Item talk:Q269155
From geokb
{
"USGS Publications Warehouse": { "@context": "https://schema.org", "@type": "Article", "additionalType": "Journal Article", "name": "Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two rainbow trout aquaculture lines confirms oligogenic architecture with several moderate effect quantitative trait loci", "identifier": [ { "@type": "PropertyValue", "propertyID": "USGS Publications Warehouse IndexID", "value": "70254581", "url": "https://pubs.usgs.gov/publication/70254581" }, { "@type": "PropertyValue", "propertyID": "USGS Publications Warehouse Internal ID", "value": 70254581 }, { "@type": "PropertyValue", "propertyID": "DOI", "value": "10.3389/fgene.2024.1394656", "url": "https://doi.org/10.3389/fgene.2024.1394656" } ], "journal": { "@type": "Periodical", "name": "Frontiers in Genetics", "volumeNumber": "15", "issueNumber": null }, "inLanguage": "en", "isPartOf": [ { "@type": "CreativeWorkSeries", "name": "Frontiers in Genetics" } ], "datePublished": "2024", "dateModified": "2024-06-03", "abstract": "Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV), which can cause substantial mortality and economic losses in rainbow trout aquaculture and fisheries enhancement hatchery programs. In a previous study on a commercial rainbow trout breeding line that has undergone selection, we found that genetic resistance to IHNV is controlled by the oligogenic inheritance of several moderate and many small effect quantitative trait loci (QTL). Here we used genome wide association analyses in two different commercial aquaculture lines that were na\u00efve to previous exposure to IHNV to determine whether QTL were shared across lines, and to investigate whether there were major effect loci that were still segregating in the na\u00efve lines. A total of 1,859 and 1,768 offspring from two commercial aquaculture strains were phenotyped for resistance to IHNV and genotyped with the rainbow trout Axiom 57K SNP array. Moderate heritability values (0.15\u20130.25) were estimated. Two statistical methods were used for genome wide association analyses in the two populations. No major QTL were detected despite the na\u00efve status of the two lines. Further, our analyses confirmed an oligogenic architecture for genetic resistance to IHNV in rainbow trout. Overall, 17 QTL with notable effect (\u22651.9% of the additive genetic variance) were detected in at least one of the two rainbow trout lines with at least one of the two statistical methods. Five of those QTL were mapped to overlapping or adjacent chromosomal regions in both lines, suggesting that some loci may be shared across commercial lines. Although some of the loci detected in this GWAS merit further investigation to better understand the biological basis of IHNV disease resistance across populations, the overall genetic architecture of IHNV resistance in the two rainbow trout lines suggests that genomic selection may be a more effective strategy for genetic improvement in this trait.", "description": "1394656, 14 p.", "publisher": { "@type": "Organization", "name": "Frontiers" }, "author": [ { "@type": "Person", "name": "Palti, Yniv", "givenName": "Yniv", "familyName": "Palti", "affiliation": [ { "@type": "Organization", "name": "National Center for Cool and Cold Water Aquaculture, USDA-ARS, 11861 Leetown Road, Kearneysville, WV 25430, USA" } ] }, { "@type": "Person", "name": "Vallejo, Roger L.", "givenName": "Roger L.", "familyName": "Vallejo", "affiliation": [ { "@type": "Organization", "name": "National Center for Cool and Cold Water Aquaculture, USDA-ARS, 11861 Leetown Road, Kearneysville, WV 25430, USA" } ] }, { "@type": "Person", "name": "Purcell, Maureen K. mpurcell@usgs.gov", "givenName": "Maureen K.", "familyName": "Purcell", "email": "mpurcell@usgs.gov", "identifier": { "@type": "PropertyValue", "propertyID": "ORCID", "value": "0000-0003-0154-8433", "url": "https://orcid.org/0000-0003-0154-8433" }, "affiliation": [ { "@type": "Organization", "name": "Western Fisheries Research Center", "url": "https://www.usgs.gov/centers/western-fisheries-research-center" } ] }, { "@type": "Person", "name": "Gao, Guangtu", "givenName": "Guangtu", "familyName": "Gao", "affiliation": [ { "@type": "Organization", "name": "National Center for Cool and Cold Water Aquaculture, USDA-ARS, 11861 Leetown Road, Kearneysville, WV 25430, USA" } ] }, { "@type": "Person", "name": "Shewbridge, Kristy L.", "givenName": "Kristy L.", "familyName": "Shewbridge", "affiliation": [ { "@type": "Organization", "name": "National Center for Cool and Cold Water Aquaculture, USDA-ARS, 11861 Leetown Road, Kearneysville, WV 25430, USA" } ] }, { "@type": "Person", "name": "Long, Roseanna L.", "givenName": "Roseanna L.", "familyName": "Long", "affiliation": [ { "@type": "Organization", "name": "National Center for Cool and Cold Water Aquaculture, USDA-ARS, 11861 Leetown Road, Kearneysville, WV 25430, USA" } ] }, { "@type": "Person", "name": "Setzke, Christopher", "givenName": "Christopher", "familyName": "Setzke", "affiliation": [ { "@type": "Organization", "name": "School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195-5020, USA" } ] }, { "@type": "Person", "name": "Fragomeni, Breno