Understanding the contribution of host genetics, intestinal structure and microbiome diversity to gut health in broiler chickens

现代肉鸡通常是杂交的，来自三个或四个精英祖父母系之间的杂交，这些祖父母系已经经历了一系列性能和福利相关性状的强烈遗传选择。一个“金字塔”的人口结构允许从金字塔顶端的这些精英股票的选择性育种中获得的收益，通过父母的肉鸡育种一代级联到生产肉鸡，将用于肉类。已经描述了肉鸡和肉种鸡的抗病性、肠道微生物组组成和免疫能力的表型变异，所有这些都有助于肠道健康。在这里，我们建议评估两个纯肉鸡血统的变化，代表极端的“好”和“坏”的肠道健康与健康和性能，以及先进的杂交人口来自每个血统的个人，正式建立良好/坏的肠道健康的定义。产出将用于告知肉鸡育种和饲养实践，提高生产力和福利，并降低对抗生素干预的要求。该奖学金将采用整体方法来研究肠道健康，使用形态学和组织学为高绩效个体的健康肠道制定金标准，并在形态学，微生物和宿主转录组数据集中识别生物标志物，这些数据集可以在一系列商业以及低收入和中等收入国家（LMIC）设置中具有更广泛的实用性。肠道形态学、微生物学和转录的变化与商业化肉种鸡的肠道健康相关，可用于鉴定可用于育种计划和减少对抗菌药物依赖的早期生命生物标志物。目的1：定义肠道形态和完整性，在两个肉种鸡系和个人从先进的互交人口与“好”和“坏”的肠道健康。目的2：评估和比较肉种鸡肠道组织和/或粪便中的基因转录和microRNA谱目的3：比较不同肉种鸡品系中不同肠道隔室的肠道微生物组群体目的4：确定目标1-3生成的数据与性能和福利指标之间的关联目标5：评估商业肉鸡的候选生物标志物性能

Modern broiler chickens are usually hybrid, derived from crosses between three or four elite grandparental lines that have been subject to intense genetic selection for a range of performance and welfare related traits. A 'pyramid' population structure permits gains from selective breeding of these elite stock at the top of the pyramid to cascade down through a parental broiler breeder generation to production broilers that will be used for meat. Phenotypic variation has been described in broiler and broiler breeder chickens for disease resistance, enteric microbiome composition and immunocompetence, all of which contribute to intestinal health. Here, we propose to assess variation in two pure broiler pedigree lines that represent extremes of 'good' and 'bad' intestinal health with relevance to health and performance, as well as an advanced intercross population derived from individuals from each pedigree line, to formally establish definitions for good/bad gut health. Output will be used to inform broiler breeding and husbandry practices, increasing productivity and welfare, and decreasing requirements for antibiotic intervention. This studentship will take a holistic approach to investigating intestinal health, using morphometry and histology to develop a gold standard for a healthy gut in high performing individuals and identifying biomarkers within morphological, microbiological and host transcriptomic datasets that can have broader utility in a range of commercial as well as low and middle income country (LMIC) settings.HYPOTHESIS: Variation in intestinal morphology, microbiology and transcription associates with intestinal health in commercial broiler breeder chickens and can be used to identify early-life biomarkers useful for breeding programmes and reducing reliance on antimicrobial drugs.OBJECTIVE 1: Define intestinal morphology and integrity in two broiler breeder lines and individuals from an advanced intercross population with 'good' and 'bad' gut health. Chickens will be co-reared to minimise the influence of non-genetic variables.OBJECTIVE 2: Assess and compare gene transcription and microRNA profiles in intestinal tissues and/or faeces from broiler breeder chickensOBJECTIVE 3: Compare enteric microbiome populations from distinct intestinal compartments in different broiler breeder linesOBJECTIVE 4: Identify associations between data generated from Objectives 1-3 and performance and welfare indicatorsOBJECTIVE 5: Assess candidate biomarker performance in commercial broiler chickens