INFECTION AND DISEASE ADVERSELY IMPACT PERFORMANCE, GROWTH, MORBIDITY AND MORTALITY IN PRODUCTION ANIMALS AND HAS MAJOR ECONOMIC IMPACTS ON COMMERCIAL POULTRY PRODUCTION. THIS IS EXACERBATED BY CONSUMER WORRIES ABOUT ANTIBIOTIC USE, WHICH PRESSURES PRODUCERS TO USE ALTERNATIVE STRATEGIES TO PREVENT INFECTION. AN ILLUSTRATING EXAMPLE IS THE AVIAN INFLUENZA OUTBREAK OF 2015, WHICH HAS BEEN DESCRIBED AS THE WORST IN US HISTORY WITH THE LOSS OF OVER 48 MILLION BIRDS (CHICKEN AND TURKEY). THIS EVENT UNDERSCORES THE NEED TO FUNCTIONALLY ANNOTATING THE CHICKEN GENOME TO UNDERSTAND COMPLEX GENETIC TRAITS SUCH AS DISEASE RESISTANCE, WHICH IN TURN COULD SERVE AS A POWERFUL TOOL TO ENSURE SUSTAINABLE AGRICULTURAL SYSTEMS. FURTHERMORE, IN POULTRY PRODUCTION, ADDITIONAL FACTORS AFFECTING COMMERCIAL AND ECONOMIC PERFORMANCE NEED TO BE CONSIDERED IN BREEDING. FACTORS INCLUDING INTESTINAL HEALTH, EGG LAYING PERFORMANCE OR GROWTH EFFICIENCY IN BROILERS CERTAINLY ARE OF PARTICULAR ECONOMIC SIGNIFICANCE.TO IMPROVE OUR UNDERSTANDING OF THE UNDERLYING MECHANISMS CONTROLLING THESE AND OTHER TRAITS, IDENTIFICATION OF CIS-REGULATORY ELEMENTS ON THE GENOME IS WARRANTED. THESE REGULATORY ELEMENTS CONTROL THE EXPRESSION OF GENES AND CONSEQUENTLY PHENOTYPE; HOWEVER, THE TARGETED TISSUES AND CELLS FOR ANALYSIS NEED TO BE DETERMINED FOR EACH TRAIT OF INTEREST, AS THESE REGULATORY ELEMENTS ARE TISSUE SPECIFIC, AND EVEN DIFFER FROM CELL TO CELL WITHIN A GIVEN TISSUE. ADDITIONALLY, ENVIRONMENTAL FACTORS SUCH AS NUTRITION INTERACT WITH EPIGENETIC MODIFIERS WORKING AT THESE REGULATORY ELEMENTS, THUS MAKING IT POSSIBLE TO PROMOTE THE EXPRESSION OF DESIRABLE PRODUCTIVE TRAITS BY MANAGEMENT.IN THE PAST, SELECTIVE BREEDING OF POULTRY HAS RESULTED IN IMPROVED FEED CONVERSION RATIOS IN BROILERS, ALBEIT AT THE COST OF DECREASED IMMUNE COMPETENCE AND GREATER SUSCEPTIBILITY TO DISEASE. IN CONTRAST, SOME LINES OF BIRDS ARE KNOWN TO BE MORE RESISTANT TO A VARIETY OF PATHOGENS.THE EMERGENCE OF ANTIMICROBIAL RESISTANCE SUGGESTS THAT GENETIC RESISTANCE TO DISEASE WOULD PROVIDE AN ADVANTAGE OVER THE USE OF ANTIMICROBIALS. WHILE PARAMETERS OF IMMUNE COMPETENCE, SUCH AS ANTIBODY PRODUCTION, PHAGOCYTIC ACTIVITY AND CYTOKINE PRODUCTION OF THE HOST ARE KNOWN, THE GENETIC AND MOLECULAR BASIS FOR DISEASE RESISTANCE IS STILL NOT WELL UNDERSTOOD. IT HAS BECOME APPARENT THAT PATHOGENS INTERACT WITH EPIGENETIC REGULATORS OF THE HOST, AIDING IMMUNE EVASION AND REPLICATION OF THE PATHOGEN.IDENTIFICATION OF REGULATORY ELEMENTS AND THEIR INFLUENCE ON TARGET GENES DIRECTLY RESPONSIBLE FOR ENHANCED IMMUNITY IN POULTRY IS CRUCIAL IN ORDER TO SELECT FOR TRAITS THAT IMPROVE DISEASE RESISTANCE FOR BREEDING PURPOSES AND FLOCK HEALTH.