A comparison of microsatellites and SNPs in parental assignment in the GIFT strain of Nile tilapia (Oreochromis niloticus): The power of exclusion

In this study, parental assignment was studied in the 10th generation of a pedigreed selected Nile tilapia (Oreochromis niloticus) population (GIFT) and their offspring, by comparing two types of molecular markers, microsatellites and SNPs, using an exclusion-based (Vitassign) and a likelihood-based (Cervus) method. For the experiment, G10 parents were divided in 4 groups (cohorts) and allowed to produce offspring by natural group mating. In total 173 offspring were tested against 238 parents, using either 12 microsatellites (PIC = 0.639; exclusion power 68.0%) or 122 SNPs (PIC = 0.341; exclusion power 99.9%). In this study, more than half of the candidate parents were either full-or half-sibs with other parents. Furthermore, 13.8% of the parents died before being sampled for DNA. When offspring were assigned to parents in the same cohort, using Vitassign, for microsatellites, allowing up to 2 mismatches, 37.6% offspring got unique assignments, 45.1% got multiple assignments, and 17.3% were not assigned; for SNPs with up to 15 mismatches allowed, 83.8% offspring got unique assignments while 13.9% got multiple assignments. Only 2.3% were not assigned. Using Cervus, for microsatellites, the mean 'strict' (>95% CF) assignment rate across the 4 cohorts was 18%, the 'relax' (80-95% CF) assignment rate was 43%, and 39% were not assigned; for SNPs, 39% 'strict' assignments were obtained (mean across 4 cohorts); the remaining offspring were not assigned. In general assignment rates were higher when cohort offspring were assigned to all parents combined, irrespective of method (Vitassign or Cervus) or marker used. However, consistency of assignments between microsatellites and SNPs was low: 28% with Vitassign and 16% with Cervus. Consistency of assignments between Cervus and Vitassign was high with SNPs (65%), but was low with microsatellites (31%). We conclude that missing parents and relatedness among candidate parents resulted in low assignment rates. Furthermore, low exclusion power of the microsatellite set resulted in low assignment rates and multiple parent pair assignments irrespective of method used. Exclusion methods and likelihood-based methods can be equally good for parental assignments, providing that good marker sets with high exclusion power are available. (C) 2013 Elsevier B.V. All rights reserved.