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Fig. 5 | Genome Biology

Fig. 5

From: AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data

Fig. 5

Intermediate data produced by AFLAP when analyzing two F1 populations of B. lactucae. Two populations generated by crossing SF5 (center) to C82P24 (left) or C98622b (right). Black arrows indicate the path of 31-mers derived from each parental isolate. Ultimately, only those derived from SF5 were used for linkage analysis. a JELLYFISH histograms were generated to determine the boundaries of single-copy, heterozygous 31-mers, (dashed lines). 31-mers common to both parents of each cross were discarded (gray arrows). Unique 31-mers to each parental isolate were assembled (vertical arrows). b The modal assembled fragment size was 61 bp (SNPs), except for C98O622b. Fragments < 61 bp were discarded (gray arrows). One representative 31-mer marker was extracted from each fragment ≥ 61 bp, verified against the parents, and used for downstream genotyping (vertical arrows). c Kinship heatmaps for parent specific, pseudo-test cross markers from each parent. Left: 73 progeny isolates from SF5 x C82P24 tested with C82P24-derived markers ≥ 61 bp. Center: 96 progeny isolates from both crosses tested with SF5-derived markers ≥ 61 bp. Right: 23 progeny isolates from SF5 x C98O622b tested with C98O622b-derived markers equal to 61 bp. One isolate was selected when clusters of isolates (colored blue) were formed using markers of both parents. The additional pattern observed for C82P24 (left) is due to heterokaryosis (see 6). d Segregation of 31-mer pseudo-test cross markers in the F1. For C82P24 (left) and SF5 (center), both marker types ≥ 61 bp segregate at the same frequency. The discordance observed for markers derived from C98O622b may be due to contamination (see a). Distortion is observed for C82P24 because this isolate is heterokaryotic (see c and 6). SF5 is homokaryotic so all gametes are derived from a single nucleus. Therefore, only SF5-derived markers were suitable for linkage map construction

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