*2.6. SLAF-seq Data Grouping and Genotyping*

In this study, reads with a quality score below Q30 (quality score < 30e) were filtered out. After that, high-quality reads were mapped to the pepper reference genome utilizing

BWA software, with the paired-end mapped reads at the identical position and >95% identity divided into a single SLAF locus. In each SLAF, a polymorphism locus was observed between the parents, of which most were SNPs. All of the polymorphism SLAF loci were then genotyped with consistency at SNP loci of the offspring and parents. SLAFs that consisted of more than eight SNPs were screened out, and then the parental SLAFs with a sequencing depth of <10-fold were discarded. A high-density linkage map was then created using polymorphic SLAFs showing parental homozygosis (aa × bb).
