Ptr haplotype analysis in IRRI 3 K sequenced rice germplasm

To investigate the distribution of the resistant Ptr allele observed in Katy, we characterized haplotypes in the IRRI 3 K SNP Seek database^19,20. The SNP data were extracted for the Ptr gene (LOC_Os12g18729) from the 4.8 M SNP database and haplotypes were characterized using 173 polymorphic sites within the exon regions of the gene. Data were obtained for 3,024 lines and lines that had missing data at SNP 10,833,409 were excluded, this SNP was correlated to the SNP InDel in sequence data presented in Supplementary Table ¹. Lines with over 15% total missing data, with heterozygous alleles considered as missing, were excluded. Upon filtering, 2215 lines remained for haplotype characterization. Haplotypes were defined by having no SNP polymorphisms among lines in the same haplotype group. A total of 35 lines contained rare haplotypes (<10 lines within haplotype group) and these haplotype groups were not considered, and 13 lines were not able to be assigned to a haplotype group due to missing data. A total of 2167 lines were assigned to a haplotype group. The association of Ptr haplotypes to Pi-ta was conducted by comparing the functional Pi-ta SNP at 10,607,554 with the assigned Ptr haplotype group. Based on the sequence data, there appeared to be a single SNP difference between the haplotype groups that contained ‘Katy’ and ‘Drew’. These groups were not treated as separate haplotypes as it is known from pedigree that ‘Drew’ and ‘Katy’ contain the same allele through decent, as ‘Katy’ is the parent of ‘Drew’. SNPs of each Ptr haplotype of IRRI 3 K rice varieties in the coding regions were used to build the sliding window with DNasp v5 and a phylogenetic tree that was constructed with the software MEGA 7.0. See additional resource for varieties in each haplotype and predicted disease reaction and details of SNPs.