{"id":"https://openalex.org/W7225810023","doi":"https://doi.org/10.21203/rs.3.rs-11167872/v1","title":"Research Paper Ultra-low-depth whole-genome sequencing with reference panel-based imputation illuminates sex chromosome evolution and enables growth rate and disease-resistance GWAS and genomic prediction in sablefish (Anoplopoma fimbria)","display_name":"Research Paper Ultra-low-depth whole-genome sequencing with reference panel-based imputation illuminates sex chromosome evolution and enables growth rate and disease-resistance GWAS and genomic prediction in sablefish (Anoplopoma fimbria)","publication_year":2026,"publication_date":"2026-11-11","ids":{"openalex":"https://openalex.org/W7225810023","doi":"https://doi.org/10.21203/rs.3.rs-11167872/v1"},"language":"en","primary_location":{"id":"doi:10.21203/rs.3.rs-11167872/v1","doi":"https://doi.org/10.21203/rs.3.rs-11167872/v1","is_oa":true,"landing_page_url":"https://doi.org/10.21203/rs.3.rs-11167872/v1","pdf_url":null,"source":{"id":"https://openalex.org/S4306525896","display_name":"Research Square","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Research Square","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.21203/rs.3.rs-11167872/v1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102689088","display_name":"Zhaoze Liu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I212119943","display_name":"University of Victoria","ror":"https://ror.org/04s5mat29","country_code":"CA","type":"education","lineage":["https://openalex.org/I212119943"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Zhaoze Liu","raw_affiliation_strings":["University of Victoria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Victoria","institution_ids":["https://openalex.org/I212119943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009892327","display_name":"Briony Campbell","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Briony Campbell","raw_affiliation_strings":["Golden Eagle Sable Fish"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Golden Eagle Sable Fish","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024814762","display_name":"Mary Lesperance","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I212119943","display_name":"University of Victoria","ror":"https://ror.org/04s5mat29","country_code":"CA","type":"education","lineage":["https://openalex.org/I212119943"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Lesperance Mary","raw_affiliation_strings":["University of Victoria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Victoria","institution_ids":["https://openalex.org/I212119943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056521783","display_name":"Isabel Ma","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I212119943","display_name":"University of Victoria","ror":"https://ror.org/04s5mat29","country_code":"CA","type":"education","lineage":["https://openalex.org/I212119943"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Isabel Ma","raw_affiliation_strings":["University of Victoria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Victoria","institution_ids":["https://openalex.org/I212119943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090281546","display_name":"Xuekui Zhang","orcid":"https://orcid.org/0000-0003-4728-2343","observed_orcids":["https://orcid.org/0000-0003-4728-2343"]},"institutions":[{"id":"https://openalex.org/I212119943","display_name":"University of Victoria","ror":"https://ror.org/04s5mat29","country_code":"CA","type":"education","lineage":["https://openalex.org/I212119943"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Xuekui Zhang","raw_affiliation_strings":["University of Victoria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Victoria","institution_ids":["https://openalex.org/I212119943"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101941545","display_name":"John Taylor","orcid":"https://orcid.org/0000-0001-9003-4076","observed_orcids":["https://orcid.org/0000-0001-9003-4076"]},"institutions":[{"id":"https://openalex.org/I212119943","display_name":"University of Victoria","ror":"https://ror.org/04s5mat29","country_code":"CA","type":"education","lineage":["https://openalex.org/I212119943"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"John Taylor","raw_affiliation_strings":["University of