Abstract
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 (R 2 > 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.
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Acknowledgements
This work was supported by the National Natural Science Foundation of China (No. 31572612); Natural Science Foundation of Guangdong Province, China (No. 2015A030313150); and the Special Program for Marine Fishery, Science, Technology and Industry Development Foundation of Guangdong Province (A201501A04). We would like to thank Mr. Baoqing Ye for editing English of this paper.
Author Contributions
JHX and GHY coordinated and supervised the project. BJL, LHL, ZNM, ZY, HRL, and GHY designed the research and performed experiments. JHX and BJL analyzed the data and wrote the paper. GHY finalized the paper.
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Supplementary Table S1
Summary for the CNVs identified in all 47 samples (XLSX 1386 kb)
Supplementary Table S2
Primer sequences for CNVs confirmation in this study (XLSX 10 kb)
Supplementary Table S3
The identified CNVs that significantly associated with the population types (XLSX 39 kb)
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Li, B.J., Li, H.L., Meng, Z. et al. Copy Number Variations in Tilapia Genomes. Mar Biotechnol 19, 11–21 (2017). https://doi.org/10.1007/s10126-017-9733-0
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DOI: https://doi.org/10.1007/s10126-017-9733-0