Tracing the genetic impact of farmed turbot Scophthalmus maximus on wild populations

Abstract

The impact of escapees from aquaculture is of general concern for the sustainability of natural resources. Turbot Scophthalmus maximus is a marine flatfish of great commercial value whose land-based aquaculture started approx. 40 yr ago; hence, a low impact of escapees is expected on wild populations. However, enhancement of wild stocks using farmed turbot has been carried out along the Northeast Atlantic coasts in the last decades. Recently, a broad panel of single nucleotide polymorphism (SNP) markers (755 SNPs; 1 SNP Mb −1 ) has been used to evaluate the genetic structure of turbot throughout its distribution range, constituting the baseline to evaluate the impact of farmed fish in the wild. Two distinct origins were identified for farmed turbot (F _ORI1 and F _ORI2 ; F ST = 0.049), which differentiated from wild populations after 5 generations of selection (average F ST = 0.059), and consistent evidence of adaptation to domestication was detected. A notable proportion of fish of farmed ancestry was detected in the wild (15.5%), mainly in the North Sea, where restocking activities have taken place, determining genetic introgression in wild populations. Conversely, effects of land-based aquaculture appear negligible. A simulation exercise supported panels of 40 and 80 SNPs to identify fishes of F _ORI1 and F _ORI2 ancestry in the wild, respectively. Application to empirical data showed an assignment success (wild/farmed ancestry) of approx. 95% in comparison with the full SNP dataset. The SNP tools will be useful to monitor turbot of farmed ancestry in the wild, which might represent a risk, considering the lower fitness of farmed individuals.

Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Scophthalmus maximus)

“…When the study was performed, the four active European hatcheries were founded with individuals from the Atlantic, where populations are genetically rather homogeneous (F ST = 0.0024; do Prado et al, 2018b). The broodstock of CETGA (Aquaculture Cluster of Galicia, Ribeira, Spain), constituted by a mix of these four hatcheries, provided a good representation of domestic turbot (do Prado et al, 2018a), and it was used to analyze both the ROHi (Runs of Homozygosity islands) and the distribution of genetic diversity in our study. Despite different breeding strategies, the same traits have been targeted in the turbot breeding programs, i.e., growth-related traits and resistance to major infectious diseases affecting turbot production (Sánchez-Molano et al, 2011;Rodríguez-Ramilo et al, 2014), suggesting that processes of convergent selection may have shaped the genome of the different turbot broodstock.…”

“…Linkage maps (Bouza et al, 2007(Bouza et al, , 2012Martínez et al, 2008;Hermida et al, 2013) have been used in this species to localize QTL related to the main traits for selective breeding programs, namely sex determination (Martínez et al, 2009), growth (Sánchez-Molano et al, 2011;Rodríguez-Ramilo et al, 2014) and resistance to various pathogens (Rodríguez-Ramilo et al, 2011, as a step toward marker assisted selection (Sciara et al, 2018). Furthermore, studies have also provided outlier markers and candidate genomic regions related to adaptive variation in wild (do Prado et al, 2018b) and domestic turbot (do Prado et al, 2018a). Recent advances in genotyping by sequencing and whole-genome resequencing have provided a large number of SNP loci covering the 567-Mb turbot genome (Maroso et al, 2018).…”

GENETIC IMPLICATIONS OF RESTOCKING PROGRAMS ON WILD POPULATIONS OF STREAKED PROCHILOD <i>Prochilodus lineatus<i>

“…Genetic differentiation between and within wild and farmed fish is a clear signal that restocking using farmed fish may, indeed, compromise the genetic diversity of wild stocks, resulting in genetic introgression, which occurs when exogenous genetic material is different from that of the wild population (Ryman et al, 1995;Prado et al, 2018). Furthermore, the genetic constitution of the wild population can be permanently altered by the loss of important genetic material.…”

“…Thus, limited genetic diversity and effective population size of broodstock may pose a risk to wild populations restocked under these conditions (Small et al, 2009;Fonseca et al, 2017;Prado et al, 2018). In addition, restocking programs that avoid introduction of genotypes unrepresentative of the augmented population, low genetic diversity and inbreeding can have negative effects (Ward, 2006;Roques et al, 2018).…”

Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

“…2) This approach has been explored extensively in salmonoid aquaculture [71,72], as well as in other species (e.g. turbot [73]).…”