Application of whole-eDNA sequencing for monitoring broodstock genetic diversity in breeding groups of gilthead seabream (Sparus aurata)

Environmental DNA (eDNA) analysis represents a non-invasive approach for assessing biodiversity and its use is expanding in several fields. However, its potential to recover population genomic information remains largely unexplored. In this study we evaluated the feasibility of whole eDNA sequencing to infer broodstock genetic diversity in a breeding aquaculture population, using the gilthead seabream (Sparus aurata) as a model species. Water samples were collected from four broodstock tanks and filtered through three pore sizes (0.2, 1.2, and 5 μm), along with tissue samples from the fish in each tank. DNA extracted from the filters (eDNA) and pooled from the fish in each of the four tanks was sequenced using next-generation sequencing and reads were mapped to the gilthead seabream reference genome. Q20 mapped reads were used for variant calling and single nucleotide polymorphisms were utilised to calculate heterozygosity-based indices (FIS-like) and Fixation index (FST) within and across DNA pools derived from the four tanks and corresponding eDNA samples. Mapping rates confirmed the expected predominance of non-target DNA in eDNA samples across filters, with the 5 μm filters showing the highest rate of mapped reads (from 34% to 51% in three out of 4 tanks), resulting in a genome coverage that ranges from 7.05 to 12.89× of Q20 mapped reads. Moreover, FIS-like and FST values were similar between DNA pools and eDNA datasets, with low differentiation observed across tanks and filters (ΔFIS≤0.01 for the depth-balanced dataset). These results indicate that whole eDNA sequencing can recover genome-wide estimates of genetic diversity comparable to those obtained from fish tissue samples, representing a first proof-of-concept for its application in breeding aquaculture populations.