Fig. 4: Fate of dSVs in domestication and inbred line development.
From: Leveraging a phased pangenome for haplotype design of hybrid potato
a, The pipeline for identifying dSVs includes the joint criteria of derived state of low-frequency SVs (≤0.05) in gene-coding and/or evolutionarily constrained regions. b, The percentage of homozygous and heterozygous dSVs in wild and cultivated potato populations. c, The number of dSVs per chromosome in the founder PG6359 (average of the two haplotypes) and its derivative inbred line A6-26. d, Schematic diagram of recombination events in chromosome 2 (left) and haplotype selection in chromosome 4 (right). The potential recombination events are marked with dashed lines. Deleterious variants from the H1 and H2 haplotypes are shown in different colours. e, Pearson correlation coefficient (r = 0.78) and P value (2.6 × 10−16) between numbers of dSNPs and dSVs across all chromosomes (n = 696). The shaded area represents the bootstrapped 95% confidence interval. f, Distribution of the number of dSNPs flanking focal dSVs for 10-kb non-overlapping windows in the dSV coupling phase (orange) and the dSV repulsion phase (grey). The points represent means of 58 haplotypes and error bars represent 95% confidence intervals. g, Average distance of a focal dSV to the nearest dSV in coupling phase (same haplotype; dis-coupling) and to the nearest dSV in syntenic regions of the other haplotype (dis-repulsion). Only distances <1 Mb are included. The boxes represent 75% and 25% quartiles, the central line indicates the median and the whiskers extend to 1.5 times the interquartile range; P < 2.2 × 10−16, two-tailed Student’s t-test, n = 13,717 (dis-coupling) and 11,679 (dis-repulsion). h, A zoomed-in view of biased dSNP accumulation (blue bars) around a heterozygous dSV (red triangle) within a 20-kb segment of chromosome 4 in E86-69 H2.
