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Aubrac cow. © INRA, SLAGMULDER Christian

High throughput genomics: a rapidly changing field

Revolutionising the breeding of dairy cattle 

Today, scientists are able to predict the genetic value of an animal with a test using a DNA chip that contains tens of thousands of markers. This genetic evaluation, which takes into account new criteria such as fertility, disease resistance or quality of meat and dairy products, is speeding up the genetic enhancement of animals.

In 2012, 60% of cows of the three major French dairy breeds were born of bulls whose genomes had been previously evaluated. © MAITRE Christophe
In 2012, 60% of cows of the three major French dairy breeds were born of bulls whose genomes had been previously evaluated. © MAITRE Christophe
In 2012, 60% of cows of the three major French dairy breeds were born of bulls whose genomes had been previously evaluated! Whereas in the past, the choice of a breeding animal depended on the quality of his progeny, today we are able to predict the genetic value of an animal thanks to a test performed with a DNA chip containing tens of thousands of genetic markers. Genomic selection allows us therefore to choose breeding animals based on their genetic profile, using genetic markers that cover the entire genome. This is made possible by the development of chips containing 50,000-60,000 SNP markers for a growing number of species.

Genomics, transcriptomics, the boom in "-omics" sciences

In livestock species, genomics began in the 1990s with the development of genetic marker maps covering the entire genome, banks of DNA fragments of differing sizes - granting access to different regions of the genome - and comparing the genetic maps of different species. In the early 2000s, advances in sequencing technologies and bioinformatics led to the acquisition of sequence data for the RNA fragment of genomes known as transcriptomes, and shortly thereafter to the sequencing of entire genomes of livestock animals. While genome sequences, available online to the international community, are still far from perfect, they are contributing significantly to a better understanding of living organisms. Genome sequencing has many applications: comparison of sequences between different species, and especially what it can teach us about their respective evolution; identification of DNA polymorphisms between different individuals of the same species and rapid genotyping of many animals, made possible by new high throughput genotyping tools such as SNP chips; analysis of  genome expression in its entirety thanks to transcriptome chips and new methods to assess protein expression, and eventually proteomes; analysis of the non-coding part of genomes and discovery of new ways to regulate gene expression (small RNA, methylation, epigenetics).

Direct access to the genetic value of animals

This genomic selection accelerates genetic improvement in a species, as breeders can access online information about potential breeding animals regarding fertility, disease resistance and quality of meat and dairy products. This revolutionary step also allows for the genetic diversity of a species to remain intact, since the genome itself is not subject to selection. Michel Cètre, livestock breeder of some 40 Montbeliarde cows, and President of the French national union of cooperatives for animal insemination, UNCEIA, explains:“Today, I am able to evaluate with great precision the genetic quality of each one of my cows through genotyping. This speeds up the genetic enhancement of the entire herd as I am able to select the traits I want. The livestock of tomorrow will adapt to these new techniques. Breeding methods will evolve as we rethink how we feed and raise animals...”Genomics and related sciences are rising to the new challenges now facing animal production. The key is to incorporate them into the broader goal of agricultural sustainability, with animals that are healthy, even disease-resistant, with improved dietary assimilation. Another major challenge is to do so while responding to the new demands of society in terms of animal welfare, environmental impact and quality of animal products. According to Maurice Barbezant, former director of UNCEIA,“A hands-on approach was taken in research from the very start, applying knowledge and technologies directly to livestock sectors. Today we are able to select traits of low heritability, responding directly to the needs of society, such as the quality of udders and the hardiness of animals… It’s about broadening the genetic biodiversity of livestock animals by exploring genetic families that have been ignored up to now.”


Thanks to research carried out at INRA, France is a world leader in prediction methods based on genomic selection in dairy and suckler cows.