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This dissertation develops mixed family selection for Pacific oysters using marker-based pedigree reconstruction. It focuses on improving the efficiency of parentage assignment, determining the optimum life stage to mix oyster families for rearing and selection, comparing mixed-family and separate-family selective breeding in the field, and applying the mixed method to estimate the heritability of shell shape. We developed novel computer software, P-LOCI (available at http://marineresearch. oregonstate. edu/genetics/PLOCI. html), which identifies the most efficient set of codominant markers for assigning parentage, accounting for marker linkage, mating design, null alleles and genotyping error, and found that the most efficient group of loci for assignment is not necessarily comprised of the top individually ranked loci, or best for all populations. We determined the optimum time to mix oyster families for rearing and …