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，由三到四个优秀的祖父母系杂交而来，这些祖辈系在一系列性能和福利相关性状上经历了激烈的遗传选择。“金字塔”种群结构允许从金字塔顶端的这些精英品种的选择性育种中获得收益，通过亲本肉鸡育种者一代，生产将用于肉类的肉鸡。肉鸡和肉鸡种鸡在抗病、肠道微生物组成和免疫能力方面的表型变异已被描述，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家系的变异，这两个家系代表了与健康和生产性能相关的“好”和“坏”肠道健康的极端，以及来自每个家系个体的高级杂交群体，以正式建立好/坏肠道健康的定义。产出将用于肉鸡育种和饲养实践，提高生产力和福利，并减少抗生素干预的需求。该学生将采用整体方法研究肠道健康，使用形态计量学和组织学为高性能个体的健康肠道制定黄金标准，并在形态学，微生物学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中低收入国家（LMIC）环境中具有更广泛的用途。假设：肠道形态、微生物学和转录的变化与商业肉鸡种鸡的肠道健康有关，可用于鉴定对育种计划有用的早期生物标志物，并减少对抗菌药物的依赖。目的1：确定两个肉鸡种系和肠道健康“好”和“坏”的高级杂交群体个体的肠道形态和完整性。鸡将被共同饲养，以尽量减少非遗传变量的影响。目的2：评估和比较肉鸡肠道组织和/或粪便中的基因转录和microRNA谱目的3：比较不同肉鸡种系不同肠室的肠道微生物群目的4：确定目的1-3产生的数据与性能和福利指标之间的关联目的5：评估候选生物标志物在商品肉鸡中的性能

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