Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon
<p>Abstract</p> <p>Background</p> <p>Restriction site-associated DNA sequencing (RAD-Seq) is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing. Recent applications of RAD-Seq have included linkage and QTL...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-06-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/244 |
| _version_ | 1811293272469929984 |
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| author | Houston Ross D Davey John W Bishop Stephen C Lowe Natalie R Mota-Velasco Jose C Hamilton Alastair Guy Derrick R Tinch Alan E Thomson Marian L Blaxter Mark L Gharbi Karim Bron James E Taggart John B |
| author_facet | Houston Ross D Davey John W Bishop Stephen C Lowe Natalie R Mota-Velasco Jose C Hamilton Alastair Guy Derrick R Tinch Alan E Thomson Marian L Blaxter Mark L Gharbi Karim Bron James E Taggart John B |
| author_sort | Houston Ross D |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Restriction site-associated DNA sequencing (RAD-Seq) is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing. Recent applications of RAD-Seq have included linkage and QTL mapping with a particular focus on non-model species. In the current study, we have applied RAD-Seq to two Atlantic salmon families from a commercial breeding program. The offspring from these families were classified into resistant or susceptible based on survival/mortality in an Infectious Pancreatic Necrosis (IPN) challenge experiment, and putative homozygous resistant or susceptible genotype at a major IPN-resistance QTL. From each family, the genomic DNA of the two heterozygous parents and seven offspring of each IPN phenotype and genotype was digested with the SbfI enzyme and sequenced in multiplexed pools.</p> <p>Results</p> <p>Sequence was obtained from approximately 70,000 RAD loci in both families and a filtered set of 6,712 segregating SNPs were identified. Analyses of genome-wide RAD marker segregation patterns in the two families suggested SNP discovery on all 29 Atlantic salmon chromosome pairs, and highlighted the dearth of male recombination. The use of pedigreed samples allowed us to distinguish segregating SNPs from putative paralogous sequence variants resulting from the relatively recent genome duplication of salmonid species. Of the segregating SNPs, 50 were linked to the QTL. A subset of these QTL-linked SNPs were converted to a high-throughput assay and genotyped across large commercial populations of IPNV-challenged salmon fry. Several SNPs showed highly significant linkage and association with resistance to IPN, and population linkage-disequilibrium-based SNP tests for resistance were identified.</p> <p>Conclusions</p> <p>We used RAD-Seq to successfully identify and characterise high-density genetic markers in pedigreed aquaculture Atlantic salmon. These results underline the effectiveness of RAD-Seq as a tool for rapid and efficient generation of QTL-targeted and genome-wide marker data in a large complex genome, and its possible utility in farmed animal selection programs.</p> |
| first_indexed | 2024-04-13T04:58:56Z |
| format | Article |
| id | doaj.art-8764d138ef8b403185d99f1afe069ce4 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T04:58:56Z |
| publishDate | 2012-06-01 |
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| series | BMC Genomics |
| spelling | doaj.art-8764d138ef8b403185d99f1afe069ce42022-12-22T03:01:23ZengBMCBMC Genomics1471-21642012-06-0113124410.1186/1471-2164-13-244Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmonHouston Ross DDavey John WBishop Stephen CLowe Natalie RMota-Velasco Jose CHamilton AlastairGuy Derrick RTinch Alan EThomson Marian LBlaxter Mark LGharbi KarimBron James ETaggart John B<p>Abstract</p> <p>Background</p> <p>Restriction site-associated DNA sequencing (RAD-Seq) is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing. Recent applications of RAD-Seq have included linkage and QTL mapping with a particular focus on non-model species. In the current study, we have applied RAD-Seq to two Atlantic salmon families from a commercial breeding program. The offspring from these families were classified into resistant or susceptible based on survival/mortality in an Infectious Pancreatic Necrosis (IPN) challenge experiment, and putative homozygous resistant or susceptible genotype at a major IPN-resistance QTL. From each family, the genomic DNA of the two heterozygous parents and seven offspring of each IPN phenotype and genotype was digested with the SbfI enzyme and sequenced in multiplexed pools.</p> <p>Results</p> <p>Sequence was obtained from approximately 70,000 RAD loci in both families and a filtered set of 6,712 segregating SNPs were identified. Analyses of genome-wide RAD marker segregation patterns in the two families suggested SNP discovery on all 29 Atlantic salmon chromosome pairs, and highlighted the dearth of male recombination. The use of pedigreed samples allowed us to distinguish segregating SNPs from putative paralogous sequence variants resulting from the relatively recent genome duplication of salmonid species. Of the segregating SNPs, 50 were linked to the QTL. A subset of these QTL-linked SNPs were converted to a high-throughput assay and genotyped across large commercial populations of IPNV-challenged salmon fry. Several SNPs showed highly significant linkage and association with resistance to IPN, and population linkage-disequilibrium-based SNP tests for resistance were identified.</p> <p>Conclusions</p> <p>We used RAD-Seq to successfully identify and characterise high-density genetic markers in pedigreed aquaculture Atlantic salmon. These results underline the effectiveness of RAD-Seq as a tool for rapid and efficient generation of QTL-targeted and genome-wide marker data in a large complex genome, and its possible utility in farmed animal selection programs.</p>http://www.biomedcentral.com/1471-2164/13/244Atlantic salmonRAD sequencingAquacultureInfectious pancreatic necrosisRecombinationSingle nucleotide polymorphismParalogous sequence variant |
| spellingShingle | Houston Ross D Davey John W Bishop Stephen C Lowe Natalie R Mota-Velasco Jose C Hamilton Alastair Guy Derrick R Tinch Alan E Thomson Marian L Blaxter Mark L Gharbi Karim Bron James E Taggart John B Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon BMC Genomics Atlantic salmon RAD sequencing Aquaculture Infectious pancreatic necrosis Recombination Single nucleotide polymorphism Paralogous sequence variant |
| title | Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon |
| title_full | Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon |
| title_fullStr | Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon |
| title_full_unstemmed | Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon |
| title_short | Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon |
| title_sort | characterisation of qtl linked and genome wide restriction site associated dna rad markers in farmed atlantic salmon |
| topic | Atlantic salmon RAD sequencing Aquaculture Infectious pancreatic necrosis Recombination Single nucleotide polymorphism Paralogous sequence variant |
| url | http://www.biomedcentral.com/1471-2164/13/244 |
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