Fig. 3

Representation of plate- and droplet-based methods for isolating and sequencing gametes and in silico map construction pipeline. a Schematic representation of plate- and bead-based approaches for profiling gametes. Gametes collected from a donor can be processed through plate-based methods; the single gamete is projected to individual compartments, and DNA amplification is carried out within each chamber for each gamete that can further be used for genotyping using SNP array or DNA sequencing. Bead-based methods either encapsulate single gametes or HMW DNA in a droplet with beads that contain a barcode. Pooled barcode-tagged reads are sequenced in parallel and provide gamete sources or HMW DNA sources. b General pipeline for crossover detection for individuals using gamete-based data. Reads from multiple gametes are aggregated for hetSNP identification. hetSNPs are phased based on SNP co-appearance in gametes. Genotypes of gametes and phased hetSNPs are used for constructing haplotypes of gametes that can be further used for crossover detection. c Illustration of marker ordering for an individual which shows different ordering and distancing from the reference genetic map