Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout ( Oncorhynchus mykiss ) Breeding Strains by Using Next-Generation Sequencing
Selective breeding can significantly improve the establishment of sustainable and profitable aquaculture fish farming. For rainbow trout ( ), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the...
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| Veröffentlicht in: | Genes 2020-07, Vol.11 (8), p.841 |
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| creator | de Los Ríos-Pérez, Lidia Brunner, Ronald Marco Hadlich, Frieder Rebl, Alexander Kühn, Carsten Wittenburg, Dörte Goldammer, Tom Verleih, Marieke |
| description | Selective breeding can significantly improve the establishment of sustainable and profitable aquaculture fish farming. For rainbow trout (
), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the genetic variation between the local Born strain, selected for survival, and the commercially available Silver Steelhead strain, selected for growth. We sequenced the transcriptome of six tissues (gills, head kidney, heart, liver, spleen, and white muscle) from eight healthy individuals per strain, using RNA-seq technology to identify strain-specific gene-expression patterns and single nucleotide polymorphisms (SNPs). In total, 1760 annotated genes were differentially expressed across all tissues. Pathway analysis assigned them to different gene networks. We also identified a set of SNPs, which are heterozygous for one of the two breeding strains: 1229 of which represent polymorphisms over all tissues and individuals. Our data indicate a strong genetic differentiation between Born and Silver Steelhead trout, despite the relatively short time of evolutionary separation of the two breeding strains. The results most likely reflect their specifically adapted genotypes and might contribute to the understanding of differences regarding their robustness toward high stress and pathogenic challenge described in former studies. |
| doi_str_mv | 10.3390/genes11080841 |
| format | Article |
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), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the genetic variation between the local Born strain, selected for survival, and the commercially available Silver Steelhead strain, selected for growth. We sequenced the transcriptome of six tissues (gills, head kidney, heart, liver, spleen, and white muscle) from eight healthy individuals per strain, using RNA-seq technology to identify strain-specific gene-expression patterns and single nucleotide polymorphisms (SNPs). In total, 1760 annotated genes were differentially expressed across all tissues. Pathway analysis assigned them to different gene networks. We also identified a set of SNPs, which are heterozygous for one of the two breeding strains: 1229 of which represent polymorphisms over all tissues and individuals. Our data indicate a strong genetic differentiation between Born and Silver Steelhead trout, despite the relatively short time of evolutionary separation of the two breeding strains. The results most likely reflect their specifically adapted genotypes and might contribute to the understanding of differences regarding their robustness toward high stress and pathogenic challenge described in former studies.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes11080841</identifier><identifier>PMID: 32722051</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Animal breeding ; Animals ; Aquaculture ; Breeding ; Comparative analysis ; Deoxyribonucleic acid ; DNA ; DNA methylation ; DNA sequencing ; Epigenetics ; Fish hatcheries ; Fisheries ; Gene expression ; Gene Regulatory Networks ; Genes ; Genetic aspects ; Genetic diversity ; Genetic Markers ; Genetic transcription ; Genomes ; Genotype & phenotype ; Gills ; Growth ; High-Throughput Nucleotide Sequencing - methods ; Kidneys ; Methods ; Molecular Sequence Annotation ; Next-generation sequencing ; Nucleotide sequencing ; Oncorhynchus mykiss ; Oncorhynchus mykiss - classification ; Oncorhynchus mykiss - genetics ; Oncorhynchus mykiss - growth & development ; Pipelines ; Polymorphism, Single Nucleotide ; Quality control ; Rainbow trout ; Ribonucleic acid ; RNA ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Species Specificity ; Spleen ; Strains (organisms) ; Transcriptome ; Trout</subject><ispartof>Genes, 2020-07, Vol.11 (8), p.841</ispartof><rights>COPYRIGHT 2020 MDPI AG</rights><rights>2020. This work is licensed under http://creativecommons.org/licenses/by/3.