{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T16:48:29Z","timestamp":1771951709131,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,25]],"date-time":"2022-05-25T00:00:00Z","timestamp":1653436800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Project of Sanya Yazhouwan Science and Technology City Management Foundation","award":["SKJC-KJ-2019KY01"],"award-info":[{"award-number":["SKJC-KJ-2019KY01"]}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFD1200805"],"award-info":[{"award-number":["2021YFD1200805"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32002388"],"award-info":[{"award-number":["32002388"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32072976"],"award-info":[{"award-number":["32072976"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013142","name":"Key R & D Project of Hainan Province","doi-asserted-by":"publisher","award":["ZDYF2021XDNY133"],"award-info":[{"award-number":["ZDYF2021XDNY133"]}],"id":[{"id":"10.13039\/501100013142","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key R&D Project of Shandong Province","award":["2021ZLGX03"],"award-info":[{"award-number":["2021ZLGX03"]}]},{"name":"Major Science and Technology Program of Hainan Province","award":["ZDKJ2021017"],"award-info":[{"award-number":["ZDKJ2021017"]}]},{"DOI":"10.13039\/501100019048","name":"Science Foundation of Ministry of Education of China","doi-asserted-by":"publisher","award":["2021ZL09"],"award-info":[{"award-number":["2021ZL09"]}],"id":[{"id":"10.13039\/501100019048","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>It is of vital importance to understand the population structure, dissect the genetic bases of performance traits, and make proper strategies for selection in breeding programs. However, there is no single webserver covering the specific needs in aquaculture. We present Aquaculture Molecular Breeding Platform (AMBP), the first web server for genetic data analysis in aquatic species of farming interest. AMBP integrates the haplotype reference panels of 18 aquaculture species, which greatly improves the accuracy of genotype imputation. It also supports multiple tools to infer genetic structures, dissect the genetic architecture of performance traits, estimate breeding values, and predict optimum contribution. All the tools are coherently linked in a web-interface for users to generate interpretable results and evaluate statistical appropriateness. The webserver supports standard VCF and PLINK (PED, MAP) files, and implements automated pipelines for format transformation and visualization to simplify the process of analysis. As a demonstration, we applied the webserver to Pacific white shrimp and Atlantic salmon datasets. In summary, AMBP constitutes comprehensive resources and analytical tools for exploring genetic data and guiding practical breeding programs. AMBP is available at http:\/\/mgb.qnlm.ac.<\/jats:p>","DOI":"10.1093\/nar\/gkac424","type":"journal-article","created":{"date-parts":[[2022,5,9]],"date-time":"2022-05-09T11:10:00Z","timestamp":1652094600000},"page":"W66-W74","source":"Crossref","is-referenced-by-count":31,"title":["Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture"],"prefix":"10.1093","volume":"50","author":[{"given":"Qifan","family":"Zeng","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"},{"name":"Key Laboratory of Tropical Aquatic Germplasm of Hainan Province , Sanya Oceanog Inst, Ocean Univ China, Sanya \u00a0572000, Peoples R China"},{"name":"Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology , Qingdao \u00a0266237, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8303-0330","authenticated-orcid":false,"given":"Baojun","family":"Zhao","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"}]},{"given":"Hao","family":"Wang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"}]},{"given":"Mengqiu","family":"Wang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"}]},{"given":"Mingxuan","family":"Teng","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"}]},{"given":"Jingjie","family":"Hu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"},{"name":"Key Laboratory of Tropical Aquatic Germplasm of Hainan Province , Sanya Oceanog Inst, Ocean Univ China, Sanya \u00a0572000, Peoples R China"}]},{"given":"Zhenmin","family":"Bao","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"},{"name":"Key Laboratory of Tropical Aquatic Germplasm of Hainan Province , Sanya Oceanog Inst, Ocean Univ China, Sanya \u00a0572000, Peoples R China"},{"name":"Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology , Qingdao \u00a0266237, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7000-4213","authenticated-orcid":false,"given":"Yangfan","family":"Wang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"},{"name":"Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology , Qingdao \u00a0266237, China"}]}],"member":"286","published-online":{"date-parts":[[2022,5,25]]},"reference":[{"key":"2022070500021162900_B1","volume-title":"The state of world fisheries and aquaculture","author":"Food and Agricultural Organization","year":"2020"},{"key":"2022070500021162900_B2","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/s41586-020-2616-y","article-title":"The future of food from the sea","volume":"588","author":"Costello","year":"2020","journal-title":"Nature"},{"key":"2022070500021162900_B3","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1111\/cobi.13295","article-title":"Aquaculture and the displacement of fisheries captures","volume":"33","author":"Longo","year":"2019","journal-title":"Conserv. Biol."