*3.5. Variant Analysis and Filtering for Selection of Transcripts*

A variant analysis was conducted to confirm the genetic variations between the gray mold disease-resistant and -susceptible lines. The total raw variants was 359,288, which was generated using haplotypeCaller of the Genome Analysis Tool Kit (GATK, Broad Institute, Cambridge, MA, USA). These variants were confirmed to have occurred in 28,602 transcripts out of a total of 87,427 acquired transcripts. To remove the low-quality genotypes, the minimum depth coverage was set to five, and the maximum depth coverage was set to 100. The minimum genotype quality was filtered to 20%. As a result, the total filtered-out variants were 28,602, including 27,303 SNPs and 1299 indels. Among them, the variants that matched the following conditions were selected: four resistant lines showed the same genotype within a group, and three susceptible lines also showed the same genotype within a group but showed differences between the resistant and susceptible groups. A total of 233 variants were obtained that matched these conditions, and 118 corresponding transcripts were selected.
