Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

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• 作者：Ross D Houston (1)
  John B Taggart (2)
  Timothé Cézard (3)
  Micha?l Bekaert (2)
  Natalie R Lowe (1)
  Alison Downing (4)
  Richard Talbot (4)
  Stephen C Bishop (1)
  Alan L Archibald (1)
  James E Bron (2)
  David J Penman (2)
  Alessandro Davassi (5)
  Fiona Brew (5)
  Alan E Tinch (6)
  Karim Gharbi (3)
  Alastair Hamilton (6)
  
• 关键词：Atlantic salmon ; Salmo salar ; Polymorphism ; Single nucleotide polymorphism ; SNP ; Next ; generation sequencing ; Array ; Genomics ; Mapping ; Genome duplication
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：386 KB
• 作者单位：Ross D Houston (1)
  John B Taggart (2)
  Timothé Cézard (3)
  Micha?l Bekaert (2)
  Natalie R Lowe (1)
  Alison Downing (4)
  Richard Talbot (4)
  Stephen C Bishop (1)
  Alan L Archibald (1)
  James E Bron (2)
  David J Penman (2)
  Alessandro Davassi (5)
  Fiona Brew (5)
  Alan E Tinch (6)
  Karim Gharbi (3)
  Alastair Hamilton (6)
  
  1. The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
  2. Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
  3. Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3JT, UK
  4. Edinburgh Genomics, The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK
  5. Affymetrix UK Ltd, Voyager, Mercury Park, Wycombe Lane, Wooburn Green, High Wycombe, HP10 0HH, UK
  6. Landcatch Natural Selection Ltd, 15 Beta Centre, Stirling University Innovation Park, Stirling, FK9 4NF, UK
  
• ISSN：1471-2164

文摘

Background Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. Results SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom? myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. Conclusions This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection.