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United States Department of Agriculture

Agricultural Research Service

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Research Project: Development of the SNP Platform and Its Application for Genetic Mapping in Catfish

Location: Warmwater Aquaculture Research Unit

2011 Annual Report


1a.Objectives (from AD-416)
Produce 6000 single nucleotide polymorphism (SNP) markers for channel catfish.


1b.Approach (from AD-416)
Genomic DNA from multiple individuals will be pooled and sequenced using next-generation sequencing technology. SNP loci will be identified using computational methods.


3.Progress Report

The objective of this Reimbursible Agreement was to produce 6,000 single nucleotide polymorphism (SNP) markers for channel catfish as part of a larger project to produce a SNP mapping array for large scale genotype analysis. Genomic DNA from multiple individual catfish was pooled and digested with restriction enzymes, and the fragments were resolved by agarose gel electrophoresis. Restriction fragments of varying sizes (300-400bp, 400-500bp, 500-600bp) were isolated and sequenced using high throughput next-generation DNA sequencing. The sequences were aligned to genomic contigs and high-likelihood DNA polymorphisms were identified using bioinformatic methods. The research revealed 9,764 high-likelihood SNPs in 6,640 (17.6%) of the genomic contigs that were interrogated in this sample population. Further testing showed 93% of the predicted variable loci were variable in the individuals, and the predicted and realized allele frequencies were strongly correlated. ADODR used site visit, email and telephone conferences to monitor activities of the project.


Last Modified: 11/1/2014
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