The practice - recently intensified with artificial insemination - has its potential drawbacks, as the focus on a small gene pool has led to in-breeding in industrial livestock. However, a European Union (EU)-funded research project, NEXTGEN, is working on countering the risks by analysing more than 450 whole genomes for identifying the potential genetic resources and for designing new breeding strategies.
The project team is gathering data on an unprecedented scale for all major types of genetic variation in the genomes – the entire genetic information - of cattle, sheep and goats. The researchers are devising precise methodology for studying the biodiversity aspect of disease resistance and the relationships between genomes and the environment.
NEXTGEN’s coordinator, Pierre Taberlet from the French National Centre for Scientific Research (CNRS) in Grenoble, points to research from the Food and Agriculture Organisation (FAO) that shows some 300 of 6,000 farm animal breeds becoming extinct over the past 15 years. “We are dealing with a pressing conservation need,” he says.
The sharp fall in fertility of the Holstein cattle, as well as the recent emergence of new hereditary diseases, is a sign that in-breeding is becoming a serious concern in the short term. “When a few animals are providing sperm to many, then vital genes are lost generation by generation. In a few decades, we might lose most of the highly valuable genetic resources that humanity has gradually selected over the past 10,000 years,” explains Taberlet. The NEXTGEN project is a research effort to identify these resources, which are essential to ensure global and sustainable food security.
The team is taking advantage of recent developments in next generation sequencing technologies to understand genetic resources not only in diverse domestic breeds, but also in their wild relatives. The researchers have built new bioinformatic methods and tools, have taken sampling in remote farms, and conducted experiments for improving bio-banking technologies - notably preserving undamaged DNA in 60% of cells whose nuclei were freeze-dried.
The sampling in farms is currently carried out in Uganda (where cattle have been affected by vectors or microorganisms that carry diseases in well defined endemic areas), Morocco (where adaptation in sheep and goats is being investigated in a region showing marked variation in environmental conditions), and Iran (where wild ancestors and traditional breeds of sheep and goat from the domestication centre are being evaluated as reservoirs of genetic diversity for the respective domestic species).
In addition, the team is designing breeding programmes to exploit whole genome data in order to maximise genetic progress in livestock populations while maintaining diversity. Furthermore, strategies are being developed to decide which animal genomes to put in the biobank.
Taberlet admits that “the real value of biodiversity is difficult to assess. “We also do not know which feature will be useful to exploit in the future, and which breed carries this feature today,” he adds.
“The NEXTGEN project is about long term benefits and being able to revive breeds in the future. We need to future-proof DNA-based analysis in livestock conservation against upcoming changes in technology and analysis. If we lose the genetic resources now, they may be gone forever,” he concludes.