Genomic tools have been applied in agriculturally significant species such as pigs to assess questions such as parentage and inbreeding and to develop selective breeding programs. However, the aquaculture industry is just beginning to apply genomic tools to improve broomstick management and product quality. Olive Flounder, Paralichthys olivaceus, is a popular aquaculture species in the Republic of Korea and Japan, with most of the United States supply being imported from those countries. Studies using this species have generally used micro-satellite markers (highly repeated segments of DNA) to analyze brood stock relationships and parentage. Most genomic studies have been genome-wide association studies and transcriptome analyses of disease resistance and developmental pathways, while some questions concerning industry applications remain unanswered.
In this study, low-coverage whole genome sequencing (lcWGS), a type of next-generation sequencing that interrogates the whole genome of an organism and provides many thousands of genetic markers at a lower depth (0.5-2X) and lower cost than Whole Genome Sequencing, will be used to identify parentage and sex markers for P. olivaceus from an experimental hatchery. Fin clips were collected from 20 brood stock P. olivaceus and 60 fish from 2 groups of offspring from the same cohort, a “Runt” group, and a “Future Brood Stock” group which were isolated due to a faster growth rate post-hatch. The samples were sequenced using a lcWGS approach and single nucleotide polymorphisms (SNPs) will be used to identify parentage relationships between brood stock and offspring. Results will be used to determine the relative contribution of specific brood stock to each offspring group (runt versus future broomstick). In addition, an association study will be used to identify SNP markers for sex that will allow for sex identification in a species that has no morphological distinction between males and females. These results will provide valuable broodstock management data and further prove the utility of lcWGS approaches as cost-effective methods of answering questions significant to aquaculture operations.