High-Throughput Sequencing of Backcross Pools

Sequencing libraries were generated from each backcross pool, using the Illumina Nextera kit. These libraries were sequenced on an Illumina NextSeq machine by the USC Epigenome Center, using 75 × 75 base reads. Rough pools were sequenced to an average of 246-fold and control pools were sequenced to an average of 162-fold coverage. Reads were aligned to either a BY or 3S reference genome, using the Burrows–Wheeler Aligner version 7 with option mem −t 20 (ref. 39 (link)) and mpileup files were generated with SAMtools40 (link). Sequencing data can be accessed from the Sequence Read Archive using Biosample accession numbers SAMN04126845 through SAMN04126912 or the Bioproject accession number PRJNA301897. The specific accession number for each pool is listed in Supplementary Table 6.