Genomic predictions of mastitis resistance in dairy goats using computational genomics

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.

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 breeding of healthy goats with resistance to bacterial infections leading to mastitis. This project aims to identify sires with daughters that have lower susceptibility to mastitis and generate genomic predictions of merit for this trait. The exploitation of such ability to the wider commercial goat industry in the UK and abroad will be enabled via genomic predictions for mastitis resistance via the development in this project of a low density (LD), lower cost customised single nucleotide polymorphism (SNP) array for UK goats. This allows the imputation from LD to the higher density arrays and genotyping more animals. 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.

This project offers a unique and innovative approach to prepare the UK goat milk industry to address the challenges it will face. The immediate beneficiaries will be Yorkshire Dairy Goats (YDG) and their customers, who will benefit through having goats that are more resistant to mastitis and a more efficient farming enterprise with less wastage of young animals. YDG benefits from this project because the LD array (or 'chip') development requires knowledge from their existing project from the 50K array to produce the required SNPs, and through including mastitis resistance , it will become their unique selling point. The LD chip enables the proposed work to be more widely exploited and revenue generated for YDG because a 50k chip plus profit is too expensive for commercial goat producers. Once developed, their value is in enabling other goat producers to improve their animals either by buying YDG animals or in testing their own animals for traits they find difficult to record, such as mastitis.They also benefit through having healthier, longer-living animals, through the inclusion of mastitis, functional fitness and longevity into the genomic breeding programme. YDG benefits through their interaction with applied animal scientists at SRUC, which is reciprocated such that scientists are better able to understand and meet industry needs through their interaction with YDG staff. The UK goat industry as a whole benefits from having access to, and increased knowledge from the results of this project through open days, published articles and shared committees (Goat Veterinary Society). This has already been demonstrated through their (and other) invitations to YDG and SRUC staff to provide advice and deliver presentations (outputs) on goat breeding and health issues. The international scientific community benefits through having colleagues with which to compare results and foster closer collaborations in the pursuit of improving and enhancing methodologies. For instance, using the 50K array in the existing TSB-funded project had not been undertaken for a crossbred goat population in the world, neither had including females as well as males in the genotyped animal pool. The Government will benefit from their investment as this project supports a viable rural business and employer (YDG), whose profits are a source of tax revenue. It also benefits throughenhanced food security, lower imports and export of superior genetics. Environmental benefits will be realised in this project through having fewer replacement animals waiting until their progeny are lactating, as the identification of potentially superior males can be done soon after birth with the new technology. Environmental benefits are also apparent as genetic selection is a cumulative and sustainable way to improve performance and reduce the inefficiencies. International governments in poorer countries (where subsistence farming is reliant on small ruminants such as many African countries) will also benefit from this project as they often do not have sufficient research capital available to undertake such a project to benefit their own farmers. The results and experience from this project may enable a step-change to occur in these countries through the generation of the LD arrays because they will be able to leap-frog the large investment required to replicate this project elsewhere and benefit from the lower cost LD technology.