Species identification in Haliotis genus from the northeastern Pacific Ocean using genome-wide RAD-SNPs

Abalone is a marine gastropod mollusk that belongs to the genus Haliotis high-priced and with commercial importance worldwide. Because of its high demand, its products are susceptible to retail fraud by substituting lower-value products or protected species instead of higher-value ones. Therefore, species identification is a crucial traceability element, and restriction-site-associated DNA sequencing (RAD-seq) is a genomic tool that permits achieving this goal in non-model species with few developments in genetic data. This study analyzed five ecological and socio-economically important abalone species that inhabit the west coast and islands of the Baja California Peninsula (BCP), Mexico: green H. fulgens, pink H. corrugata, red H. rufescens, black H. cracherodii and threaded/pinto H. kamtschatkana abalones. The number of putative bi-allelic single nucleotide polymorphisms (SNPs) found across the five species was 150 326 loci. After filtering data, 1 127 SNPs (Total panel) were retained from 223 sequenced abalones. Subsequently, two criteria were used to identify the most informative SNPs markers: private alleles (species-specific) and FST outliers (adaptive markers). The reduced 66 Private SNPs allele panel performs similarly to the Total panel with a 100% correct assignment among the five species, whereas the 24 SNPs FST outlier panel could only correctly assign four out of five species, confusing the threaded/pinto and red abalones. Furthermore, both reduced panels successfully identify black abalone individuals, which has a commercial and conservation importance for seafood trade in Mexico. Therefore, all these markers can be used in seafood traceability and specimen identification in enforcing fishery management measures among these five abalone species.