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Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus)
Wang, Juan1,2; Xue, Dong-Xiu1,2; Zhang, Bai-Dong1,2,3; Li, Yu-Long1,2,3; Liu, Bing-Jian1,2,3; Liu, Jin-Xian1,2
2016-06-23
Source PublicationPLOS ONE
Volume11Issue:6
SubtypeArticle
AbstractNext-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (Pi) for each population was 0.0028 +/- 0.0001 in Dandong and 0.0018 +/- 0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (F-ST = 0.0550, P < 0.001) and the putatively neutral SNPs (F-ST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (F-ST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by F-ST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus.
DOI10.1371/journal.pone.0157809
Indexed BySCI
Language英语
WOS IDWOS:000378389200052
Citation statistics
Cited Times:4[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Version出版稿
Identifierhttp://ir.qdio.ac.cn/handle/337002/130971
Collection海洋生态与环境科学重点实验室
Affiliation1.Chinese Acad Sci, Inst Oceanol, Key Lab Marine Ecol & Environm Sci, Qingdao, Shandong, Peoples R China
2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao, Peoples R China
3.Univ Chinese Acad Sci, Beijing, Peoples R China
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Wang, Juan,Xue, Dong-Xiu,Zhang, Bai-Dong,et al. Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus)[J]. PLOS ONE,2016,11(6).
APA Wang, Juan,Xue, Dong-Xiu,Zhang, Bai-Dong,Li, Yu-Long,Liu, Bing-Jian,&Liu, Jin-Xian.(2016).Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus).PLOS ONE,11(6).
MLA Wang, Juan,et al."Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus)".PLOS ONE 11.6(2016).
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