DOI: 10.17882/106440
title: SNP dataset for Haliotis tuberculata tuberculata: 158 markers for population genetics of wild and hatchery-raised European abalone

description: This dataset includes 158 loci of 896 abalones genotyped by LGC Genomics using Kompetitive Allele Specific PCR (KASP) assays. Populations of Haliotis tuberculata tuberculata declined sharply over the last two decades, mainly due to pathogenic bacteria, Vibrio Harveyi. In this context, restocking or stock-enhancement operations based on hatchery juveniles might be relevant to restore populations and ensure sustainable fisheries. Maintaining the genetic diversity of wild populations and hatchery individuals is a primary concern in supplementation programs. Therefore, the present study aimed at assessing the distribution of genetic variability among wild and hatchery samples of H. t. tuberculata, to evaluate the effect of hatchery breeding on the diversity of hatchery-raised cohorts, and to explore the spatial distribution of the genetic variability among wild populations.
Hatchery samples (467 individuals) were collected in two successive generations produced in, France Haliotis (Plouguerneau, Brittany), the only commercial farm producing H. t. tuberculata. From 2014, a directional selection program was applied where the largest 5 % (95th percentile) 3-year-old males and 4-year-old females were selected and used as broodstock each year (Generation 4 to Generation 5). The broodstock samples corresponded to 3-year-old males and 4-year-old females hatched in 2014 to 2016 respectively, and belonged to the hatchery generation G4 (G4-18F1, G4-18F2, G4-18F3, G4-18M1, G4-18M2, G4-18M3, G4-19-1, G4-19-2, G4-19-3). Sex was not individually determined for the broodstock used in 2019. The offspring corresponded to the hatchery generation G5 (G5-17-1, G5-17-2, G5-18-1, G5-18-2, G5-18-3).
Wild individuals (429 individuals) were sampled by scuba-diving over ten sites located across most of the distribution range of the subspecies H. t. tuberculata. Sampling was conducted from March to June 2019 along the coasts of Brittany and Normandy (NW France). For each site, specimens were collected within a 50 metres radius of an anchored vessel during a single dive (N = 10-30; Locmariaquer (LOC), Molène (MOL), Bay of Brest (BOB), Aber-Wrac’h (ABW), Guissény (GUI), Saint-Quay-Portrieux (SQP), Saint-Malo (SMA), Chausey (CHA), Blainville-Sur-Mer (BLA), Cherbourg (CHE). Multiple size classes were sampled (i.e. from 20 to 115 mm) to avoid sampling a single cohort each time. For the Molène, Bay of Brest and Aber-Wrac’h sites, sampling was replicated three to four times in order to evaluate the robustness of the genetic signal. At each of these three sites, replicated sampling points were separated by one to five kilometres (BOB-1, BOB-2, BOB-3, MOL-1, MOL-2, MOL-3, MOL-4, ABW-1, ABW-2, ABW-3).
For each individual, a mantle epipodium was sampled from the periphery of the foot, for DNA extraction. Wild individuals were systematically released to their original site after tissue collection. Samples were transferred to 1.5 mL microtubes filled with 70 % ethanol and stored at 4°C. DNA extractions were performed by LGC Genomics (Ostendstraße 25, 12459 Berlin, Germany) according to their standard protocol (tissue lysis with Proteinase K, subsequent binding, washing and elution steps achieved using proprietary buffers). High throughput SNP genotyping was conducted by LGC Genomics using Kompetitive Allele Specific PCR (KASP) assays, allowing bi-allelic SNP scoring. Out of 192 SNP markers (Harney et al., 2018, https://doi.org/10.1016/j.aquaculture.2018.03.006), 158 SNPs were unambiguously genotyped and used for subsequent data analysis.
 
01-Haliotis_SNPs_Dataset.csv: Dataset used for the 896 abalone of this study. The table contains SNPs for 158 loci genotyped by LGC genomics.
02-Haliotis_SNPs_Amorces: List of SNPs used in this study. Referenced in this table are the SNP ID, contig name, position of the SNP, the original SNP used as reference and its alternate, known sense of the sequence and the SNP sequence.