Aubrac cow. © INRA, SLAGMULDER Christian

High throughput genomics: a rapidly changing field

Boosting our knowledge of genomics for a brighter future in livestock breeding

Animal genomics has tremendous potential in the livestock sector as evidenced by recent research on the identification of several genomic zones (QTL) responsible for a decline in the fertility of dairy cows. Likewise, genomic research on sheep has led to the identification of the mutation and unique processes that spur the production of muscle tissue, ultimately producing an animal that yields high-quality meat. 

Animal genomics has tremendous potential in the livestock sector © BOCHE Jennifer
Animal genomics has tremendous potential in the livestock sector © BOCHE Jennifer
Because of its tremendous potential for improving species through genetic engineering, but also for optimising the pairing of breeding methods and animals, animal genomics is a major focus of research in animal sciences. Thanks to animal genomics, our general knowledge of the structure and functioning of genomes is increasing, as scientists gather information from molecular data obtained, for the most part, by ever-improving technology. In addition to genomic data, phenotypic data is also being collected by the careful study of different traits at different stages of their biological development. This allows for a highly detailed and extremely precise analysis of the animals studied, in a variety of environments. INRA is particularly committed to research programmes geared toward improving the fertility of dairy cows and the quality of sheep meat.

Fertility in high-producing dairy cows

The breeding of dairy cows has led to a tremendous and sustained increase of dairy production over the past 30 years, but also to a steady decline in female fertility. Several research programmes have been initiated to get to the genetic and physiological causes at the root of this. One programme in particular revealed several QTLs responsible for this phenomenon in the top three French dairy breeds. Great progress has been made with high throughput genotyping tools that allow scientists to pinpoint the location of these QTLs in the bovine genome, thus exposing the genes at the root of the problem. Moreover, detailed phenotyping, coupled with genetic data, make the study of the underlying physiological mechanisms behind the phenomenon possible. Thanks to research, scientists are also now able to identify markers that reveal the quality of cattle oocytes, or egg cells. These advances taken together should eventually allow science to eliminate the alleles that are responsible for a decline in fertility in herds, and/or to adapt breeding methods to the genotype in question.  

Improving the quality of meat products

Improving the quality of animal products is a top priority for the livestock industry, and recent findings show that genomics has a lot to offer in achieving this goal. The identification of the gene mutation and unique biological processes responsible for remarkable muscle development in the Belgian Texel breed of sheep, which is known to yield high-quality meat, has been a major achievement of research in recent years. Encouraging results have also been reported when it comes to the genetic make-up of tender, high-quality bovine meat as well. In chickens, a gene that determines the colour of meat has recently been identified. Scientists are also hoping to find, through genome-focused research, an alternative to castrating male swine for the production of high-quality pork.

Key dates

From the discovery of DNA to high throughput sequencing

1953: discovery of the molecular structure of DNA

1961-1965: the genetic code is revealed

1977: DNA is sequenced for the first time

1980: genetic mapping is invented, using anonymous molecular markers

1987: the first automatic DNA sequencing machine is invented

1990: the BLAST algorithm for comparing DNA sequences is developed

Sequencing the human genome:

• first map of genetic markers of human genome in 1987

• inception of sequencing project in 1988 and first draft produced in 2001

• sequencing the human genome declared complete in 2004

Sequencing the Arabidopsis thaliana genome:

• project launched in 1992

• sequencing accomplished in 2000

Sequencing the genomes of livestock animals:

• genetic marker maps established for cows, pigs and chickens starting in the 1990s

• analysis of transcriptome starting in 2000

• first draft of genome sequence for chicken in 2004 (sequencing initiated in 2002), cow in 2006, horse in 2007 and pig in 2009