Victoria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Victoria","institution_ids":["https://openalex.org/I212119943"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5101941545"],"corresponding_institution_ids":["https://openalex.org/I212119943"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.9634000062942505,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.9634000062942505,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.02410000003874302,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0032999999821186066,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7739999890327454},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.7164000272750854},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.6758000254631042},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.6496999859809875},{"id":"https://openalex.org/C106208931","wikidata":"https://www.wikidata.org/wiki/Q1098876","display_name":"Genome-wide association study","level":5,"score":0.6251000165939331},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6003000140190125},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.5331000089645386},{"id":"https://openalex.org/C186413461","wikidata":"https://www.wikidata.org/wiki/Q744727","display_name":"Genetic association","level":5,"score":0.508899986743927},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.499099999666214},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.46239998936653137},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.42719998955726624},{"id":"https://openalex.org/C163691529","wikidata":"https://www.wikidata.org/wiki/Q7391886","display_name":"SNP genotyping","level":5,"score":0.4108000099658966},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.34360000491142273},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.3337000012397766},{"id":"https://openalex.org/C59701697","wikidata":"https://www.wikidata.org/wiki/Q6895959","display_name":"Molecular Inversion Probe","level":5,"score":0.28999999165534973},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.28139999508857727},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.27959999442100525},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.2696000039577484},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.26100000739097595},{"id":"https://openalex.org/C2779729001","wikidata":"https://www.wikidata.org/wiki/Q4688338","display_name":"Aeromonas salmonicida","level":3,"score":0.25519999861717224},{"id":"https://openalex.org/C3641667","wikidata":"https://www.wikidata.org/wiki/Q1295959","display_name":"Effective population size","level":4,"score":0.25200000405311584}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.21203/rs.3.rs-11167872/v1","doi":"https://doi.org/10.21203/rs.3.rs-11167872/v1","is_oa":true,"landing_page_url":"https://doi.org/10.21203/rs.3.rs-11167872/v1","pdf_url":null,"source":{"id":"https://openalex.org/S4306525896","display_name":"Research Square","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Research Square","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.21203/rs.3.rs-11167872/v1","doi":"https://doi.org/10.21203/rs.3.rs-11167872/v1","is_oa":true,"landing_page_url":"https://doi.org/10.21203/rs.3.rs-11167872/v1","pdf_url":null,"source":{"id":"https://openalex.org/S4306525896","display_name":"Research Square","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Research Square","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1928998639","https://openalex.org/W1979543168","https://openalex.org/W1980168725","https://openalex.org/W1997751006","https://openalex.org/W2010647601","https://openalex.org/W2072943194","https://openalex.org/W2104549677","https://openalex.org/W2106574010","https://openalex.org/W2108234281","https://openalex.org/W2119180969","https://openalex.org/W2122825543","https://openalex.org/W2161633633","https://openalex.org/W2166501262","https://openalex.org/W2170551349","https://openalex.org/W2230276206","https://openalex.org/W2307506820","https://openalex.org/W2511515754","https://openalex.org/W2557913812","https://openalex.org/W2592004722","https://openalex.org/W2725988230","https://openalex.org/W3017265939","https://openalex.org/W3021560172","https://openalex.org/W3120295425","https://openalex.org/W3134212955","https://openalex.org/W3175822364","https://openalex.org/W4224111903","https://openalex.org/W4366996300","https://openalex.org/W4376865198","https://openalex.org/W4389883300","https://openalex.org/W4404413400","https://openalex.