Genomic predictions of mastitis resistance in dairy goats using computational genomics

该项目通过使用新的基因和基因组技术来提高牛奶生产的质量和疾病管理，解决了奶山羊奶生产面临的主要挑战。主要的挑战是培育对导致乳房炎的细菌感染具有抵抗力的健康山羊，并识别出对乳房炎易感性较低的父羊和女儿，并对这一特征进行基因组预测。英国和海外更广泛的山羊行业将通过为英国山羊创造低密度(LD)、低成本定制单核苷酸多态性(SNP)阵列的新分子技术，获得增强乳房炎抵抗力的基因组预测。这使得可以使用更具成本效益的分子技术来预测(‘归因于’)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。该项目将确保奶山羊的长期可持续育种目标，包括将乳房炎记录的常规收集作为健康和寿命的指标，从而帮助将之前由TSB资助的研究转化为实践。据估计，在英国所有奶山羊的生殖过程中，乳房炎影响高达三分之一。尽管这在英国还没有正式量化，但我们预计YDG每年损失约286k GB。损失的生产力和额外的替换成本。乳房炎在动物育种中被称为“复杂性状”，即决定动物是否会死于临床(或亚临床)疾病的基因很多。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，以确定对乳房炎具有更强遗传抗性的动物，而不考虑致病微生物。这种做法符合欧盟法规，该法规旨在限制使用活性化合物控制农业疾病，这增加了病原体对当前生物和化学控制措施产生抗药性的风险。饲养抗病能力更强的动物，从而改善健康状况，将使这些动物更好地实现其产奶的遗传潜力。EBV和GEBV的使用将能够准确地消除对乳房炎高度敏感的动物，从而作为早期识别潜在疾病的一种措施。这项提议是一个合作项目，将刺激英国高质量山羊奶的生产。这将通过开发新的基因组技术(一种针对英国山羊品种量身定做的低密度(LD)、单核苷酸多态(SNP)阵列)来实现，以确定高遗传和基因组优势的乳山羊对乳房炎的抵抗力、功能适应性、健康和寿命，同时实现高水平的产奶量。这将导致一个平衡的养殖方案，这是可持续强化山羊奶生产所必需的。英国羊奶业面临的挑战是，在供应高基因优势牲畜用于牛奶生产方面成为国际领先参与者，同时建立提供高抗病动物的声誉。识别具有高乳房炎抵抗力的雌性公牛将大大减少由于兽医费用和牛奶供应减少而造成的损失。培育对乳房炎抵抗力增强的山羊将成为该行业合作伙伴的独特卖点。将乳房炎表型纳入山羊选择指数的常规做法可能会提高乳房炎的抵抗力，这与最近采用新的奶牛繁殖力指数对奶牛的繁殖力产生的影响类似。

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.