Abstract
Red sea bream, a popular fish resource in Korea and Japan, is being bred in fish farms of the two countries. It is hypothesized that the genomes of red sea bream are influenced by decades of artificial selection. This study investigates the impact of artificial selection on genomes of red sea bream. Whole genome sequencing was conducted for 40 samples of red sea bream either from Ehime, Nagasaki and Tongyeong fish farms or from the wild. Population stratification based on whole genome data was investigated and the genomic regions of fish farm populations under selection were identified using XP-EHH and relative nucleotide diversity. Gene ontology analysis revealed that different functions were enriched in different fish farms. In conclusion, this study highlights the difference between independently cultured red sea bream populations by showing that influence of artificial selection acted upon completely different genes related to different functions including metabolic and developmental processes.
Highlights
IntroductionA popular fish resource in Korea and Japan, is being bred in fish farms of the two countries
Red sea bream, a popular fish resource in Korea and Japan, is being bred in fish farms of the two countries
Red sea bream populations were collected from three different fish farms (1 Korean and 2 Japanese farms) and pair-wise comparisons were made against a wild-type population collected from Korea using the statistics mentioned above
Summary
A popular fish resource in Korea and Japan, is being bred in fish farms of the two countries. Tilapia which is native cichlid fish from Middle East and Africa, exists in various commercial lines due to breeding program[12] Regarding this fish, a previous study performed whole genome sequencing on selection lines and wild-type samples and performed selective sweep analysis to detect many genes under selection related to growth, immune system, response to chemical, stress and drug[12]. The aim of this publication is to investigate population genomes of red sea bream from various fish farms in Korea and Japan, and to detect genomic regions with selective sweep signature in each fish farm. Red sea bream populations were collected from three different fish farms (1 Korean and 2 Japanese farms) and pair-wise comparisons were made against a wild-type population collected from Korea using the statistics mentioned above. This is the first study to perform population analysis on whole genome sequencing data of red sea bream
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