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Genetic diversity and signatures of selection in the mito-gynogenetic olive flounder Paralichthys olivaceus revealed by genome-wide SNP markers
Wang, Lijuan1,2; Wu, Zhihao1,2; Zou, Congcong1,2,3; Lu, Yunliang4; Yue, Xinlu5; Song, Zongcheng5; Yang, Runqing6; You, Feng1,2
2022-05-15
Source PublicationAQUACULTURE
ISSN0044-8486
Volume553Pages:10
Corresponding AuthorYang, Runqing(runqingyang@cafs.ac.cn) ; You, Feng(youfeng@qdio.ac.cn)
AbstractThe artificial gynogenesis technique has been proven to be an effective genetic tool and has been widely used in fish breeding. The evaluation of the genetic basis of the artificial gynogenetic population is essential for breeding and farming, and the detection of the signatures of selection is potential to elucidate genes and mutations associated with important phenotypic traits. Olive flounder Paralichthys olivaceus is a commercially important flatfish species cultured in China, Japan, and Korea, and artificial gynogenesis has been used for its genetic breeding. In this study, the genetic variation of the artificial mito-gynogenetic population and common population of the flounder were analyzed using SNP markers with 2b-RAD genotyping technique. A total of 162 mitogynogenetic and 90 common flounders were used, and 39,018 high-quality genome-wide single nucleotide polymorphisms (SNPs) were identified across two populations. The average observed heterozygosity (Ho) and average expected heterozygosity (He) of SNP were 0.1895 and 0.2413, and 0.0222 and 0.2974 in the common and mito-gynogenetic populations, respectively. Most loci significantly deviated from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction in the former population. However, the genetic distance between the two populations suggested no significant genetic differentiation. Furthermore, analysis of run of homozygosity (ROH) showed low level of genomic inbreeding in the common population (inbreed coefficient was 0.2171) compared to higher inbreeding in the mito-gynogenetic population (inbreed coefficient was 0.9227). Short ROHs were more frequent in the common population, while long ROHs were more frequent in the mito-gynogenetic population, providing insight in the developmental history of the flounder. A total of 580 genes with putative selection signatures were identified across the two populations based on selective sweeps. These genes were involved in 39 KEGG pathways associated with some important traits, such as reproduction (e.g., sox8 and sox9) and immune response (e.g., dctn5 and socs-1). These results would be helpful for molecular marker-assisted breeding and conservation of genetic resources in the olive flounder and other marine culture fish.
KeywordOlive flounder Paralichthys olivaceus Mito-gynogenesis Genetic diversity Run of homozygosity Selective sweep
DOI10.1016/j.aquaculture.2022.738062
Indexed BySCI
Language英语
Funding ProjectNational Natural Science Foundation of China[31702337] ; National Natural Science Foundation of China[31772834] ; Youth Research Fund of Marine Biology and Biotechnology Laboratory, Pilot National Laboratory for Marine Science and Technology (Qingdao)[YQ2018NO01] ; National Key R&D Program of China[2018YFD0900202] ; Key R&D (public welfare) program of Shandong Province[2019GHY112005] ; National Marine Genetic Resource Center
WOS Research AreaFisheries ; Marine & Freshwater Biology
WOS SubjectFisheries ; Marine & Freshwater Biology
WOS IDWOS:000765399600010
PublisherELSEVIER
Citation statistics
Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/178706
Collection实验海洋生物学重点实验室
Corresponding AuthorYang, Runqing; You, Feng
Affiliation1.Chinese Acad Sci, Ctr Ocean Mega Sci, Inst Oceanol, CAS & Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China
2.Pilot Natl Lab Marine Sci & Technol Qingdao, Lab Marine Biol & Biotechnol, Qingdao 266237, Peoples R China
3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
4.Qingdao Agr Univ, Marine Sci & Engn Coll, Qingdao 266109, Peoples R China
5.Weihai Shenghang Aquat Sci & Technol Co Ltd, Weihai 264200, Peoples R China
6.Chinese Acad Fishery Sci, Res Ctr Aquat Biotechnol, Beijing 100141, Peoples R China
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Corresponding Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Wang, Lijuan,Wu, Zhihao,Zou, Congcong,et al. Genetic diversity and signatures of selection in the mito-gynogenetic olive flounder Paralichthys olivaceus revealed by genome-wide SNP markers[J]. AQUACULTURE,2022,553:10.
APA Wang, Lijuan.,Wu, Zhihao.,Zou, Congcong.,Lu, Yunliang.,Yue, Xinlu.,...&You, Feng.(2022).Genetic diversity and signatures of selection in the mito-gynogenetic olive flounder Paralichthys olivaceus revealed by genome-wide SNP markers.AQUACULTURE,553,10.
MLA Wang, Lijuan,et al."Genetic diversity and signatures of selection in the mito-gynogenetic olive flounder Paralichthys olivaceus revealed by genome-wide SNP markers".AQUACULTURE 553(2022):10.
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