As cost-effective high-throughput genotyping tools become more widely available, the application of genomic selection in oyster breeding is becoming more common. A critical step in this process is the non-lethal DNA biopsy of candidate broodstock for genotyping and generation of genomic estimated breeding values (GEBV). However, non-lethal biopsy can be challenging because oysters must be ‘relaxed’ with MgSO4 to access tissues, and extraction of mantle or hemolymph can be time consuming and damaging.
Here we present results examining multiple non-lethal biopsy methods – mantle clipping, swabbing of viscera, and filtered culture water of individual oysters (eDNA) – for their effect on DNA concentration/quality and genotype call rate using the Eastern oyster 66K HD SNP array. Genotype correspondence was also assessed between non-lethal biopsy DNA and DNA extracted from the adductor muscle of the same individual. DNA yields were substantially higher from the brush swabs, followed by mantle clips, and eDNA extractions. Genotype call rates were >94% for all mantle and brush samples and not significantly different – call rates were lower for the eDNA extractions but still generally above 90%. DNA from swab samples (cytology brush, mascara brush, and cotton tipped swab) had similar and very high genotype correspondence with adductor-derived DNA (less than 1% genotype error) with cytology swabs providing the lowest error rate. Overall, non-lethal cytology brush biopsy DNA provides high quality SNP array genotype data, similar to mantle or adductor-derived DNA, and are easier and faster to implement when sampling.