Fig. 4: Diagrammatic illustration of the exclusively uniparental-inherited genomic segment on Chr. 6 and three transposed functional genes in Nipponbare, and structural differences in the OsSOG1 gene between the parental alleles.
a, Heat maps depicting the exclusive uniparental (9311) inheritance of a single genomic segment in all TRILs of both crossing directions, its homoeologue ratios in 73 S1 tetraploid individuals and 202 earlier generation (S4) tetraploid individuals. The core segment shared by all 202 TRILs is delimited by two dashed vertical orange lines. b, Heat maps displaying the same chromosomal segment (as in a) in 6 randomly selected TRILs by mapping the resequencing reads against the parental Nipponbare and 9311 reference genomes, respectively, to test for potential influence of different reference genomes, which showed no difference. In a and b, each row represents 1 tetraploid individual. Different colours refer to different homoeologue ratios of Nipponbare and 9311. Information on chromosome and genomic location is given in the graph. c, Gene position and annotation of the 3 functional genes that had transposed from this segment to other genomic loci in the Nipponbare genome. d, Structures of gene OsSOG1 in Nipponbare (top) and 9311 (bottom). Each exon is labelled, along with its corresponding starting position. Vertical lines denote 3 SNPs present in exons, and the corresponding amino acid variants are shown. The annotations of Nipponbare and 9311 OsSOG1 alleles are based on the Nipponbare (NPB) IRGSP-1.0 and 9311 reference genomes, respectively. The gene structure image was created with IBS 2.0.
