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INRA Team Uses Illumina Chips to Study French Beef Cattle; Plans Industry-Specific Panel


NEW YORK (GenomeWeb) – Investigators at INRA, the French National Institute for Agricultural Research, recently conducted a microarray-based study that yielded quantitative trait loci associated with meat quality in three of the country's most important beef cattle breeds.

The results of the effort are described in a recent Journal of Animal Science paper.

According to Gilles Renand, corresponding author on the study, the work is a step toward crafting an array that will be used for genomic selection. "The objective is obviously to develop a panel specific to the French cattle industry," said Renand, who is a director of research at GABI, INRA's animal genetics and integrative biology unit in Paris.

He also noted that while the INRA researchers used Illumina's BovineSNP50 DNA Analysis BeadChip to generate the results in the JAS paper, the BovineSNP50 results and QTLs are "not tight enough" to be used for genomic selection, necessitating the design of a lower-density array in closer linkage disequilibrium with the identified QTLs.

Such chips are already used by beef cattle breeders in several countries for genomic selection. Lincoln, Neb.-based GeneSeek, for instance, offers a service called Genomic Profiler for Beef Cattle-LD that is based on a custom, 10,000-SNP genotyping array manufactured by Illumina.

INRA's efforts are focused on three beef cattle breeds raised in France: Charolais, Limousin, and Blonde d'Aquitaine. While cattle breeders in the US, Canada, and Australia maintain all three populations, they are indigenous to France, and named after the regions in which they originated.

According to Renand, there are 3.6 million dairy cattle and 4.1 million beef cattle in France. Of the 4.1 million beef cattle raised in the country, there are 1.6 million Charolais, a million Limousin, and 530,000 Blonde d'Aquitaine cows, he said.

Though some of the world's top-bred beef cattle originated in France, the country's industry is struggling, Renand said, providing the impetus for INRA's research. Within GABI, he directs research related to beef cattle breeding, with a focus on the genetic determinism of production traits from heifer development traits, growing male and female residual feed intake, and the carcass and meat quality of beef animals.

"Beef meat consumption has been slowly but continuously decreasing for 30 years now, while the beef producers are facing economy difficulties," said Renand. "They are seeking new information that could help keep beef consumption to a sufficiently high level and give them an advantage."

Obtaining such information is not easy though. As noted in the recent JAS paper, improving the traits that underlie meat quality is a "major challenge" in the French beef industry. Renand himself is a co-author on dozens of papers about French beef cattle.

However, the availability of bovine genotyping arrays has made it possible for bovine researchers to better detect QTLs associated with sensory meat quality traits. Both Illumina and Affymetrix offer high-density bovine genotyping chips, and Renand said that INRA has already used Illumina's 770,000 SNP BovineHD BeadChip to genotype cattle in France, generating a dataset that enabled the researchers to use the lower-density BovineSNP50 in the most recent study.

"The price is the first argument for the choice of the 50K chip," said Renand of the team's platform choice. "The possibility to impute the 700K SNP on the 50K is the second argument since we have a research program where we genotyped thousands of bulls from different breeds with the Illumina HD chip," he noted.

Study results

In the recent JAS study, the authors set out to detect QTLs linked to sensory meat quality traits in domestically raised cattle. To do this, they used the BovineSNP50 to genotype 1,059, 1,219, and 947 young bulls and their sires belonging to the Charolais, Limousin, and Blonde d'Aquitaine breeds, respectively.

After estimating relevant genetic parameters, they performed a linkage disequilibrium and linkage analysis on four distinct meat traits: intramuscular fat content, muscle lightness, shear force, and tenderness. According to the paper, heritability coefficients largely ranged between 0.10 and 0.24, but they reached a maximum of 0.44 and 0.50 for intramuscular fat content and tenderness, respectively, in the Charolais breed.

The traits of shear force and tenderness were strongly genetically correlated in all three breeds, indicating that they are two different measures of approximately the same trait, according to the authors. The genetic correlation between tenderness and intramuscular fat content, however, differed across breeds.

In total, the authors found more than 200 significant positions across the 29 autosomal chromosomes for the four traits in the Charolais and Blonde d'Aquitaine breeds. However, there were only 78 significant positions in the Limousin breed, and only a few QTLs were common across breeds.

Of the three, the results related to the Blonde d'Aquitaine breed seemed to differ most from the other two. While the authors detected QTLs for intramuscular fat content located near the GDF8 gene in all three breeds, no mutation in the gene has so far been reported for Blonde d'Aquitaine, leading the authors to suggest that an unknown mutation could be segregating in the breed.

The authors said they also discovered new QTLs on chromosome 3 that are significantly associated with meat tenderness in Blonde d'Aquitaine.

"Overall, these results greatly contribute to the goal of building a panel of markers that can be used to select animals of high meat quality," the authors wrote.