*3.1. GBS Library Sequencing and SNP Calling*

The Hiseq 2500 platform was used to conduct the paired-end (100 bp each) sequencing of the GBS library for the parents and 62 progenies. A total of 422,282,974 reads and 42,650,580,374 bases (42.65 Gb) were generated. A total of 97,772 SNPs and InDels were detected using the GATK's VariantsToTable command. Among these, only 80,283 SNPs were called, and then 22,158 SNPs that have all of the parental genotypes were selected again. SNPs were evenly distributed throughout the genome.