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2020 by the authors. 2020</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c443t-6830d3eca3d7756403b557cb3bd1107dea3c0f13f59720fe7d5dc53e3158d14e3</citedby><cites>FETCH-LOGICAL-c443t-6830d3eca3d7756403b557cb3bd1107dea3c0f13f59720fe7d5dc53e3158d14e3</cites><orcidid>0000-0001-8392-2657 ; 0000-0002-5141-5818 ; 0000-0003-1215-5504 ; 0000-0002-2918-7433</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464081/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464081/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,882,27905,27906,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32722051$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>de Los Ríos-Pérez, Lidia</creatorcontrib><creatorcontrib>Brunner, Ronald Marco</creatorcontrib><creatorcontrib>Hadlich, Frieder</creatorcontrib><creatorcontrib>Rebl, Alexander</creatorcontrib><creatorcontrib>Kühn, Carsten</creatorcontrib><creatorcontrib>Wittenburg, Dörte</creatorcontrib><creatorcontrib>Goldammer, Tom</creatorcontrib><creatorcontrib>Verleih, Marieke</creatorcontrib><title>Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout ( Oncorhynchus mykiss ) Breeding Strains by Using Next-Generation Sequencing</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>Selective breeding can significantly improve the establishment of sustainable and profitable aquaculture fish farming. For rainbow trout (
), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the genetic variation between the local Born strain, selected for survival, and the commercially available Silver Steelhead strain, selected for growth. We sequenced the transcriptome of six tissues (gills, head kidney, heart, liver, spleen, and white muscle) from eight healthy individuals per strain, using RNA-seq technology to identify strain-specific gene-expression patterns and single nucleotide polymorphisms (SNPs). In total, 1760 annotated genes were differentially expressed across all tissues. Pathway analysis assigned them to different gene networks. We also identified a set of SNPs, which are heterozygous for one of the two breeding strains: 1229 of which represent polymorphisms over all tissues and individuals. Our data indicate a strong genetic differentiation between Born and Silver Steelhead trout, despite the relatively short time of evolutionary separation of the two breeding strains. The results most likely reflect their specifically adapted genotypes and might contribute to the understanding of differences regarding their robustness toward high stress and pathogenic challenge described in former studies.</description><subject>Animal breeding</subject><subject>Animals</subject><subject>Aquaculture</subject><subject>Breeding</subject><subject>Comparative analysis</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA methylation</subject><subject>DNA sequencing</subject><subject>Epigenetics</subject><subject>Fish hatcheries</subject><subject>Fisheries</subject><subject>Gene expression</subject><subject>Gene Regulatory Networks</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetic Markers</subject><subject>Genetic transcription</subject><subject>Genomes</subject><subject>Genotype & phenotype</subject><subject>Gills</subject><subject>Growth</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Kidneys</subject><subject>Methods</subject><subject>Molecular Sequence Annotation</subject><subject>Next-generation sequencing</subject><subject>Nucleotide sequencing</subject><subject>Oncorhynchus mykiss</subject><subject>Oncorhynchus mykiss - classification</subject><subject>Oncorhynchus mykiss - genetics</subject><subject>Oncorhynchus mykiss - growth & development</subject><subject>Pipelines</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Quality control</subject><subject>Rainbow trout</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Species Specificity</subject><subject>Spleen</subject><subject>Strains (organisms)</subject><subject>Transcriptome</subject><subject>Trout</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpdkk1v1DAQhiMEolXpkSuyxKUcAv5cZy9IywIFqWordnu2HGey65LYW9tpyY_iP-JoS2nxxZbnmXfesacoXhP8nrE5_rABB5EQXOGKk2fFIcWSlZxT8fzR-aA4jvEa58UxxVi8LA4YlZRiQQ6L30vf73TQyd4CWjjdjdFG5FuUtoDWQbtogt0l3wPSrkGfbUzB1kOy3k3U5ZD2qavzy4isQ-s7j35o62p_l9P9kNAJunDGh-3ozHaIqB9_2hjRO_QpADTWbdAqhZwQUT2iqzhdnMOvVJ7m1iZbuc4KbgZwJodeFS9a3UU4vt-PiquvX9bLb-XZxen35eKsNJyzVM4qhhsGRrNGSjHjmNVCSFOzusmPJRvQzOCWsFbMJcUtyEY0RjBgRFQN4cCOio973d1Q99AYcNljp3bB9jqMymurnkac3aqNv1WS52oVyQIn9wLBZ_Mxqd5GA12nHfghKsppJQSf0wl9-x967YeQf2JPES4Jqf5RG92Bsq71ua6ZRNVixtlM4gxmqtxTJvgYA7QPlglW08SoJxOT-TeP-3yg_84H-wNykb6M</recordid><startdate>20200724</startdate><enddate>20200724</enddate><creator>de Los Ríos-Pérez, Lidia</creator><creator>Brunner, Ronald Marco</creator><creator>Hadlich, Frieder</creator><creator>Rebl, Alexander</creator><creator>Kühn, Carsten</creator><creator>Wittenburg, Dörte</creator><creator>Goldammer, Tom</creator><creator>Verleih, Marieke</creator><general>MDPI AG</general><general>MDPI</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-8392-2657</orcidid><orcidid>https://orcid.org/0000-0002-5141-5818</orcidid><orcidid>https://orcid.org/0000-0003-1215-5504</orcidid><orcidid>https://orcid.org/0000-0002-2918-7433</orcidid></search><sort><creationdate>20200724</creationdate><title>Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout ( Oncorhynchus mykiss ) Breeding Strains by Using Next-Generation Sequencing</title><author>de Los Ríos-Pérez, Lidia ; 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For rainbow trout (
), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the genetic variation between the local Born strain, selected for survival, and the commercially available Silver Steelhead strain, selected for growth. We sequenced the transcriptome of six tissues (gills, head kidney, heart, liver, spleen, and white muscle) from eight healthy individuals per strain, using RNA-seq technology to identify strain-specific gene-expression patterns and single nucleotide polymorphisms (SNPs). In total, 1760 annotated genes were differentially expressed across all tissues. Pathway analysis assigned them to different gene networks. We also identified a set of SNPs, which are heterozygous for one of the two breeding strains: 1229 of which represent polymorphisms over all tissues and individuals. Our data indicate a strong genetic differentiation between Born and Silver Steelhead trout, despite the relatively short time of evolutionary separation of the two breeding strains. The results most likely reflect their specifically adapted genotypes and might contribute to the understanding of differences regarding their robustness toward high stress and pathogenic challenge described in former studies.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>32722051</pmid><doi>10.3390/genes11080841</doi><orcidid>https://orcid.org/0000-0001-8392-2657</orcidid><orcidid>https://orcid.org/0000-0002-5141-5818</orcidid><orcidid>https://orcid.org/0000-0003-1215-5504</orcidid><orcidid>https://orcid.org/0000-0002-2918-7433</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Genes, 2020-07, Vol.11 (8), p.841 |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central Open Access; MDPI - Multidisciplinary Digital Publishing Institute; PubMed Central |
| subjects | Animal breeding Animals Aquaculture Breeding Comparative analysis Deoxyribonucleic acid DNA DNA methylation DNA sequencing Epigenetics Fish hatcheries Fisheries Gene expression Gene Regulatory Networks Genes Genetic aspects Genetic diversity Genetic Markers Genetic transcription Genomes Genotype & phenotype Gills Growth High-Throughput Nucleotide Sequencing - methods Kidneys Methods Molecular Sequence Annotation Next-generation sequencing Nucleotide sequencing Oncorhynchus mykiss Oncorhynchus mykiss - classification Oncorhynchus mykiss - genetics Oncorhynchus mykiss - growth & development Pipelines Polymorphism, Single Nucleotide Quality control Rainbow trout Ribonucleic acid RNA Single nucleotide polymorphisms Single-nucleotide polymorphism Species Specificity Spleen Strains (organisms) Transcriptome Trout |
| title | Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout ( Oncorhynchus mykiss ) Breeding Strains by Using Next-Generation Sequencing |
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