},{"key":"2022070500021162900_B4","doi-asserted-by":"crossref","first-page":"5295","DOI":"10.1073\/pnas.1801692115","article-title":"Comparative terrestrial feed and land use of an aquaculture-dominant world","volume":"115","author":"Froehlich","year":"2018","journal-title":"P Natl Acad Sci USA."},{"key":"2022070500021162900_B5","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.margen.2017.11.013","article-title":"Application of genomics in salmon aquaculture breeding programs by ashie norris: who knows where the genomic revolution will lead us?","volume":"36","author":"Norris","year":"2017","journal-title":"Mar Genomics"},{"key":"2022070500021162900_B6","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1093\/genetics\/157.4.1819","article-title":"Prediction of total genetic value using genome-wide dense marker maps","volume":"157","author":"Meuwissen","year":"2001","journal-title":"Genetics"},{"key":"2022070500021162900_B7","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1146\/annurev-animal-021815-111422","article-title":"Genomic selection in dairy cattle: the USDA experience","volume":"5","author":"Wiggans","year":"2017","journal-title":"Annu Rev Anim Biosci"},{"key":"2022070500021162900_B8","doi-asserted-by":"crossref","first-page":"210","DOI":"10.3389\/fgene.2016.00210","article-title":"Efficient breeding by genomic mating","volume":"7","author":"Akdemir","year":"2016","journal-title":"Front Genet."},{"key":"2022070500021162900_B9","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1146\/annurev.genom.9.081307.164242","article-title":"Genotype imputation","volume":"10","author":"Li","year":"2009","journal-title":"Annu. Rev. Genomics Hum. Genet."},{"key":"2022070500021162900_B10","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/s12711-019-0487-1","article-title":"Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach","volume":"51","author":"Zan","year":"2019","journal-title":"Genet. Sel. Evol."},{"key":"2022070500021162900_B11","doi-asserted-by":"crossref","first-page":"3028","DOI":"10.1111\/mec.12105","article-title":"Population genomics based on low coverage sequencing: how low should we go?","volume":"22","author":"Alex\u00a0Buerkle","year":"2013","journal-title":"Mol. Ecol."},{"key":"2022070500021162900_B12","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1007\/s00439-013-1266-7","article-title":"Imputation across genotyping arrays for genome-wide association studies: assessment of bias and a correction strategy","volume":"132","author":"Johnson","year":"2013","journal-title":"Hum. Genet."},{"key":"2022070500021162900_B13","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.aquaculture.2018.03.004","article-title":"Accuracy of genotype imputation and genomic predictions in a two-generation farmed atlantic salmon population using high-density and low-density SNP panels","volume":"491","author":"Yoshida","year":"2018","journal-title":"Aquaculture"},{"key":"2022070500021162900_B14","doi-asserted-by":"crossref","first-page":"736323","DOI":"10.1016\/j.aquaculture.2020.736323","article-title":"Evaluation for the effect of low-coverage sequencing on genomic selection in large yellow croaker","volume":"534","author":"Zhang","year":"2021","journal-title":"Aquaculture"},{"key":"2022070500021162900_B15","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013"},{"key":"2022070500021162900_B16","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"2022070500021162900_B17","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience."},{"key":"2022070500021162900_B18","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/nmeth.2307","article-title":"Improved whole-chromosome phasing for disease and population genetic studies","volume":"10","author":"Delaneau","year":"2013","journal-title":"Nat. Methods"},{"key":"2022070500021162900_B19","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/j.ajhg.2018.07.015","article-title":"A one-penny imputed genome from next-generation reference panels","volume":"103","author":"Browning","year":"2018","journal-title":"Am. J. Hum. Genet."},{"key":"2022070500021162900_B20","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/s41588-020-00756-0","article-title":"Efficient phasing and imputation of low-coverage sequencing data using large reference panels","volume":"53","author":"Rubinacci","year":"2021","journal-title":"Nat. Genet."},{"key":"2022070500021162900_B21","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1038\/s41598-018-37216-z","article-title":"Genome wide association study of body weight and feed efficiency traits in a commercial broiler chicken population, a re-visitation","volume":"9","author":"Mebratie","year":"2019","journal-title":"Sci. Rep."},{"key":"2022070500021162900_B22","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1093\/jas\/skx002","article-title":"Modeling heterotic effects in beef cattle using genome-wide SNP-marker genotypes","volume":"96","author":"Akanno","year":"2018","journal-title":"J. Anim. Sci."