Species identification of two closely exploited flatfish, turbot (Scophthalmus maximus) and brill (Scophthalmus rhombus), using a ddRADseq genomic approach

Abstract

Abstract Application of genomics tools for conservation purposes (i.e. conservation genomics) allows looking deep into the genetic structure and adaptations of populations and species in order to define management units, trace exploited stocks, and identification of species. In this work, a double‐digestion restriction‐site‐associated DNA sequencing (ddRADseq) approach was performed to identify individuals belonging to two important commercial flatfish, the turbot (Scophthalmus maximus) and the brill (Scophthalmus rhombus), and their potential hybrids. A total of 83 diagnostic single nucleotide polymorphisms (SNPs) between brill and turbot were detected in the genomic RAD‐tag database created with 122 turbot and 20 brill individuals. Markers consisted of an SNP with alternative alleles fixed in each species. From these diagnostic markers, a molecular tool comprising 10 SNPs located far apart in the turbot genome (>100 kb) was successfully designed and validated using the SNaPshot® method from a new sample set of 154 brill and turbot samples distributed throughout the natural range of both species. Additionally, 10 individuals (two turbot and eight brill) previously genotyped with ddRADseq were genotyped with SNaPshot to check for genotyping accuracy. ddRADseq and SNaPshot genotyping of these 10 markers were identical in the 10 individuals used as controls. Species assignment based on the SNP tool corresponded with phenotypic identification for all samples. Using the SNP tool in a set of 29 unknown samples, all individuals were identified as S. maximus except one identified as a hybrid (heterozygous for all diagnostic SNPs). The methodology (i.e. ddRADseq) has enabled the development of a helpful traceability tool for sustainable management and conservation of turbot and brill resources. Similar approaches could also be applied to other non‐model organisms despite lacking an assembled genome.