HOPS ARE PERENNIAL BINES, BEST KNOWN FOR THEIR ROLE IN BEER PRODUCTION. THE GOAL OF BREEDING PROGRAMS IS TO DEBUT NEW VARIETIES WITH DISTINCT FLAVOR PROFILES, DISEASE RESISTANCE, AND/OR SUITABILITY TO A NEW ENVIRONMENT. WHAT IS LACKING IN HOPS, THAT HAS ACCELERATED RESEARCH FOR OTHER CROPS, IS QUALITY GENOME REFERENCES. IMPORTANTLY, IN THE HOP GENUS,HUMULUS,ONLY FEMALES DEVELOP THE VALUABLE "HOP CONES" THAT ARE ENRICHED IN THE BITTER ACIDS AND OTHER ESSENTIAL OILS USED IN BEER PRODUCTION. THISSUGGESTSTHERE ARE GENOMIC DIFFERENCES BETWEEN FEMALES AND MALES THATCONTROL HOP CONEDEVELOPMENT. IDENTIFYING THEGENES INVOLVED IN INITIATING FEMALE HOP CONE DEVELOPMENT VERSUS MALE POLLEN DEVELOPMENT IN HUMULUS WOULDREDUCELABOR AND CROP LOSS FROM UNINTENDED CROSSES. ADDITIONALLY, SUPERIOR MARKERS FOR EARLY IDENTIFICATION OF FEMALES AND MALES ACROSS ALL CULTIVARS AND VARIETIES IN BREEDING PROGRAMS WOULD REDUCE RESOURCE USAGE BY EARLY IDENTIFICATION OF THE MALES THAT HAVE NO ECONOMIC VALUE. WITH THIS RESEARCH, I WILL USE CUTTING-EDGETECHNOLOGIES TO GENERATE A GENOMIC TOOLKIT TO HELP SUSTAINABLE ACCELERATE HOP BREEDING PROGRAMS. TO ACCOMPLISH THIS, I WILL FIRSTGENERATE HIGH-QUALITY GENOME REFERENCES FOR THE FIVE VARIETIES OF HUMULUS LUPULUS AND ITS SISTER SPECIES H. JAPONICUS THAT I WILLMAKE PUBLICALLY AVAILABLE.I WILL ALSO EXAMINE DIFFERENCES IN GENES EXPRESSED IN HOP CONES AND OTHER TISSUES TO DETERMINE THOSE INVOLVED IN HOP CONE DEVELOPMENT. I WILL ALSO DEVELOP MARKERS FOR EARLY IDENTIFICATION OF FEMALES, AS WELL AS VARIETY AND ISOLATE-SPECIFIC MARKERS ACROSS HUMULUS. FINALLY, I WILL ESTABLISH THE SOUTHEASTERN HOP ALLIANCE, WHERE OURCOMMUNITY OF HOP SCIENTISTS CAN ORGANIZE GERMPLASM, KEEP TRACK OF CROSSES, AND COMMUNICATE RESEARCH FINDINGS.