Extended Data Fig. 1: Pseudomolecule construction for 20× tetraploid simulated GBS data.

A total of 42,715 SNPs located on 678 scaffolds were used for linkage analysis. These scaffolds of ~482Mb covered approximately 99.6% of the genome. a, Dot plot for the RF estimations for scaffold pairs mapped to the same reference chromosome. The x- and y-axis represents the physical distances and the estimated RFs, respectively. b, Histogram of the RF estimations for scaffold pairs mapped to different reference chromosomes. c, Collinear plots of pseudomolecules mapped to reference chromosomes. The x- and y-axis represents physical positions (Mb) on the reference chromosomes and pseudomolecules, respectively. Each line represents a collinear block between the reference chromosome and the pseudomolecule. The diagonal line in each plot indicates a high correlation between the reference chromosome and the pseudomolecule constructed from scaffolds.