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The Association |
Hansruedi Vonlanthen
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The Association |
Hansruedi Vonlanthen
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Scientists agree: genomic selection is the future of horse breeding
The seminar section of the WBFSH Annual General Meeting was devoted to a complex topic which, however, was of great interest to the representatives of the breeding associations, as it is likely to transform horse breeding in the coming years to a similar extent to the way it has already revolutionised cattle breeding: genomic selection. Hardly any other field of scientific research has undergone such rapid development in recent years as molecular biology, on which genomic selection is based. Whereas, until a few years ago, an animal’s genetic potential – or breeding value – could only be determined by its own performance or that of its relatives, scientists are now able to read an animal’s genetic predisposition directly from its genome and use this information for breeding purposes.
Significant improvement in breeding progress
The first speaker, the German vet Dr Kathrin Stock, who works in the field of breeding value estimation at the company Vereinigte Informationssysteme Tierhaltung (VIT), refreshed the participants’ memories of past biology lessons and explained the basic concepts of genetics, as well as the increasingly efficient methods that make it possible to extract information from genetic material on a large scale and at a relatively low cost. ‘The new genomic tools offer enormous potential for horse breeding,’ said Kathrin Stock. Breeding progress in riding horses could be significantly improved using these new methods. However, genomically enhanced breeding programmes require high-quality data collection, which enables the prediction models to be continually expanded and refined. The Equine Commission of the European Association for Animal Science (EAAP), of which Kathrin Stock is a board member, has therefore set itself the aim of promoting and supporting the exchange and transfer of knowledge between all relevant stakeholders in the equine sector and the scientific community. “With the transition to genomically enhanced breeding programmes for horses, breeding organisations for sport horses will be able to benefit from joint research and development activities,” says Kathrin Stock with conviction.
Already established
Genomic selection in livestock breeding has long since ceased to be a distant dream. “Advances in genome analysis, combined with new statistical methods, have made genomic selection a widely used tool in cattle breeding,” said Dr Fritz Schmitz-Hsu. And the agronomist and geneticist at Swissgenetics is convinced that the insights gained from livestock breeding will also be of benefit to the equine industry. Genomic selection is based on the analysis of thousands of markers distributed across an animal’s entire genome. Today, tens of thousands or even hundreds of thousands of these can be determined quickly and cost-effectively, enabling a direct genomic breeding value to be calculated. Combining this with the traditionally estimated breeding value yields a genomically improved breeding value estimate, which is more reliable than the traditional breeding value. ‘This enables young animals, particularly bulls, to be sired and selected in a more targeted manner and with a shorter generation interval, leading to significant breeding progress,’ said Schmitz-Hsu.
In dairy cattle, genomic selection has become the norm in less than a decade, and since then all major breeding nations have been publishing the genomically improved breeding values of their young bulls in the key dairy breeds. The length of time required to test a bull, the associated costs, the widespread use of artificial insemination in the livestock industry, and the insemination industry’s willingness to invest in this new technology have led to the rapid adoption of genomic selection. Today, millions of cattle worldwide have been genotyped. In Fritz Schmitz-Hsu’s view, genomic selection is therefore the most significant technical achievement in cattle breeding since the introduction of artificial insemination.
Applied research on Freiberger
Dr Markus Neuditschko, a research associate at Agroscope’s Swiss National Stud, presented several examples of applied research in the field of genomics in Freiberger horses (FM). His aim was to investigate the suitability of data obtained through genetic marker analysis for breeding, genetic diversity, trait mapping and selection within a small, genetically closed horse population. To this end, he had access, on the one hand, to 43 traits from the Freiberger breeding programme, for which breeding values have been estimated since 2006, and, on the other hand, to complete or partial genetic data from around 1,200 Freiberger horses. He first investigated the genetic diversity of the FM population using pedigree information and molecular markers, known as SNPs, applying various statistical methods. ‘We found the marker data particularly useful in situations where no pedigree data is available or where the existing data needs to be verified,’ said Markus Neuditschko. Furthermore, the genome-wide analysis revealed signs of association on chromosomes 1, 3, 6 and 9 for the trait of withers height and various conformation traits. Causal gene variants were identified for height. In addition, a gene region on chromosome 6 was discovered that is associated with the trait of correct conformation. Other gene regions influence, for example, the development of white markings. Furthermore, the study demonstrated that the genome-based breeding value for Freiberg data can generally be predicted earlier and more accurately than the traditional breeding value. Markus Neuditschko went on to highlight the importance of the quality of trait recording for horse breeding and provided examples from the breeding programmes for Freibergers and Swiss sport horses.
Findings regarding French show jumpers
The fourth speaker, agricultural engineer Dr Anne Ricard from the French National Institute for Agricultural Research (INRA) in Toulouse, presented her findings on genomic selection in show jumpers in France. “The first thing people always ask me is whether genomic selection works for French horses – and I have to answer ‘yes’,” said Anne Ricard. In 2009, she launched a project in which around 1,000 show jumpers were genotyped. The data from 900 horses with strong individual and family performance records were then used to develop a formula linking the genotypes to the horses’ performance. This formula was subsequently applied to a group of 100 horses without any prior knowledge of their performance. “Nevertheless, we were able to make a prediction about performance based on the genomic data,” said Anne Ricard. Admittedly, the accuracy of these predictions is still low, which is why a further test group of 2,000 horses has now been established, in which additional traits are also being investigated. Like her predecessors, Anne Ricard also emphasised the need for international collaboration between research institutions and breeding associations, as the accuracy of genomic breeding values increases with the growing volume of available data.
Mixed feelings among breeding
In the ensuing discussion, moderated by Dr Stefan Rieder, Head of Research at Agroscope’s Swiss National Stud, it became clear that many breeding associations – particularly smaller ones – were uncertain about the introduction of genomic selection. Kathrin Stock once again emphasised the importance of collaboration: “Not every breeding association needs to set up its own system.” When setting up such a system, an association’s financial resources would be the main determining factor. Genotyping a horse’s genome costs around 200 euros. Data analysis and the estimation formulas for breeding values should be carried out jointly rather than developed by each association on its own. This allows synergies to be harnessed, the quality of the data and, ultimately, the genomic breeding values to be improved, and costs to be shared.
Fritz Schmitz-Hsu emphasised the importance of establishing universally applicable definitions for specific traits. Furthermore, a breeding association must secure the rights to publish data relevant to genomic selection in good time. According to Kathrin Stock, sharing this data with other, potentially competing breeding associations need not be a contradiction: “Each breeding association can continue to determine for itself what the ideal horse looks like and how it wishes to breed it.”
For Markus Neuditschko, establishing a clear strategy is the key: “Decide where you want to go with your breeding programme and how you want to get there – genomic selection will help you achieve this breeding goal more quickly.”
In response to a further question from the floor as to whether it would be possible to establish genomic selection in sport horse breeding within ten years, Fritz Schmitz-Hsu quoted Barack Obama’s former election campaign slogan: “Yes, you can”, whilst Anne Ricard even considers a timeframe of five years to be realistic.
HRH Princess Benedikte of Denmark, patron of the WBFSH and an enthusiastic horse breeder herself, had listened attentively to the presentations by the four speakers and came to the following conclusion: “It is clear that each of us wants to breed the best horse. However, we mustn’t forget that even the best horse can only realise its potential if it finds the right rider.”
Angelika Nido Wälty