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Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis)
Zhang, Bai-Dong1,2; Xue, Dong-Xiu1; Wang, Juan1; Li, Yu-Long1,2; Liu, Bing-Jian1,2; Liu, Jin-Xian1
2016-05-01
Source PublicationMOLECULAR ECOLOGY RESOURCES
Volume16Issue:3Pages:755-768
SubtypeArticle
AbstractRecent advances in high-throughput sequencing technologies have offered the possibility to generate genomewide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters and to evaluate potential adaptive divergence. Here, we identified 27556 single nucleotide polymorphisms for the small yellow croaker (Larimichthys polyactis) using restriction-site-associated DNA (RAD) sequencing of 24 individuals from two populations. Significant sources of genetic variation were identified, with an average nucleotide diversity () of 0.00105 +/- 0.000425 across individuals, and long-term effective population size was thus estimated to range between 26172 and 261716. According to the results, no differentiation between the two populations was detected based on the SNP data set of top quality score per contig or neutral loci. However, the two analysed populations were highly differentiated based on SNP data set of both top F-ST value per contig and the outlier SNPs. Moreover, local adaptation was highlighted by an F-ST-based outlier tests implemented in LOSITAN and a total of 538 potentially locally selected SNPs were identified. blast2go annotation of contigs containing the outlier SNPs yielded hits for 37 (66%) of 56 significant blastx matches. Candidate genes for local adaptation constituted a wide array of biological functions, including cellular response to oxidative stress, actin filament binding, ion transmembrane transport and synapse assembly. The generated SNP resources in this study provided a valuable tool for future population genetics and genomics studies of L.polyactis.
KeywordEffective Population Size Larimichthys Polyactis Population Genomics Rad-seq Single Nucleotide Polymorphism Marker
DOI10.1111/1755-0998.12476
Indexed BySCI
Language英语
WOS IDWOS:000373954100015
Citation statistics
Cited Times:18[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Version出版稿
Identifierhttp://ir.qdio.ac.cn/handle/337002/131005
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, Peoples R China
2.Univ Chinese Acad Sci, Beijing, Peoples R China
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Zhang, Bai-Dong,Xue, Dong-Xiu,Wang, Juan,et al. Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis)[J]. MOLECULAR ECOLOGY RESOURCES,2016,16(3):755-768.
APA Zhang, Bai-Dong,Xue, Dong-Xiu,Wang, Juan,Li, Yu-Long,Liu, Bing-Jian,&Liu, Jin-Xian.(2016).Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis).MOLECULAR ECOLOGY RESOURCES,16(3),755-768.
MLA Zhang, Bai-Dong,et al."Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis)".MOLECULAR ECOLOGY RESOURCES 16.3(2016):755-768.
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