Li Bi Jun, Li Hong Lian, Meng Zining, Zhang Yong, Lin Haoran, Yue Gen Hua, Xia Jun Hong
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.
Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
Mar Biotechnol (NY). 2017 Feb;19(1):11-21. doi: 10.1007/s10126-017-9733-0. Epub 2017 Feb 6.
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 > 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.
发现基因组变异的本质和模式是理解种群间表型多样性的基础。尽管罗非鱼中已发现数百万个单核苷酸多态性（SNP），但尚未对较大的结构变异进行全基因组表征，如拷贝数变异（CNV）区域。我们对来自三个罗非鱼种群的47个个体进行了全基因组CNV扫描。基于254Gb高质量双端测序读数，我们鉴定出4642个不同的高可信度CNV。这些CNV占所用尼罗罗非鱼参考基因组的1.9%（12.411Mb）。共发现1100个预测的CNV与蛋白质基因的外显子区域重叠。基于线性模型回归的进一步关联分析发现，85个长度在300至27000个碱基对之间的CNV与种群类型显著相关（R > 0.9且P > 0.001）。我们的研究首次揭示了罗非鱼全基因组CNV的情况。罗非鱼种群间和种群内的这些CNV可能对表型和对特定环境的适应性具有功能影响。
