Use of SNP Chip data to support breeding programs
The research use of SNP chips or “marker panels” to study signatures of selection or conduct genome wide association studies can be extended to their direct use in breeding programmes. Genome wide SNP marker panels can be used to derive genomic estimated breeding values (GEBV) of selection candidate animals, using prediction equations based on large reference populations for which accurate genotypic and phenotypic data is available. The feasibility of using marker panels in breeding programmes depends on a trade-off between their cost and accuracy, and also on the local infrastructures available for their deployment. High-density (HD) SNP panels, for example, are still very costly for routine use in genetic improvement of livestock species, especially in smallholder systems. Within CTLGH there is interest in developing (i) low-density custom SNP assays that can complement more expensive dairy cattle HD panels and (ii) a new HD panel designed specifically for indigenous tropical poultry breeds.
Further reading
Genome editing and bio-banking for livestock resilience and productivity
The CTLGH Reproductive Technologies program focuses on novel tools and technologies needed to conserve and deliver the improved genetic resources required by livestock breeding programs. A major barrier to the adoption of genomic selection in tropical livestock systems has been the reliance on techniques, such as artificial insemination of cattle, which require skills and infrastructure that are not always easily accessible to farming communities. Gene editing, or precision breeding, allows targeted adjustments to be made to animal genomes under controlled conditions, with the resulting gene edited animals being introduced directly to the breeding population. In the case of chickens, the ability to cryopreserve specialized cell lines from indigenous breeds supports long term safeguarding and management of local genetic resources.