From Traditional Methods to Modern DNA Precision
For millennia, cattle selection relied on careful observation of animals: Does this cow produce more milk? Does this bull produce more robust calves? Today, a silent revolution is underway, radically transforming these ancestral practices. It no longer resides in the stables, but in the very genetic code of the animals. Bovine genomics has entered farms, promising not only to improve productivity but also animal health and the sustainability of livestock farming.
This revolution is based on a simple but powerful principle: by reading the DNA of cattle, we can predict their potential long before they express their most valuable traits.
Millions of genetic variations are thus scrutinized to guide breeders' choices with unprecedented precision. Let's review the mechanisms of this profound transformation, from its fundamental concepts to its concrete applications, by dissecting a landmark experiment that paves the way for the livestock farming of tomorrow.
Genomic selection has reduced breeding cycles from 6+ years to immediate assessment, dramatically accelerating genetic progress.
Modern genomic tools analyze thousands of genetic markers simultaneously, providing comprehensive genetic profiles.
Animal selection dates back to domestication, but it was only from the 18th century that the first standardized bovine breeds appeared. Breeders then selected breeding stock based on visible criteria: size, color, musculature, or horns. The real leap forward occurred with the appearance of genealogical records and the development of objective performance controls, such as milk weighing 2 .
The mid-20th century marked a turning point with the emergence of quantitative genetics. Mathematicians like Ronald Fisher and Sewall Wright laid the theoretical foundations of genetic values and heritability. In the 1940s, Lanoy N. Hazel developed the theory of indexes, linear combinations of performances allowing estimation of an individual's genetic value considering their own results and those of their relatives 2 .
First standardized breeds based on visible traits
Quantitative genetics and performance indexes
Artificial insemination and progeny testing
Genomic selection introduced in bovine breeding
It was in 2009 that genomic selection entered the bovine world, disrupting established practices. Its fundamental principle? Predicting the genetic value of animals no longer based on their performance or that of their descendants, but directly from their genetic profile 2 .
From 6+ years to immediate assessment
Compared to traditional progeny testing
Of genomic predictions in major breeds
While association studies can identify genetic variants correlated with traits of interest, they are not sufficient to establish a causal link. How do these variations precisely influence complex traits such as milk production, fertility, or udder health? To answer this question, researchers from INRAE designed an innovative approach, published in 2025 in the journal Nature Communications 1 .
Their objective was ambitious: to move from simple statistical correlation to demonstrating the functional role of identified variants. A central question guided them: how do variants in the bovine genome influence the variability of major agronomic traits? 1
Three-step methodology combining statistical analysis, AI screening, and molecular validation
This approach identified 38 functional genomic variants that modify how genes are expressed and interpreted by the cell. More specifically, these variants alter a crucial molecular process: splicing 1 .
Splicing occurs during gene expression and modulates, by modifying messenger RNAs, the quantity or sequence of proteins produced. The identified variants disrupt this mechanism, altering cell functioning and, on a larger scale, leading to observable modifications on bovine agronomic traits 1 .
The study demonstrated that variants affecting splicing play a predominant role in the elaboration of bovine traits, a major advance in understanding the functioning of the genome of this species, where this mechanism had been little studied 1 .
Splicing-affecting variants with demonstrated functional impact
| Trait Category | Specific Examples | Impact of Variants |
|---|---|---|
| Milk Production | Milk quantity, milk composition | Modification of production levels and quality |
| Health | Udder health | Improved resistance to mastitis |
| Reproduction | Fertility | Improved conception rates |
| Morphology | Body conformation | Adaptation of physical characteristics |
The genomic revolution relies on a range of technological tools that are increasingly sophisticated and accessible. The cost of these technologies has continued to decrease, making genomics accessible to breeders. In 2025, genotyping a heifer costs about 30 to 40 euros for farms engaged in a collective approach, compared to several hundred thousand euros for the old progeny testing 5 6 .
Genotyping thousands of genetic markers simultaneously
Complete genome analysis for rare variants
| Tool/Technology | Function | Practical Use |
|---|---|---|
| SNP Chip | Genotyping thousands of genetic markers simultaneously | Evaluation of breeding stock potential |
| Whole Genome Sequencing | Complete genome analysis | Identification of rare variants and fundamental studies |
| Resequencing | Identification of variants relative to a reference genome | Study of genetic diversity at lower cost |
| AI Algorithms | Predictive analysis of genomic data | Identification of functional variants and performance prediction |
Genomics is no longer reserved for selection schemes alone: it is now accessible to all breeders 5 . Its applications transform daily work:
Breeders can early identify females with high genetic potential to inseminate them with sexed semen, and reserve the less promising ones for meat crossbreeding 5 .
By knowing the genetic qualities and defects of each female, it becomes possible to compose parental couples that complement each other to correct defects 5 .
Genomics allows indexing traits difficult to select previously, such as fertility, disease resistance (ketosis, foot health), or milk composition 5 .
The accuracy of genomic evaluation now reaches remarkable levels: in breeds with large populations like Prim'Holstein, the coefficient of determination (CD, measuring the accuracy of the index) is between 0.7 and 0.75, approaching the accuracy previously obtained by progeny testing 5 .
In 2025, the indexing system for beef breeds switches to Single Step, a major innovation already operational in dairy cattle. This method provides a single index, simultaneously integrating pedigree, phenotypic observations and genomic data 7 .
Single Step presents several decisive advantages:
Single Step seamlessly integrates genomic data, performance records, and pedigree information into a unified evaluation system.
Bovine genomics also fits into a dynamic of open science and data sharing. Projects of the "1000 genomes" type, inspired by the eponymous initiative in human genetics, aim to facilitate information extraction by grouping sequencing data obtained by different partners 6 .
This collaborative approach, encouraged by research funding agencies and institutions like INRAE, allows to accelerate research and optimize exploitation of data expensive to produce. It is accompanied by an effort of standardization and documentation of data (metadata) to facilitate their reuse 6 .
Open data initiatives in bovine genomics enable researchers worldwide to access comprehensive datasets, accelerating discoveries and validation of findings across different cattle populations and environments.
Collaborative genomic databases following the "1000 genomes" model are expanding access to bovine genetic information worldwide.
The genomic revolution in the bovine world goes far beyond the technological framework. It represents a paradigm shift that affects both the scientific foundations of selection, the organization of sectors, and the daily work of breeders.
Reduced selection cycle and gain in precision in identifying good breeding stock
Better consideration of animal health and adaptation to environmental issues
Tools within reach of a growing number of breeders, at reasonable costs
Development of animals more resistant to diseases and better adapted to their breeding conditions
As genomics continues to progress, with the arrival of new technologies like genomic editing and increasingly fine analysis of functional variants, one thing is certain: reading bovine DNA has not finished surprising us and offering us levers to reconcile economic performance, animal health and environmental sustainability. The genomic revolution, born in laboratories, has now taken up residence in our farms, for the greater benefit of breeders, animals and society as a whole.