Private haplotype barcoding facilitates inexpensive high-resolution genotyping of multiparent crosses

Inexpensive, high-throughput sequencing has led to the generation of large numbers of sequenced genomes representing diverse lineages in both model and non-model organisms. Such resources are well suited for the creation of new multiparent populations to identify quantitative trait loci that contribute to variation in phenotypes of interest. However, despite significant drops in per-base sequencing costs, the costs of sample handling and library preparation remain high, particularly when many samples are sequenced. We describe a novel method for pooled genotyping of offspring from multiple genetic crosses, such as those that that make up multiparent populations. Our approach, which we call “private haplotype barcoding” (PHB), utilizes private haplotypes to deconvolve patterns of inheritance in individual offspring from mixed pools composed of multiple offspring. We demonstrate the efficacy of this approach by applying the PHB method to whole genome sequencing of 96 segregants from 12 yeast crosses, achieving over a 90% reduction in sample preparation costs relative to non-pooled sequencing. In addition, we implement a hidden Markov model to calculate genotype probabilities for a generic PHB run and a specialized hidden Markov model for the yeast crosses that improves genotyping accuracy by making use of tetrad information. Private haplotype barcoding holds particular promise for facilitating inexpensive genotyping of large pools of offspring in diverse non-model systems.