*3.1. Sequencing and Genotyping Based on SLAF-seq*

In this study, genotyping of 150 F2 individuals and their parents was performed using the SLAF-seq technology. The sequencing data generated in this work were sent to the NCBI SRA database (http://www.ncbi.nlm.nih.gov/sra/ accessed on: 20 October 2020) as accession no. PRJNA669602. Approximately 76.22 GB of raw bases and 381.15 Mb of paired-end reads were generated, of which 94.37% achieved or exceeded quality score of 30

(Q30), and GC (guanine-cytosine) content was 38.86% (Table 1). *Oryza sativa* L. was used as control for evaluating the effectiveness of library construction. In addition, 12,250,440 reads representing 139,046 SLAFs with average depths of 63.83 were obtained from the male parent (PI201234), and 13,232,257 reads representing 141,584 SLAFs with average depths of 72.32 were obtained from the female parent (1287) (Table 1). In the offspring (F2 population), 2,371,153 reads that were representing 124,582 SLAFs with average depths of 14.66 were generated (Table 1).

**Table 1.** Specific-locus amplified fragment sequencing (SLAF)-seq data statistics of the *Capsicum* F2 population.


After filtration of low-depth SLAF tags, approximately 174,193 high-quality SLAF markers were obtained, of which 19.77% (34,432) were polymorphic SLAFs (Table 2). In addition, 25,839 of the 34,432 polymorphic SLAFs were cultured into eight segregation patterns (aa×bb, ab×cc, ab×cd, cc×ab, ef×eg, hk×hk, lm×ll, and nn×np) (Figure 1). As the parents were homozygous (i.e., with genotype aa or bb), 21,069 SLAFs exhibited the aa×bb segregation pattern and were successfully selected for map construction.

**Table 2.** Description on basic characteristics of the 12 linkage groups.

