Summary of Japonica introgressions in the Indica outliers.

Indica outliers ranged from 94.6–97.6% Indica ancestry throughout the genome. Six regions were identified where the outliers shared unique introgressions from Japonica that were observed only in Al tolerant Indica outliers and were not present in any other Indica. Five of the six introgressed segments encompass regions identified in GWA analysis or bi-parental QTL analysis. Three introgressed regions encompass SNPs identified within the indica (IND) subpopulation, across all subpopulations (All), or both. Two of the introgressions encompass previously reported QTLs.aLine 142: introgression 2.1 is 21.93–23.80 Mb and TRG-RRG = 1.15.bLine 30: introgression 7.1 is 27.05–29.65 Mb and TRG-RRG = 0.76.cLine 66: introgression 7.1 is 27.05–27.62 Mb and TRG-RRG = 1.00.dLine 142: introgression 7.1 is 27.05–29.65 Mb and TRG-RRG = 1.15.eLine 163: introgression 7.1 is 25.98–29.65 and TRG-RRG = 0.80.fIntrogression 8.1 is a novel locus that does not co-localize with GWA or QTL loci.gLine 163: introgression 8.2 is 7.61–10.14 Mb and TRG-RRG = 0.80.hLine 163: introgression 11.1 is 18.43–20.05 Mb and TRG-RRG = 0.80.