org/W4408134736","https://openalex.org/W4414138652","https://openalex.org/W4416329796"],"related_works":[],"abstract_inverted_index":{"Abstract":[0],"Genome-wide":[1],"association":[2],"studies":[3],"and":[4,8,57,108,112,172,200,212,215,326,334,340,358,381],"genome":[5,83],"prediction":[6,314],"(GWAS":[7],"GP)":[9],"in":[10,69,140,276,383],"non-model":[11,385],"species":[12],"are":[13,262],"often":[14],"limited":[15],"by":[16,24,86,159,173],"the":[17,120],"lack":[18],"of":[19,95,144,153,189,244,299,338,352,376],"dense":[20],"genotyping":[21,170],"arrays":[22],"or":[23],"high":[25],"sequencing":[26,30,87],"costs.":[27],"Low-depth":[28],"whole-genome":[29],"(WGS)":[31],"combined":[32],"with":[33,51,71,230,253,286,291,302,320,331,363],"genotype":[34],"imputation":[35,364],"can":[36,49],"be":[37],"a":[38,77,92,141,150,167,295,348,366],"cost-effective":[39],"alternative.":[40],"However,":[41],"it":[42],"is":[43],"not":[44],"clear":[45],"how":[46],"low":[47,321],"one":[48],"go":[50],"respect":[52],"to":[53,91,137,149,163,180,264],"target":[54,142,209,219],"sample":[55],"depth":[56,94,152],"reference":[58,84,135,370],"panel":[59,85,136,171,371],"size.":[60],"In":[61],"addition,":[62],"these":[63],"approaches":[64],"have":[65],"rarely":[66],"been":[67],"evaluated":[68],"populations":[70],"extensive":[72],"family":[73],"structure.":[74],"We":[75,132],"generated":[76],"sablefish":[78,147],"(":[79,129,281,310],"Anoplopoma":[80],"fimbria":[81],")":[82,283],"65":[88],"wild-caught":[89],"individuals":[90,221],"mean":[93,151],"14x.":[96],"Approximately":[97],"4.9":[98],"million":[99,191],"SNPs":[100,192,249,275,289,319],"were":[101,196,250,273,284,316,329],"observed.":[102],"SNP":[103,169,239],"density":[104],"varied":[105],"among":[106],"chromosomes":[107],"along":[109],"chromosome":[110,116,233,300],"arms":[111],"was":[113,157,240,258],"lowest":[114,236],"on":[115],"14,":[117],"which":[118],"contains":[119],"Master":[121],"Sex-Determining":[122],"gene,":[123],"gonodal":[124],"somatic":[125],"cell":[126],"derived":[127],"factor":[128],"gsdf":[130,245],").":[131,312],"used":[133],"this":[134,384],"impute":[138],"genotypes":[139,162,175],"population":[143,210,220],"1,380":[145],"farm-raised":[146],"sequenced":[148],"0.4x.":[154],"Imputation":[155],"accuracy":[156],"estimated":[158],"comparing":[160,174],"imputed":[161,184],"those":[164,181],"obtained":[165,176,182],"from":[166,177,183],"PCR-based":[168],"14x":[178],"alignments":[179],"down-sampled":[185],"data.":[186],"A":[187],"total":[188],"1.2":[190],"(MAF":[193],"\u2265":[194],"0.05)":[195],"utilized":[197],"for":[198,202,213,379],"GWAS":[199,322,380],"GP":[201,382],"weight":[203,254,287],"at":[204],"age":[205],"2.5":[206],"years":[207],"(all":[208],"individuals)":[211],"sex":[214,231],"disease":[216,292,327],"status":[217,293,328],"(603":[218],"sampled":[222],"during":[223],"an":[224,373],"Aeromonas":[225],"salmonicida":[226],"outbreak).":[227],"Significant":[228],"associations":[229],"spanned":[232,294],"14.":[234],"The":[235,343],"p":[237,323],"-value":[238],"9":[241],"kb":[242],"upstream":[243],".":[246],"Chromosome":[247],"14":[248],"also":[251],"associated":[252,285,290],"variation.":[255,288],"This":[256],"result":[257],"anticipated":[259],"because":[260],"females":[261],"known":[263],"grow":[265],"faster":[266],"than":[267],"males.":[268],"When":[269],"only":[270],"female":[271],"data":[272],"analyzed,":[274],"macrophage":[277],"mannose":[278],"receptor":[279],"1":[280],"mrc1":[282],"46":[296],"Kb":[297],"region":[298],"20":[301],"several":[303],"candidate":[304],"genes":[305],"including":[306],"peroxynitrite":[307],"isomerase":[308],"THAP4":[309],"thap4":[311],"Genomic":[313],"models":[315,333],"developed":[317],"using":[318,365],"-values.":[324],"Sex":[325],"predicted":[330,359],"multi-locus":[332],"had":[335],"classification":[336],"accuracies":[337],"0.95":[339],"0.71,":[341],"respectively.":[342],"best":[344],"weight-prediction":[345],"model":[346],"achieved":[347],"Pearson":[349],"correlation":[350],"coefficient":[351],"r":[353],"=":[354],"0.65":[355],"between":[356],"observed":[357],"weights.":[360],"Ultra-low-depth":[361],"WGS":[362],"diverse":[367],"but":[368],"small":[369],"provided":[372],"enormous":[374],"set":[375],"reliable":[377],"markers":[378],"aquaculture":[386],"species.":[387]},"counts_by_year":[],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2026-11-12T00:00:00"}