A comparative assessment of GBS-SNPs aligned to scaffold and pseudo-chromosome level of the pear reference genome

We compared genetic information of GBS-SNPs produced by aligning sequencing reads to scaffold and pseudo-chromosome level of the reference genome to identify more suitable SNPs information according to levels of the reference genome. Two SNP matrixes were obtained by aligning raw sequencing reads to scaffold and pseudo-chromosome levels of the reference genome, respectively. Four criteria were used for SNP filtering: (1) bi-allele; (2) missing value <10%; (3) minor allele frequency (MAF) >5%; and (4) polymorphism information content (PIC) value ≥0.3. As a result, the number of filtered SNPs was 4,987 and 6,505 in the scaffold and pseudo-chromosome level, respectively. The values of expected heterozygosity and PIC in scaffold and pseudo-chromosome level were similar. The averages of MAF and observed heterozygosity (Ho) values, which were 0.361 and 0.360, in the pseudo-chromosome level were larger than those which were 0.350 and 0.328, in scaffold level. Development of genetic markers based on a pseudo-chromosome level will be appropriate for genetic analysis since the number of SNPs and values of MAF and Ho were higher than the scaffold level.