How Long Can Dead Fish Tell Tales? Effects of Time, Tissue, Preservation, and Handling on Genotyping Success

Abstract

Genetic analyses have become increasingly powerful, more readily available to biologists, and have made ever more degraded DNA potentially useful. Single nucleotide polymorphisms (SNP) are a relatively new “class” of markers that show promise for use with degraded or archived samples. We sequenced a panel of 298 SNPs from Chinook salmon (Oncorhynchus tshawytscha) tissue in three comparative studies to determine the effect of DNA quality at sampling, time in archive, and tissue type and preservation method on SNP genotyping success using logistic regression. The first study evaluated pristine DNA from live adults sampled at three hatcheries and archived up to 6 years. The second study compared samples from carcasses with varying levels degradation (i.e., condition) and archived up to 15 years. The third study compared heart and fin samples preserved either in ethanol or on paper from carcasses with varying levels of degradation and processed within 6 months. Genotyping success for fresh tissue did not decline over the 6-year archive period at two of the three hatcheries, suggesting sample handling techniques may be more influential than time in archive. Genotyping success of archived carcass samples depended more on carcass condition than time in archive. Heart tissue genotyped consistently more often than fin samples from all but poor condition carcasses. Based on these results, we make tissue-sampling recommendations for different intended purposes. We also provide simple, post-collection sample handling procedures that can increase genotyping success regardless of tissue or preservation method.