Fig. 6

Identification of female-specific putative W-linked genomic region. a Schematic diagram of the method used to identify the female-specific putative W-linked genomic region. De novo assembled genome sequences of female (P3-DDN) and male (P4-DDN) parents were combined to serve as a reference sequence. Short reads of bulked DNA from F1 female and F1 male progeny were separately mapped onto this combined reference sequence. The majority of reads mapped to two duplicated homologous locations in the reference genome (indicated as “common regions”), which gave low MAPQ scores (<60) in the BWA alignment. Female parental contigs that were mapped only with reads belonging to the F1 female bulk corresponded to female-specific genomic regions. Sequence reads mapped to such positions were identified by their high MAPQ scores (=60). b An example of a female-specific contig (contig Female917_flattened_line_87512_3057). Alignment depths of F1 female bulk (red) and F1 male bulk (blue) are shown (top). Frequency of reads mapped with MAPQ score = 60. The red line corresponds to genomic regions that were covered by short reads, > 90% of which had a MAPQ score of 60 (middle). A genomic region that is covered only by female reads (not by male reads) and > 90% of mapped reads had MAPQ score = 60 (indicated by gray bars) (bottom). Red arrowheads indicate the positions of PCR primers for the DNA marker sp16. c Location of the female-specific genomic region. Thick gray horizontal line denotes pseudo-chromosome 11 (top), scaffolds on chromosome 11 (middle), and scaffold206 (bottom). The thin blue lines shown under the first, second, and third horizontal lines indicate the positions of female contigs (P3-DDN) specifically mapped by F1 female bulk reads. The square box at the bottom indicates alignment depth of reads of F1 female bulk (red) and F1 bulk of progeny in which sp16 amplification was not observed (sp16-minus) (blue) to scaffold206. Red triangles indicate the position of DNA marker sp16