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A novel transcriptome-derived SNPs array for tench (Tinca tinca L.).

Girish Kumar1, Jorge Langa2, Iratxe Montes2

  • 1Research Institute of Fish Culture and Hydrobiology, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Czech Republic.

Plos One
|March 20, 2019
PubMed
Summary
This summary is machine-generated.

Researchers developed new genetic markers for tench (Tinca tinca L.) by sequencing its genome. These validated single nucleotide polymorphisms (SNPs) can differentiate tench breeds and aid in aquaculture and conservation efforts.

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Area of Science:

  • Aquaculture and Fisheries Science
  • Genomics and Bioinformatics
  • Conservation Genetics

Background:

  • Tench (Tinca tinca L.) possesses significant economic value, attributed to its high fecundity and longevity.
  • Previous population genetic studies identified Eastern and Western phylogroups but were hampered by a lack of genomic resources.
  • Developing genetic markers is crucial for understanding tench population structure and facilitating selective breeding.

Purpose of the Study:

  • To generate novel genomic resources for tench (Tinca tinca L.) through transcriptome and genome sequencing.
  • To identify and validate single nucleotide polymorphisms (SNPs) for use as genetic markers.
  • To assess the genetic differentiation between two tench breeds using the validated SNPs.

Main Methods:

  • High-throughput sequencing was employed to analyze the tench transcriptome and genome.
  • A computational pipeline was used to identify putative single nucleotide polymorphisms (SNPs) from transcriptome data.
  • A set of 96 SNPs was selected for validation, with 92 successfully validated (95.83% conversion rate).

Main Results:

  • A total of 60,414 putative SNPs were identified in the tench transcriptome.
  • The validated SNP array successfully genotyped 140 individuals from two tench breeds (Tabor and Hungarian).
  • Low but significant genetic differentiation (FST = 0.0450, P < 0.0001) was observed between the two breeds.

Conclusions:

  • The validated SNP set provides a valuable tool for distinguishing tench breeds.
  • These genomic resources will advance population genetics, fish stock management, and aquaculture applications for tench.
  • The high SNP validation rate demonstrates the effectiveness of the developed computational pipeline for non-model species.