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Identification of candidate variants and genes associated with temperature
tolerance in olive flounders by Genome-Wide Association Study (GWAS)
H.M.V. Udayantha a,b,1, Sukkyoung Lee a,b,1, D.S. Liyanage a,b,1, Chaehyeon Lim a,b,c,
Taehyug Jeong a,b, W.K.M. Omeka a,b, Hyerim Yang c, Gaeun Kim a,b,c, Joungeun Kim a,b,c,
Jihun Lee a,b,c, Kishanthini Nadarajapillai a,b,c, Subothini Ganeshalingam a,b,c,
Cheong-Uk Park a,b,c, Jiwon Lee a,b,c, Seong-Rip Oh d, Po Gong d, Yeounghwan Jang d,
Jaemin Hyun d, Aejeon Park d, Hyoung-Bum Koh d, Mun-Kwan Kim a,b, David B. Jones e,
Cecile Massault e, Dean R. Jerry e,f,*, Jehee Lee a,b,c,*
a Marine Science Institute, Jeju National University, Jeju Self-Governing Province 63333, Republic of Korea
b Center for Genomic Selection in Korean Aquaculture & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 63333, Republic of Korea
c Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea
d Ocean and Fisheries Research Institute, Jeju Self-Governing Province 63629, Republic of Korea
e Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
f Tropical Futures Institute, James Cook University, Singapore
A B S T R A C T
The Republic of Korea is one of the largest producers of farm-raised olive flounder (Paralichthys olivaceus), accounting
for nearly half of the global production. However, global warming has affected the aquaculture industry
worldwide as it impacts survival, growth, and immunity and accelerates increases in pathogen load. In this study,
we identified thermal stress-related genes in olive flounder using a genome-wide association study (GWAS) to
provide a basis for marker-assisted selection and the development of temperature-resistant olive flounder in
response to global warming. In total, 768 healthy olive flounder (weight of 159 ± 29.9 g and length of 25.42 ±
1.63 cm) were subjected to thermal stress (19.4–32.5 ◦C), and dead fish (537) were collected every 30 min. The
fin tissues were isolated from all dead and surviving fish (231) and used for gDNA extraction. A high-quality 70 K
SNP chip was used for genotyping, and 58,920 SNPs were obtained from 726 individuals after quality filtering.
The GWAS identified 216 statistically significant SNPs at the Bonferroni cutoff (8.5 × 10? 7). All significant SNPs
were located on chromosome (chr) 18 (39 SNPs), chr 19 (176 SNPs), and contig 28 (AGQT02031776.1). After the
SNP annotation, 13, 67, and 135 SNPs were identified in exons, introns, and intergenic regions, respectively.
Gene and functional annotations revealed that almost all significant SNPs were directly or indirectly associated
with the thermal stress response. Annotated genes were further categorized into the following functional groups:
metabolic, neural and neuroendocrine, molecular and cellular, and physiological and behavioral responses. The
significant SNP-harboring genes identified in this study could be used for marker-assisted genomic selection in
future breeding programs.
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