Genomic predictions of mastitis resistance in dairy goats using computational genomics

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This project addresses the key challenges facing dairy goat milk production by using new genetic and genomic technologies to improve the quality of milk production and disease management. The main challenge is to breed healthy goats with resistance to bacterial infections leading to mastitis, and to identify sires with daughters that have lower susceptibility to mastitis and generate genomic predictions of merit for this trait. The wider goat industry in the UK and abroad will access genomic predictions of enhanced mastitis resistance via new molecular technology from the creatipon of a low density (LD), lower cost customised single nucleotide polymorphism (SNP) array for UK goats. This allows for the use of more cost-effective molecular technology to predict ('impute') the information that was previously generated by the more expensive, more comprehensive SNP array and enabling more animals to be genotyped. The project will ensure sustainable breeding objectives for dairy goats in the long-term, by including routine collection of mastitis records as indicators of health and longevity, thereby helping to translate previous TSB-funded research into practice.It is estimated that mastitis affects up to a third of all UK dairy goats during their reproductive life. Even thoughthis hasn't been formally quantified in the UK, we anticipate that YDG loses around £286K p.a. in lost productivity and additional replacement costs. Mastitis is termed a 'complex trait' in animal breeding terms, i.e. whereby many genes are involved in determining whether or not animals succumb to clinical (or subclinical) disease. For this reason, using well recorded goats, the overall aim of the project is to generate genetic (EBV) and genomic (GEBV) breeding values that will identify genetically more resistant animals to mastitis, irrespective of the causative organisms. Such approach is in line with the EU regulations, which are aiming to restrict the use of active compounds to control agricultural diseases, which increases the risk of pathogens developing resistance to current biological and chemical control measures. Breeding of animals with increased disease resistance and thus improved health will allow the animals to better realise their genetic potential for milk production. The use of EBVs and GEBVs will allow for accurate elimination of animals with high susceptibility to mastitis, thus acting as a measure of early identification of potential disease. This proposal is a collaborative project that will stimulate the production of high quality goat milk in the UK. This will be done through the exploitation of new genomic technology (a low-density (LD), single nucleotide polymorphism, (SNP) array that is tailored to UK goat breeds), to identify high genetic and genomic merit dairy goats for mastitis resistance, functional fitness, health, and longevity, whilst attaining high levels of milk production. This will result in a balanced breeding programme, which is necessary for sustainable intensification of goat milk production. The challenge is for the UK goat milk industry to become a leading international player in the supply of high genetic merit livestock for milk production, whilst building a reputation for the supply of animals of high disease resistance. The identification of sires with daughters with high mastitis resistance will greatly reduce losses due to veterinary costs and decreased milk supply. Breeding of goats with increased resistance for mastitis will become a unique selling point for the industrial partner. The routine inclusion of mastitis phenotyping for the goat selection index is likely to improve mastitis resistance, in a similar way to that which has recently occurred for fertility in the dairy cattle, initiated by the uptake of the new dairy fertility index.