},{"key":"2022070500021162900_B23","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1186\/s12863-018-0654-3","article-title":"Comparing SNP panels and statistical methods for estimating genomic breed composition of individual animals in ten cattle breeds","volume":"19","author":"He","year":"2018","journal-title":"BMC Genet."},{"key":"2022070500021162900_B24","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"2022070500021162900_B25","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res."},{"key":"2022070500021162900_B26","doi-asserted-by":"crossref","first-page":"2867","DOI":"10.1093\/bioinformatics\/btq559","article-title":"Robust relationship inference in genome-wide association studies","volume":"26","author":"Manichaikul","year":"2010","journal-title":"Bioinformatics"},{"key":"2022070500021162900_B27","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1038\/ng.2310","article-title":"Genome-wide efficient mixed-model analysis for association studies","volume":"44","author":"Zhou","year":"2012","journal-title":"Nat. Genet."},{"key":"2022070500021162900_B28","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1534\/genetics.112.143313","article-title":"Whole-genome regression and prediction methods applied to plant and animal breeding","volume":"193","author":"de\u00a0Los\u00a0Campos","year":"2013","journal-title":"Genetics"},{"key":"2022070500021162900_B29","doi-asserted-by":"crossref","first-page":"2016","DOI":"10.1093\/jas\/sky071","article-title":"Technical note: an r package for fitting sparse neural networks with application in animal breeding","volume":"96","author":"Wang","year":"2018","journal-title":"J. Anim. Sci."},{"key":"2022070500021162900_B30","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/1471-2164-15-90","article-title":"Development and validation of a high density SNP genotyping array for atlantic salmon (Salmo salar)","volume":"15","author":"Houston","year":"2014","journal-title":"BMC Genomics"},{"key":"2022070500021162900_B31","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.1534\/g3.117.040717","article-title":"Genotype imputation to improve the cost-efficiency of genomic selection in farmed atlantic salmon","volume":"7","author":"Tsai","year":"2017","journal-title":"G3"},{"key":"2022070500021162900_B32","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1534\/genetics.118.301298","article-title":"Can deep learning improve genomic prediction of complex human traits?","volume":"210","author":"Bellot","year":"2018","journal-title":"Genetics"},{"key":"2022070500021162900_B33","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1038\/ng.3656","article-title":"Next-generation genotype imputation service and methods","volume":"48","author":"Das","year":"2016","journal-title":"Nat. Genet."},{"key":"2022070500021162900_B34","doi-asserted-by":"crossref","first-page":"D659","DOI":"10.1093\/nar\/gkz854","article-title":"Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation","volume":"48","author":"Yang","year":"2020","journal-title":"Nucleic. Acids. Res."},{"key":"2022070500021162900_B35","doi-asserted-by":"crossref","first-page":"D1480","DOI":"10.1093\/nar\/gkaa953","article-title":"Plant-ImputeDB: an integrated multiple plant reference panel database for genotype imputation","volume":"49","author":"Gao","year":"2021","journal-title":"Nucleic. Acids. Res."},{"key":"2022070500021162900_B36","doi-asserted-by":"crossref","first-page":"e0229330","DOI":"10.1371\/journal.pone.0229330","article-title":"StructuRly: a novel shiny app to produce comprehensive, detailed and interactive plots for population genetic analysis","volume":"15","author":"Criscuolo","year":"2020","journal-title":"PLoS One"},{"key":"2022070500021162900_B37","doi-asserted-by":"crossref","first-page":"W295","DOI":"10.1093\/nar\/gkv351","article-title":"SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations","volume":"43","author":"Dereeper","year":"2015","journal-title":"Nucleic. Acids. Res."},{"key":"2022070500021162900_B38","doi-asserted-by":"crossref","first-page":"D1036","DOI":"10.1093\/nar\/gku1195","article-title":"The sol genomics network (SGN)\u2013from genotype to phenotype to breeding","volume":"43","author":"Fernandez-Pozo","year":"2015","journal-title":"Nucleic. Acids. Res."},{"key":"2022070500021162900_B39","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1105\/tpc.16.00551","article-title":"easyGWAS: a cloud-based platform for comparing the results of genome-wide association studies","volume":"29","author":"Grimm","year":"2017","journal-title":"Plant Cell."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/W1\/W66\/44379926\/gkac424.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/W1\/W66\/44379926\/gkac424.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,5]],"date-time":"2022-07-05T00:08:49Z","timestamp":1656979729000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/W1\/W66\/6593105"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,25]]},"references-count":39,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2022,5,25]]},"published-print":{"date-parts":[[2022,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac424","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,7,5]]},"published":{"date-parts":[[2022,5,25]]}}}