Copy Number Variations in Tilapia Genomes.
Discovering the nature and pattern of genome variation is fundamental in understanding phenotypic diversity among populations. Although several millions of single nucleotide polymorphisms (SNPs) have been discovered in tilapia, the genome-wide characterization of larger structural variants, such as copy number variation (CNV) regions has not been carried out yet. We conducted a genome-wide scan for CNVs in 47 individuals from three tilapia populations. Based on 254 Gb of high-quality paired-end sequencing reads, we identified 4642 distinct high-confidence CNVs. These CNVs account for 1.9% (12.411 Mb) of the used Nile tilapia reference genome. A total of 1100 predicted CNVs were found overlapping with exon regions of protein genes. Further association analysis based on linear model regression found 85 CNVs ranging between 300 and 27,000 base pairs significantly associated to population types (R2> 0.9 and P > 0.001). Our study sheds first insights on genome-wide CNVs in tilapia. These CNVs among and within tilapia populations may have functional effects on phenotypes and specific adaptation to particular environments.
State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
Bi Jun
BJ
Li
State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
Hong Lian
HL
Li
State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
Zining
Z
Meng
State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
Yong
Y
Zhang
State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
Haoran
H
Lin
Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. genhua@tll.org.sg.|Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore. genhua@tll.org.sg.|School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. genhua@tll.org.sg.
Gen Hua
GH
Yue
State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China. xiajunh3@mail.sysu.edu.cn.
Jun Hong
JH
Xia
D000222:Adaptation, Physiological / Q000235:genetics; D000818:Animals; D002874:Chromosome Mapping; D056915:DNA Copy Number Variations; D063990:Gene Ontology; D005828:Genetics, Population; D016678:Genome; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D017210:Tilapia / Q000235:genetics*
Association analysis; Copy number variation; Genome-wide scan; Tilapia