Fig. 4: Relationships between eight deeply sequenced D. alata breeding lines.

a Matrix of identity-by-descent (IBD) relatedness between all pairs of individuals (Supplementary Data 3). Blue represents the degree of diploid genome identity (IBD2); white, one haplotype (IBD1); and black, no shared haplotypes (IBD0). b Pedigree of relationships. Sequenced individuals are represented in black boxes with white text, while individuals not sequenced are in gray. Relationships known via IITA records (Supplementary Table 1) are drawn with solid lines. Relationships that could be confirmed using direct sequence comparison are highlighted with solid black lines, and those that could not be are colored grey. Inferred cryptic relationships are indicated with broken lines (first- and second-degree relations are represented as thick dashed and thin dotted lines, respectively). Unexpectedly, TDa95-310 is a parent of TDa00/00005 and a likely second-degree relative of TDa02/00012. c Regions of heterozygosity, autozygosity, and possible introgression. Within a background of intraspecific genetic variation (light cyan), large homozygous blocks (runs of homozygosity [ROH], dark cyan) appear common in the resequenced individuals, suggesting autozygosity from historical inbreeding. In addition, large blocks of exceptionally high heterozygosity (yellow) can also be observed, indicating possible introgressions (interspecific variation introduced via hybridization) in one or more of the unsampled pedigree founders. The recombination rate along each chromosome is shown in the track above. d Haplotype sharing between TDa95/00328 and all other resequenced individuals, and TDa95-310 and all others. Regions of the genome where an individual shares two haplotypes (i.e., they are IBD2) with TDa95/00328 (or TDa95-310) are highlighted in blue, one shares haplotype (IBD1) in gray, or shares no haplotypes (IBD0) in black. Source data are provided as a Source Data file.