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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Differentiating diploid and triploid individuals using single nucleotide polymorphisms genotyped by amplicon

Thomas A Delomas1

  • 1Pacific States Marine Fisheries Commission, Eagle Fish Genetics Laboratory, Eagle, ID, USA.

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This study introduces a new, cost-effective method for determining fish ploidy using amplicon sequencing data. This technique accurately identifies triploid and diploid individuals, crucial for fisheries management and aquaculture.

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Area of Science:

  • Aquaculture
  • Genetics
  • Fisheries Science

Background:

  • Triploidy induction in fish and shellfish produces sterile individuals for fisheries management and aquaculture.
  • Sterile triploids prevent unwanted reproduction in stocked fish and reduce interbreeding of escaped aquaculture fish with wild populations.
  • Accurate ploidy determination is essential for monitoring triploidy treatments and identifying fish ploidy in mixed populations.

Purpose of the Study:

  • To develop and validate a cost-effective alternative to flow cytometry for determining fish ploidy.
  • To analyze amplicon sequencing data for biallelic single-nucleotide polymorphisms (SNPs) to distinguish between diploid and triploid fish.

Main Methods:

  • Developed a method analyzing amplicon sequencing data for SNPs to determine ploidy.
  • Identified heterozygous genotypes and calculated diploidy/triploidy likelihoods based on allele read counts.
  • Validated the method using triploid and diploid brook trout (234 SNPs) and Chinook salmon (298 SNPs) via GT-seq amplicon sequencing.

Main Results:

  • The amplicon-sequencing SNP analysis accurately determined the ploidy of brook trout and Chinook salmon.
  • The method provides a reliable alternative for ploidy assessment in fish populations.

Conclusions:

  • This SNP-based amplicon sequencing method offers a cost-effective and accurate approach for determining fish ploidy.
  • The technique supports effective fisheries management, aquaculture practices, and conservation efforts by enabling precise ploidy identification.