INFERTILITY AND SUBFERTILITY ARE MAJOR PROBLEMS IN DOMESTIC ANIMALS AND HUMANS. THOSE FERTILITY PROBLEMS INVOLVE PREGNANCY LOSS DUE TO EMBRYO MORTALITY, WHICH IS PARTICULARLY PREVALENT DURING THE FIRST TWO MONTHS OF PREGNANCY ESTABLISHMENT. MANY CASES OF INFERTILITY AND PREGNANCY LOSS CANNOT BE ASCRIBED TO A SPECIFIC GENETIC OR PHYSIOLOGICAL CAUSE. IN CATTLE AND HUMANS, FERTILITY ISSUES AND PREGNANCY LOSS IS DUE TO PATERNAL, MATERNAL AND/OR EMBRYONIC FACTORS. HOWEVER, OUR KNOWLEDGE OF THE UNDERLYING COMPLEX BIOLOGICAL PATHWAYS AND GENES GOVERNING ESTABLISHMENT OF PREGNANCY AND PATERNAL INFLUENCES ON EMBRYO MORTALITY AND PREGNANCY LOSS REMAINS VERY LIMITED IN AGRICULTURAL ANIMALS AND HUMANS. OUR CENTRAL HYPOTHESIS IS THAT THE PATERNAL GENOME HAS A STRONG INFLUENCE ON EMBRYO SURVIVAL AND MORTALITY DURING THE ESTABLISHMENT OF PREGNANCY AND THUS PREGNANCY SUCCESS AND LOSS. THE GOAL OF THIS PROPOSAL IS TO TEST THIS HYPOTHESIS USING AN INNOVATIVE SYSTEMS BIOLOGY APPROACH AND TO UNDERSTAND THE GENETICS OF EMBRYO MORTALITY AND PREGNANCY LOSS WITH A FOCUS ON PREGNANCY ESTABLISHMENT IN DAIRY CATTLE. TO ACHIEVE THIS GOAL, HOLSTEIN BULLS WILL BE IDENTIFIED THAT POSSESS INTRINSIC DIFFERENCES IN PREGNANCY LOSS DURING THE FIRST TWO MONTHS AFTER BREEDING BASED ON EARLY (&LT; 32 DAYS OF GESTATION) AND LATE EMBRYONIC MORTALITY (&GT; 32 DAYS). THESE PHENOTYPED BULLS WILL BE USED TO UNCOVER THE BIOLOGICAL AND GENETIC MECHANISMS GOVERNING PATERNAL EFFECTS ON EMBRYO MORTALITY AND DEVELOP GENETIC SELECTION TOOLS TO IMPROVE PREGNANCY RATES IN CATTLE. SPECIFIC AIMS ARE TO: (1) IDENTIFY SIRES WITH INCREASED EMBRYO MORTALITY. THIS AIM WILL IDENTIFY AND PHENOTYPE SUBFERTILE SIRES WHO CREATE EMBRYOS THAT HAVE A HIGHER PREVALENCE OF EARLY OR LATE MORTALITY IN THE FIRST TWO MONTHS OF PREGNANCY; (2) INVESTIGATE BIOLOGICAL MECHANISMS GOVERNING EARLY EMBRYO MORTALITY. THIS AIM WILL TEST THE HYPOTHESES THAT SUBFERTILE SIRES HAVE DEFECTS IN GENES GOVERNING EMBRYO DEVELOPMENT AND/OR CONCEPTUS IMPLANTATION AND PLACENTATION THAT IMPACT EARLY EMBRYO MORTALITY AND ESTABLISHMENT OF PREGNANCY; AND (3) DETERMINE GENETIC MECHANISMS UNDERLYING SIRE EFFECTS ON EMBRYO SURVIVAL AND MORTALITY. THIS AIM WILL TEST THE HYPOTHESIS THAT GENETIC LOCI AND GENOMIC REARRANGEMENTS ASSOCIATED WITH SUBFERTILE SIRE EFFECTS ON EARLY AND LATE EMBRYO MORTALITY CAN BE IDENTIFIED USING CUTTING-EDGE GENOMIC ANALYSES. COMPLETION OF THE RESEARCH IS EXPECTED TO FILL A SUBSTANTIAL GAP IN OUR EXISTING KNOWLEDGE BY PROVIDING NOVEL INSIGHTS INTO BULL FERTILITY AND PREGNANCY LOSS. THE SYSTEMS BIOLOGY APPROACH UTILIZING FUNCTIONAL GENOMICS AND DISCOVERY-BASED METHODS IS INNOVATIVE. EXPECTED TRANSLATIONAL OUTCOMES OF THIS RESEARCH ARE GENETIC MARKERS THAT CAN BE USED AS DIAGNOSTIC TOOLS TO IDENTIFY, SELECT AND CREATE SIRES WITH INCREASED FERTILITY, WHICH WILL INCREASE PREGNANCY RATES, PRODUCTION EFFICIENCY, PROFITABILITY AND SUSTAINABILITY OF CATTLE ENTERPRISES. TRANSLATION OF THE IDENTIFIED MARKERS (GENES IN WHICH DISRUPTI,VE HUMAN VARIANTS ARE LIKELY TO CAUSE EMBRYO LOSS) TO HUMANS IS EXPECTED TO PROVIDE NOVEL INSIGHTS INTO IDIOPATHIC MALE FERTILITY THAT CAN BE USED TO DIAGNOSE, TREAT AND PREVENT FERTILITY PROBLEMS AND ENHANCE PREGNANCY OUTCOMES IN NATURAL AND ASSISTED REPRODUCTION.