World Aquaculture Singapore 2022

November 29 - December 2, 2022



 Sukkyoung Lee1,*, Tae Hyug Jeong1, Hyerim Yang2, D.S. Liyanage2, W.K.M. Omeka,

Seong-Rip Oh3, Hyung Bum Koh3, and Jehee Lee1,2


1 Marine Science Institute, Jeju National University, Republic of Korea, Jeju 63333

2 Department of Marin Life Sciences, Jeju National University, Republic of Korea, Jeju 63243

3 Oceans and Fisheries Research Institute, Jeju Special Self-Governing Province, Republic of Korea, Jeju 63629



Aquaculture industry of olive flounder (Paralichthys olivaceus) is the major fisheries in Jeju island, South Korea. Nowadays farming of the flounder is depressed to come to grips with serious problems as diseases, high mortality, low-quality seeds, and price decline. To solve these issues, the breeding program was started to improve fish traits with the collection of fish from different places. Also, whole genome re-sequencing was performed to develop and analysis about single nucleotide polymorphisms (SNPs) in our broodstock.

Initially, 1286 fishes were collected from four different farms or places and analyzed the basic genomic structure by 11 microsatellite markers. From that, 100 fishes which represent the whole were selected to whole genome re-sequencing based on the phylogenetic tree. Total sequencing reads and data from 100 fishes were 24.31 Gb and 3,666.48 Gb, respectively. Average sequencing data per one fish was 36.69 Gb as 72X coverage to flounder whole genome. The read mapping rate to reference sequence was 95.32%.

As a result of variant calling, eighty percent of modification of sequencing data are SNPs and twenty percent are INDELs. Union variants were confirmed as 15,530,229. High-quality SNPs were filtered as 6,964,879 after hyper-variable filtering such as base quality SNPs, bi-allelic, genotyping rate, miner allele frequency (MAF) and Hardy-Weinberg equilibrium (HWE). Intergenic regions, transcripts and intron regions of the data were consisted of 45.425%, 27.283% and 24.584% of high-quality SNPs, respectively.

To select suitable candidate for development of SNP chip, the specific filtering steps like MAF, linkage disequilibrium, repeat checking were performed. After that, 154,964 SNPs were selected, and they were fairly uniformly distributed in 24 chromosomes. Average length between SNPs per each chromosome were confirmed as 2,087 to 5,342. The 100 fish could be divided into 3 populations based on phylogenetic tree and PCA analysis using 155K SNPs.

Finally, it can be concluded that identified high-quality SNPs from the Jeju olive flounder broodstock will be used to analyze genotypes of important traits such as disease resistance, fast growth, thermo tolerance and shape and these data will be applied to future genomic selection.