SNP-haplotypes: An accurate approach for parentage and relatedness inference in gilthead sea bream (Sparus aurata)

The present study has evaluated the accuracy of SNP-haplotypes (genotypic combination of single SNPs located in the same gene) as parentage and relatedness tool in gilthead sea bream (Sparus aurata). Initially, by direct sequencing of 11 genes in a set of 30 unrelated individuals with heterogeneous origin, a total of 398 putative SNPs were identified and, by means of a filtering procedure to remove false positive and SNPs in a very low frequency, 164 SNPs were selected for the final panel. Using the iPLEX Gold MassARRAY technology, a subset of 58 SNPs located in 7 genes were genotyped in 424 individuals organized into two broodstocks (54 breeders and 370 offspring with pedigree previously inferred by microsatellite loci). From the obtained genotype data, a SNP-haplotype reconstruction was carried out for each gene. According to this approach, 58 biallelic single SNPs were turned into 7 multi-allelic markers (1 gene = 1 marker) whose allele (haplotype) number ranged from 3 to 41. This SNP-haplotypes resolved parentage assignment with an accuracy higher than 99%, resulting in a 10.5% and 3.5% more accuracy than the set of 58 SNPs and 9 microsatellite loci, respectively. Likewise, under a scenario in which ancestral information was not available, SNP-haplotypes showed an accuracy similar than microsatellite loci for discriminating unrelated individuals. Using this approach, a proportion close to 94% of unrelated individuals correctly classified for the coefficient of relationship equal to zero (theoretically expected relatedness value between unrelated individuals) was achieved. The 6% of individuals, misclassified as unrelated, were largely half-sibs since the full-sibs did not exceed 0.03%. In conclusion, we report herein that SNP-haplotypes approach represents a highly efficient alternative to microsatellite loci to infer parentage and assess relatedness.