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Species-Specific Marker Discovery in Tilapia.

Mochamad Syaifudin1,2, Michaël Bekaert1, John B Taggart1

  • 1Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom.

Scientific Reports
|September 12, 2019
PubMed
Summary

Double digested restriction-site associated DNA (ddRAD) sequencing effectively identified numerous single nucleotide polymorphism (SNP) markers. These markers are crucial for distinguishing tilapia species and analyzing hybridization in aquaculture and wild populations.

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Area of Science:

  • Aquaculture and Fisheries Science
  • Genetics and Genomics
  • Molecular Biology

Background:

  • Tilapias are vital in global aquaculture and fisheries.
  • Hybridization and introgression are prevalent in tilapia but challenging to study due to a lack of species-specific genetic markers.

Purpose of the Study:

  • To evaluate double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers.
  • To develop genetic tools for distinguishing tilapia species and investigating hybridization.

Main Methods:

  • Utilized ddRAD sequencing to analyze genetic variation across 10 tilapia species.
  • Employed both de novo and reference-based analyses to identify shared and species-specific SNPs.
  • Developed and validated a panel of 24 SNP markers for four key tilapia species.

Main Results:

  • Identified 1,371 shared SNPs (de novo) and 1,204 shared SNPs (reference-based).
  • Discovered 57 species-specific SNP markers among 10 tilapia species.
  • Developed a panel of 62 species-specific SNPs for four frequently hybridized tilapia species, with 24 validated for distinguishing them.

Conclusions:

  • ddRAD sequencing is a powerful method for discovering numerous SNP markers in tilapia.
  • The identified SNP markers can effectively distinguish tilapia species and aid in the study of hybridization and introgression.
  • This approach has significant potential for managing tilapia aquaculture and conserving wild populations.