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Schematic representation of the principle of how GWAS can be used to detect the position of the duplicated genes based on linkage disequilibrium (LD). As phenotype, heterozygosity at the position of interest is coded as 1 (present) or 0 (absent). As a genotype, the SNPs matrix of the 1001 genome dataset was used (with heterozygous SNPs filtered out). Color gradients represent the strength of LD around the two loci. In this example, the reference genome does not contain locus2.

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