ANALYSIS OF SEX RELATED TRAITS IS CRUCIALLY IMPORTANT FOR AQUACULTURE SPECIES BECAUSE ONE SEX USUALLY GROW MUCH FASTER THAN THE OTHER SEX. WITH CATFISH, MALES GROW FASTER THAN THE FEMALES BY UP TO 60%. THE AVAILABILITY OF A REFERENCE GENOME SEQUENCE IS VERY IMPORTANT FOR GENETIC AND GENOMIC RESEARCH, INCLUDING THE ANALYSIS FOR SEX DETERMINATION. AS SUCH, WE HAVE DEVELOPED A HIGH-QUALITY CATFISH REFERENCE GENOME SEQUENCE. HOWEVER, THE CATFISH REFERENCE GENOME SEQUENCE WAS GENERATED FROM A DOUBLED HAPLOID GYNOGEN FISH, MISSING THE ENTIRE Y-CHROMOSOME. THE LACK OF THE SEX CHROMOSOME SEQUENCES PROHIBITS IDENTIFICATION OF SEX DETERMINATION GENE, AND HINDERS UNDERSTANDING OF THE MOLECULAR BASIS FOR SEX DETERMINATION, AND PROHIBITING THE APPLICATION OF MONO-SEX CULTURE TECHNOLOGIES AND THEIR APPLICATION IN AQUACULTURE. THIS PROJECT IS PROPOSED TO FILL THIS GAP WITH THREE SPECIFIC OBJECTIVES: 1) TO GENERATE A HIGH-QUALITY REFERENCE Y CHROMOSOME SEQUENCE OF CHANNEL CATFISH BY USING A YY MALE FISH; 2) COMPARATIVE ANALYSIS OF X AND Y CHROMOSOMAL SEQUENCES, ESPECIALLY WITHIN THE SEX DETERMINATION REGION, TO IDENTIFY POSITIONAL CANDIDATE GENES OF SEX DETERMINATION; AND 3) RNA-SEQ ANALYSIS OF EXPRESSION IN MALES AND FEMALES DURING THE CRITICAL PERIOD OF EARLY SEX DETERMINATION TO IDENTIFY DIFFERENTIALLY EXPRESSED CANDIDATE GENES FOR SEX DETERMINATION, AND PINNING DOWN THE SEX DETERMINATION CANDIDATE GENES BY CROSS ANALYSIS OF THE POSITIONAL AND EXPRESSIONAL CANDIDATE GENES. ACHIEVING THESE GOALS WILL PROVIDE GREAT INSIGHTS INTO THE MECHANISMS OF SEX DETERMINATION IN CATFISH, AND ALLOW DESIGN OF STRATEGIES TO DEVELOP MONOSEX TECHNOLOGIES. WE PROPOSED TO USE AN INNOVATIVE APPROACH TO ACHIEVE THESE GOALS BY USING THE YY MALE SEQUENCING TEMPLATE, THE IDENTIFIED SMALL GENOMIC REGION OF SEX DETERMINATION, AND TISSUE SAMPLES COLLECTED FROM MALES AND FEMALES DURING THE CRITICAL PERIOD OF EARLY SEX DETERMINATION FOR RNA-SEQ ANALYSIS. THE YY TEMPLATE AND THE XX TEMPLATE WILL AVOID TECHNICAL DIFFICULTUIES AND WILL ALLOW CLEAN ASSEMBLY OF THE SEX CHROMOSOME SEQUENCES. THIS PROJECT SHOULD GENERATE THE SEX CHROMOSOME REFERENCE SEQUENCES. WHEN THE FEMALE AND MALE CHROMOSOMES (X VS Y) ARE COMPARED, THE DIFFERENTIAL GENE MAY BE THE SEX DETERMINATION GENE, WHICH UPON BEING FOUND ALSO DIFFERENTIALLY EXPRESSED DURING SEX DETERMINATION PERIOD, SHOULD PROVIDE GOOD INFORMATION ABOUT SEX DETERMINATION GENE IN CATFISH. SUCH INFORMATION WILL BE USEFUL FOR WORKING WITH SEX SELECTION, OR FOR THE DEVELOPMENT OF STRATEGIES OF MONO-SEX CULTURE POPULATIONS.