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

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 chickens
OBJECTIVE 3: Compare enteric microbiome populations from distinct intestinal compartments in different broiler breeder lines
OBJECTIVE 4: Identify associations between data generated from Objectives 1-3 and performance and welfare indicators
OBJECTIVE 5: Assess candidate biomarker performance in commercial broiler chickens