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Fig. 2 | Genome Biology

Fig. 2

From: Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity

Fig. 2

GWAS of putative duplications. A 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. B GWAS results for three different genes with evidence of duplication, for illustration. The red lines indicate the position of the pseudo-SNP used for each gene/GWAS and the thick gray lines indicate the centromeres. The top plot shows a trans-association, the bottom a cis-association, and the middle shows a case with both (cis plus two trans). C Summary of all 26,647 GWAS results

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