Exclusion and genomic relatedness methods for assignment of parentage using genotyping-by-sequencing data

Genotypes are often used to assign parentage in agricultural and ecological settings. Sequencing can be used to obtain genotypes but does not provide unambiguous genotype calls, especially when sequencing depth is low in order to reduce costs. Therefore, standard parentage analysis methods no longer apply. A strategy for using low-depth sequencing data for parentage assignment is developed here. It entails the use of relatedness estimates along with a metric termed excess mismatch rate. The excess mismatch rate, for parent-offspring pairs or trios, is the difference between the observed mismatch rate and the rate expected under a model of inheritance and allele reads without error. When more than one putative parent has similar statistics, bootstrapping can provide a measure of the relatedness similarity. Finally, putative parent-offspring trios can be checked for consistency by comparing the offspring’s estimated inbreeding to half the parent relatedness. Suitable thresholds are required for each metric. These methods were applied to a deer breeding operation consisting of two herds of different breeds. Relatedness estimates were more in line with expectation when the herds were analysed separately than when combined, although this did not alter which parents were the best matches with each offspring. Parentage results were largely consistent with those based on a microsatellite parentage panel with three discordant parent assignments out of 1561. Some evidence was found for non-random selection of alleles and two models are given to account for this possibility. The tools and strategies given here allow parentage to be assigned from low-depth sequencing data.