Development of a high density Atlantic salmon SNP chip

  • Blaxter, Mark (Principal Investigator)
  • Archibald, Alan (Co-investigator)
  • Bishop, Stephen (Co-investigator)
  • Houston, Ross (Co-investigator)
  • Gharbi, Karim (Researcher)

Project Details

Description

Salmon farming is a key economic contributor to the UK (~£0.5bn p.a.) and provides healthy, high quality food. The competitiveness and sustainability of this rural industry depend upon selective breeding. While cutting-edge genomics tools such as high density (HD) SNP chips are now routinely employed for livestock breeding decisions, salmon aquaculture has no access to such tools. This project addresses this technology gap by developing an HD salmon SNP chip for selective breeding. Use of this chip to improve salmon resistance to sea louse infection provides a tractable exemplar of this technology’s power to deliver tangible stock improvement. The project will; 1) use high-throughput sequencing to detect genome-wide SNP variation; 2) develop an HD SNP chip; 3) use the chip to perform association mapping of loci affecting resistance to sea lice; 4) commercially verify trait-associated SNPs; 5) implement strategies for SNP use in breeding programmes to improve resistance to sea lice, a paradigm for other key economic traits.

Layman's description

Salmon farming is a key economic contributor to the UK (~£0.5bn p.a.) and provides healthy, high quality food. The competitiveness and sustainability of this rural industry depend upon selective breeding. While cutting-edge genomics tools such as high density (HD) SNP chips are now routinely employed for livestock breeding decisions, salmon aquaculture has no access to such tools. This project addresses this technology gap by developing an HD salmon SNP chip for selective breeding. Use of this chip to improve salmon resistance to sea louse infection provides a tractable exemplar of this technology’s power to deliver tangible stock improvement. The project will; 1) use high-throughput sequencing to detect genome-wide SNP variation; 2) develop an HD SNP chip; 3) use the chip to perform association mapping of loci affecting resistance to sea lice; 4) commercially verify trait-associated SNPs; 5) implement strategies for SNP use in breeding programmes to improve resistance to sea lice, a paradigm for other key economic traits.

Key findings

The project has progressed well, with the majortr part of the Uoe SBS deliverables completed using the technology of the GenePool genomics Facility. RAD sequencing has been conducted and SNP defined that have been incorporated into a first generation SNP chip for genotyping and assisted breeding of Atlantic salmon. The SNP chip is described in a publication in BMC Genomics here:
http://www.biomedcentral.com/1471-2164/15/90
StatusFinished
Effective start/end date1/08/1131/07/14

Funding

  • UK central government bodies/local authorities, health and hospital authorities: £45,749.00
  • UK central government bodies/local authorities, health and hospital authorities: £93,663.00

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