Presentation Title

Comparing genotyping methods and the characterization of two new microsatellite markers in Syngnathus

Faculty Mentor

Dr. Burnaford, Dr. Hoese, Dr. Walter

Start Date

23-11-2019 10:00 AM

End Date

23-11-2019 10:45 AM

Location

93

Session

poster 3

Type of Presentation

Poster

Subject Area

biological_agricultural_sciences

Abstract

Fin clipping, a standard tissue sampling technique for recovering DNA from fishes, has the potential to be devastating to smaller fishes or those with small fins such as pipefishes (Syngnathus). Skin swabbing has the potential to replace the traditional method of fin clipping as a tissue sampling technique; however, comparisons of multi-locus genotyping using the two methods has not been directly assessed. To address this, we swabbed and fin-clipped pipefishes in Redondo and Cabrillo Beach, Los Angeles County, CA and characterized two novel microsatellite markers (Syg8788 and Syg0910) for use in Syngnathus (n=37 individuals). We extracted DNA, PCR-amplified locus-specific alleles and compared fragment lengths between the two sampling techniques. We used principal coordinate analysis to visualize individual genetic distance, which showed that both methods produced comparable results with overlapping genetic variance. Some minor differences were noticeable among DNA recovery methods. We observed 17 alleles from skin swab method and 16 alleles from fin clips for locus Syg8788, with 70% of the sampled individuals possessed at least two out of four alleles matching between the methods. At locus Syg0910, we observed 17 alleles for skin swabs and 13 alleles for fin clips, with 60% of samples having at least two out of four alleles match between methods. Overall, the resulting genetic data has the potential to increase the number of individuals sampled in a study while potentially minimizing negative impacts of DNA sampling on individuals and their populations.

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Nov 23rd, 10:00 AM Nov 23rd, 10:45 AM

Comparing genotyping methods and the characterization of two new microsatellite markers in Syngnathus

93

Fin clipping, a standard tissue sampling technique for recovering DNA from fishes, has the potential to be devastating to smaller fishes or those with small fins such as pipefishes (Syngnathus). Skin swabbing has the potential to replace the traditional method of fin clipping as a tissue sampling technique; however, comparisons of multi-locus genotyping using the two methods has not been directly assessed. To address this, we swabbed and fin-clipped pipefishes in Redondo and Cabrillo Beach, Los Angeles County, CA and characterized two novel microsatellite markers (Syg8788 and Syg0910) for use in Syngnathus (n=37 individuals). We extracted DNA, PCR-amplified locus-specific alleles and compared fragment lengths between the two sampling techniques. We used principal coordinate analysis to visualize individual genetic distance, which showed that both methods produced comparable results with overlapping genetic variance. Some minor differences were noticeable among DNA recovery methods. We observed 17 alleles from skin swab method and 16 alleles from fin clips for locus Syg8788, with 70% of the sampled individuals possessed at least two out of four alleles matching between the methods. At locus Syg0910, we observed 17 alleles for skin swabs and 13 alleles for fin clips, with 60% of samples having at least two out of four alleles match between methods. Overall, the resulting genetic data has the potential to increase the number of individuals sampled in a study while potentially minimizing negative impacts of DNA sampling on individuals and their populations.