In this study, we describe the isolation and characterization of novel microsatellite markers for Haliotisrufescens derived from transcriptomepyrosequencing and heterologous loci obtained from expressed sequence tags previously reported for H. discus hannai. We were able to characterize 29 of 59 loci using 94 individuals from populations localized in Mexico and Chile. For the Mexican population, the number of alleles per locus ranged from 2 to 11, while the observed and expected heterozygosities varied from 0 to 0.977 and 0.1 to 0.854 respectively. For the Chilean populations, the number of alleles per locus ranged from two to eight while the observed and expected heterozygosities varied from 0 to 0.8 and 0.1 to 0.847 respectively. The average inbreeding coefficient F is was 0.282 for the Mexican and 0.245 for the Chilean populations, while the polymorphic information content ranged from 0.590 to 0.927. Pairwise fixation index F st and analysis of molecular variance indicated a significantly high genetic difference between the two studied populations (F st = 0.535). In addition, cross-amplifications of 59 loci were also evaluated in H. fulgens, H. corrugate and H. discus hannai. These markers will constitute valuable tools for management strategies in aquaculture production and also for population genetic studies.

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Parentage analysis in aquaculture determines genealogical relationships between broodstock and progeny when the parents are unknown. Thus, parentage analysis is a useful tool to establish pedigree reports in molecular-assisted selection programs. Here, we evaluated 10 heterologous microsatellite markers for parentage assignment in abalone hybrids produced from 43 abalone broodstocks of red abalone (Haliotis rufescens) and Japanese abalone (H. discus hannai). The allele frequencies, exclusion probabilities and broodstock contributions were calculated using CERVUS, PAPA and GERUD software. The polymorphic information content (PIC) values showed that most of the microsatellite loci were highly informative (>0.7) and more than 90% of parentage assignment was possible with a minimum of 5-6 microsatellite markers. Parentage assignment for hybrid and pure-red progeny showed a better performance than pure-Japanese progeny. This result could be due to the high level of allele loss in the parental genotypes. In addition, results indicated that only two sires contributed over 80% and 90% of red and hybrid progenies, respectively. This study gives a new molecular tool to support marker-assisted selection in abalone hybrids produced in Chile.