Fig. 6
From: Traces of Introgression from cAus into Tropical Japonica Observed in African Upland Rice Varieties
Genomic differentiation and population structure: a Fixation index (Fst) on chromosome 6 between Asian versus West African tropical upland Japonica rice populations. The position of the large introgression of cAus on this chromosome is represented by the segment in red. b Manhattan plot of the iHS statistic computed on the West African tropical upland Japonica rice population. The orange line corresponds to the significant threshold. The right legend shows the density of SNPs for each 1 MB window. c Highlight of the cAus genome introgression signal in the West African tropical Japonica genetic background on chromosome 6. The color in yellow identifies the chromosome locations with haplotypes assigned to cAus. d Nucleotide diversity (Pi) on chromosome 6 between tropical accessions with (Int + in blue) or without (Int- in red) the cAus introgression. The gray band identifies the region around the introgression. e Result of Tajima's D statistic on chromosome 6 between tropical accessions with (Int + in green) or without (Int- in brown) the cAus introgression. The gray band identifies the region around the introgression. f Unweighted neighbour tree constructed on the left outer edge of 100 Kb of the large introgression between 17.9 and 21.7 Mb on chromosome 6. West Africa annotated with an asterisk (*) denotes Tropical Japonica with cAus introgression