O.", "givenName": "Breno O.", "familyName": "Fragomeni", "affiliation": [ { "@type": "Organization", "name": "Department of Animal Science, University of Connecticut, 17 Manter RD, Unit 4040, Storrs, CT 06268, USADepartment of Animal Science, University of Connecticut, 17 Manter RD, Unit 4040, Storrs, CT 06268, USA" } ] }, { "@type": "Person", "name": "Cheng, Hao", "givenName": "Hao", "familyName": "Cheng", "affiliation": [ { "@type": "Organization", "name": "Department of Animal Science, University of California, One Shields AVE, Davis, CA 95616, USA" } ] }, { "@type": "Person", "name": "Martin, Kyle E.", "givenName": "Kyle E.", "familyName": "Martin", "affiliation": [ { "@type": "Organization", "name": "Hendrix Genetics, 12000 McCutcheon Road, Sumner, WA 98390, USA" } ] }, { "@type": "Person", "name": "Naish, Kerrry A.", "givenName": "Kerrry A.", "familyName": "Naish", "affiliation": [ { "@type": "Organization", "name": "chool of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195-5020, USA" } ] } ], "funder": [ { "@type": "Organization", "name": "Forest and Rangeland Ecosystem Science Center", "url": "https://www.usgs.gov/centers/forest-and-rangeland-ecosystem-science-center" }, { "@type": "Organization", "name": "Western Fisheries Research Center", "url": "https://www.usgs.gov/centers/western-fisheries-research-center" } ] }, "OpenAlex": { "_id": "https://openalex.org/w4398782423", "abstract_inverted_index": { "Infectious": [ 0 ], "hematopoietic": [ 1 ], "necrosis": [ 2 ], "(IHN)": [ 3 ], "is": [ 4, 11, 57 ], "a": [ 5, 36, 40, 297 ], "disease": [ 6, 274 ], "of": [ 7, 63, 122, 177, 203, 214, 224, 230, 256, 272, 282 ], "salmonid": [ 8 ], "fish": [ 9 ], "that": [ 10, 46, 52, 87, 112, 245, 292 ], "caused": [ 12 ], "by": [ 13, 59 ], "the": [ 14, 60, 117, 141, 165, 174, 178, 204, 215, 225, 257, 269, 278, 286 ], "IHN": [ 15 ], "virus": [ 16 ], "(IHNV),": [ 17 ], "which": [ 18 ], "can": [ 19 ], "cause": [ 20 ], "substantial": [ 21 ], "mortality": [ 22 ], "and": [ 23, 30, 66, 103, 124, 138 ], "economic": [ 24 ], "losses": [ 25 ], "in": [ 26, 81, 116, 164, 193, 210, 241, 260, 285, 304 ], "rainbow": [ 27, 42, 142, 194, 217, 288 ], "trout": [ 28, 43, 143, 218, 289 ], "aquaculture": [ 29, 85, 130 ], "fisheries": [ 31 ], "enhancement": [ 32 ], "hatchery": [ 33 ], "programs.": [ 34 ], "In": [ 35 ], "previous": [ 37, 91 ], 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"https://openalex.org/I4210126162" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5027929796", "display_name": "Paul Wheeler", "orcid": "https://orcid.org/0000-0002-5399-3531" }, "institutions": [ { "id": "https://openalex.org/I4210126162", "display_name": "National Center for Cool and Cold Water Aquaculture", "ror": "https://ror.org/026sw0405", "country_code": "US", "type": "facility", "lineage": [ "https://openalex.org/I1312222531", "https://openalex.org/I1336096307", "https://openalex.org/I4210126162", "https://openalex.org/I4210138094" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Roger L. Vallejo", "raw_affiliation_strings": [ "National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States" ], "affiliations": [ { "raw_affiliation_string": "National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States", "institution_ids": [ "https://openalex.org/I4210126162" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5065071885", "display_name": "Maureen K. Purcell", "orcid": "https://orcid.org/0000-0003-0154-8433" }, "institutions": [ { "id": "https://openalex.org/I4210166920", "display_name": "NOAA National Marine Fisheries Service Northwest Fisheries Science Center", "ror": "https://ror.org/05r7z1k40", "country_code": "US", "type": "government", "lineage": [ "https://openalex.org/I106745318", "https://openalex.org/I1308126019", "https://openalex.org/I1343035065", "https://openalex.org/I4210166920" ] }, { "id": "https://openalex.org/I1286329397", "display_name": "United States Geological Survey", "ror": "https://ror.org/035a68863", "country_code": "US", "type": "government", "lineage": [ "https://openalex.org/I1286329397", "https://openalex.org/I1335927249" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Maureen K. Purcell", "raw_affiliation_strings": [ "US Geological Survey, Western Fisheries Research Center, Seattle, WA, United States" ], "affiliations": [ { "raw_affiliation_string": "US Geological Survey, Western Fisheries Research Center, Seattle, WA, United States", "institution_ids": [ "https://openalex.org/I4210166920", "https://openalex.org/I1286329397" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5051884995", "display_name": "Guangtu Gao", "orcid": "https://orcid.org/0000-0002-6500-8164" }, "institutions": [ { "id": "https://openalex.org/I4210126162", "display_name": "National Center for Cool and Cold Water Aquaculture", "ror": "https://ror.org/026sw0405", "country_code": "US", "type": "facility", "lineage": [ "https://openalex.org/I1312222531", "https://openalex.org/I1336096307", "https://openalex.org/I4210126162", "https://openalex.org/I4210138094" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Guangtu Gao", "raw_affiliation_strings": [ "National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States" ], "affiliations": [ { "raw_affiliation_string": "National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States", "institution_ids": [ "https://openalex.org/I4210126162" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5085251784", "display_name": "Kristy Shewbridge", "orcid": null }, "institutions": [ { "id": "https://openalex.org/I4210126162", "display_name": "National Center for Cool and Cold Water Aquaculture", "ror": "https://ror.org/026sw0405", "country_code": "US", "type": "facility", "lineage": [ "https://openalex.org/I1312222531", "https://openalex.org/I1336096307", "https://openalex.org/I4210126162", "https://openalex.org/I4210138094" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Kristy L. Shewbridge", "raw_affiliation_strings": [ "National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States" ], "affiliations": [ { "raw_affiliation_string": "National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States", "institution_ids": [ "https://openalex.org/I4210126162" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5014116228", "display_name": "Roseanna L. Long", "orcid": null }, "institutions": [ { "id": "https://openalex.org/I4210126162", "display_name": "National Center for Cool and Cold Water Aquaculture", "ror": "https://ror.org/026sw0405", "country_code": "US", "type": "facility", "lineage": [ "https://openalex.org/I1312222531", "https://openalex.org/I1336096307", "https://openalex.org/I4210126162", "https://openalex.org/I4210138094" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Roseanna L. Long", "raw_affiliation_strings": [ "National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States" ], "affiliations": [ { "raw_affiliation_string": "National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States", "institution_ids": [ "https://openalex.org/I4210126162" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5098814919", "display_name": "Christopher Setzke", "orcid": null }, "institutions": [ { "id": "https://openalex.org/I201448701", "display_name": "University of Washington", "ror": "https://ror.org/00cvxb145", "country_code": "US", "type": "education", "lineage": [ "https://openalex.org/I201448701" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Christopher Setzke", "raw_affiliation_strings": [ "School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States" ], "affiliations": [ { "raw_affiliation_string": "School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States", "institution_ids": [ "https://openalex.org/I201448701" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5052621750", "display_name": "Breno Fragomeni", "orcid": "https://orcid.org/0000-0003-2504-2760" }, "institutions": [ { "id": "https://openalex.org/I140172145", "display_name": "University of Connecticut", "ror": "https://ror.org/02der9h97", "country_code": "US", "type": "education", "lineage": [ "https://openalex.org/I140172145" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Breno O. Fragomeni", "raw_affiliation_strings": [ "Department of Animal Science, University of Connecticut, Storrs, CT, United States" ], "affiliations": [ { "raw_affiliation_string": "Department of Animal Science, University of Connecticut, Storrs, CT, United States", "institution_ids": [ "https://openalex.org/I140172145" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5100705765", "display_name": "Hao Cheng", "orcid": "https://orcid.org/0000-0001-5146-7231" }, "institutions": [ { "id": "https://openalex.org/I84218800", "display_name": "University of California, Davis", "ror": "https://ror.org/05rrcem69", "country_code": "US", "type": "education", "lineage": [ "https://openalex.org/I84218800" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Hao Cheng", "raw_affiliation_strings": [ "Department of Animal Science, University of California, Davis, Davis, CA, United States" ], "affiliations": [ { "raw_affiliation_string": "Department of Animal Science, University of California, Davis, Davis, CA, United States", "institution_ids": [ "https://openalex.org/I84218800" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5069541545", "display_name": "Kyle E. 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Naish", "raw_affiliation_strings": [ "School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States" ], "affiliations": [ { "raw_affiliation_string": "School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States", "institution_ids": [ "https://openalex.org/I201448701" ] } ] } ], "best_oa_location": { "is_oa": true, "landing_page_url": "https://doi.org/10.3389/fgene.2024.1394656", "pdf_url": "https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1394656/pdf", "source": { "id": "https://openalex.org/S2597340651", "display_name": "Frontiers in Genetics", "issn_l": "1664-8021", "issn": [ "1664-8021" ], "is_oa": true, "is_in_doaj": true, "is_core": true, "host_organization": "https://openalex.org/P4310320527", "host_organization_name": "Frontiers Media", "host_organization_lineage": [ "https://openalex.org/P4310320527" ], "host_organization_lineage_names": [ "Frontiers Media" ], "type": "journal" }, 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