SNPs from 12,000 cows and bulls representing several commercial dairy breeds and an ARS research population at Beltsville. Then they’ll correlate SNP data to traits of interest, such as milk, fat, and protein production.

Eventually, information derived from the markers will help dairy producers streamline their identification and breeding efforts. And, Van Tassell says, cutting test costs while increasing the rate of genetic improvement in dairy cattle will help make the U.S. germplasm industry more competitive globally.

Cool Cows

Cows with the Slick gene. They have sleek, short hair that helps keep them cool in subtropical heat.

ARS genomics research is also helping beef cattle beat the heat, thanks to researchers at the Subtropical Agricultural Research Station (STARS) in Brooksville, Florida. They have identified molecular markers tightly linked to the Slick gene, which codes for short, sleek hair that helps keep cattle cool in subtropical heat.

The discovery is very important to the beef cattle industry, since it should greatly facilitate the Slick gene’s introgression, or movement, into other economically important breeds, such as Holstein or Angus, to improve their heat tolerance. Many studies in Florida have shown slick-haired animals to have internal temperatures about 1°F lower during summer than contemporaries with normal hair coats.

Mapping the gene’s locus is the first step towards identifying the mutation responsible for slick hair coat. STARS researchers have found a strong association between at least two closely positioned markers on chromosome 20 and the slick-haired phenotype. The markers were identified through DNA sequencing.

These results suggest a role for marker-assisted selection to identify homozygous Slick bulls—that is, sires with the same alleles—that will produce only slick-haired progeny. Some Senepol bulls were tested using these markers, and the results indicated excellent potential for identifying homozygous bulls. The same gene also appears to be responsible for the slick hair coat in Romosinuano cattle.—By Alfredo Flores, Agricultural Research Service Information Staff.

August 2008

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