Aquaculture breeding programs are increasingly using genomic technologies, for applications such as parentage assignment, marker assisted selection and genomic selection. Currently, samples are shipped to genetic labs for genomic processing. The turnaround-time to receive genotyping data can be variable and lab work can be expensive. The major drawback of this process in the context of breeding programs is that large numbers of selected animals to be potentially selected as broodstock must be maintained during this time in dedicated facilities until their estimated breeding values (EBVs) can be determined, which can be costly with daily husbandry and hatchery maintenance.
A potential solution to improve the efficiency of the selection process aquaculture breeding programs that incorporate genomics, could be the use of portable next-generation-sequencing (NGS) technologies. These tools can rapidly and affordably derive genotypes for parental verification and calculate accurate EBVs for genomic selection. In addition to sequencing selection candidates tank-side, these tools can also be used for disease monitoring. The ability sequence, identify, and treat infected organisms immediately could save aquaculture enterprises from detrimental losses.
The first step for “tank-side genotyping” is rapid extraction of DNA from fin clips. We have tested a range of rapid extraction protocols, including kits available on the market and one rapid extraction method (Table 1) . The method known as the “dipstick method” (Zou et al., 2018), was created to extract DNA with minimal lab equipment.
The dipstick method with an additional bead clean up shows promise that rapid DNA extractions are possible for tank-side genotyping. This could be the start of addressing current limitations in genomics for aquaculture.