Genomic predictions of mastitis resistance in dairy goats using computational genomics

该项目通过使用新的遗传和基因组技术来提高产奶质量和疾病管理，解决了奶山羊奶生产面临的主要挑战。主要的挑战是培育健康的山羊，使其能够抵抗导致乳腺炎的细菌感染，并确定对乳腺炎易感性较低的母羊，并对这一特性进行基因组预测。通过为英国山羊创建低密度（LD）、低成本定制单核苷酸多态性（SNP）阵列的新分子技术，英国和国外更广泛的山羊产业将获得增强乳腺炎抗性的基因组预测。这允许使用更具成本效益的分子技术来预测（“impute”）以前由更昂贵、更全面的SNP阵列产生的信息，并使更多的动物能够进行基因分型。该项目将通过定期收集乳腺炎记录作为健康和寿命指标，确保奶山羊的长期可持续繁殖目标，从而帮助将以前由tsb资助的研究转化为实践。据估计，英国三分之一的奶山羊在繁殖期间受到乳腺炎的影响。尽管这在英国还没有正式量化，但我们预计YDG每年在生产力损失和额外的重置成本方面损失约28.6万英镑。在动物育种术语中，乳腺炎被称为“复杂性状”，即许多基因参与决定动物是否屈服于临床（或亚临床）疾病。因此，利用记录良好的山羊，该项目的总体目标是产生遗传（EBV）和基因组（GEBV）育种价值，从而识别出在遗传上对乳腺炎更有抵抗力的动物，而不考虑致病生物体是什么。这种方法符合欧盟的规定，其目的是限制使用活性化合物来控制农业疾病，这增加了病原体对当前生物和化学控制措施产生耐药性的风险。培育抗病能力增强的动物，从而改善健康状况，将使动物更好地发挥其产奶的遗传潜力。ebv和gebv的使用将允许准确地消除对乳腺炎高易感性的动物，从而作为早期识别潜在疾病的一种措施。该提案是一个合作项目，将刺激英国高质量羊奶的生产。这将通过利用新的基因组技术（为英国山羊品种量身定制的低密度（LD），单核苷酸多态性（SNP）阵列）来完成，以确定具有高遗传和基因组优势的奶山羊，以抵抗乳腺炎，功能适应性，健康和长寿，同时获得高水平的产奶量。这将导致一个平衡的育种计划，这是可持续加强羊奶生产所必需的。英国羊奶业面临的挑战是，在为牛奶生产提供高遗传价值牲畜方面成为国际领先的参与者，同时在提供高抗病动物方面建立声誉。鉴定具有高抗乳腺炎能力的子代母猪将大大减少因兽医费用和奶源减少而造成的损失。饲养对乳腺炎抵抗力增强的山羊将成为工业合作伙伴的独特卖点。在山羊选择指数中常规纳入乳腺炎表型可能会提高对乳腺炎的抵抗力，这与最近在奶牛生育方面发生的情况类似，这是由采用新的奶牛生育指数引起的。

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.