French cattle breeding faces a major challenge: the management of inbreeding and its corollary, the appearance of recessive genetic anomalies affecting the health and sustainability of herds. A proof-of-concept study conducted by INRAE geneticists, in partnership with the Institut de l'élevage (IDELE), ELIANCE, the 4 French veterinary schools (ENVF) and the main French breeding organizations and companies, proposes a new approach to identifying and countering these anomalies. Taking advantage of the large databases generated for cattle breeding, this method called HHED (Homozygous Haplotype Enrichment/Depletion) has been published in Genome Biology. By analyzing genomic data and the life histories of millions of cattle, the HHED method was able to detect 33 new genome regions associated with an increased risk of juvenile death and/or reduced productive life in homozygous females. One of the major discoveries was the identification of a genetic mutation in the Holstein breed responsible for the BLIRD syndrome. This syndrome, undetected for over 40 years, causes growth retardation and affects intestinal immunity. These advances offer promising prospects for improving the health and sustainability of cattle farms.

The selection of farm animals is mainly based on so-called “reference” populations, in which we know the genetic information contained in the DNA of each animal (the genotype), as well as numerous measures of its characteristics (the phenotype). Quantifying the association between genetic and phenotypic data within reference populations then enables us to better select young animals for which we only have the genetic information.