Fig. 2

Gene extension algorithm scheme of gene- and marker-based haplotype calculations. The raw SNP-based allele frequency (2nd row; “Raw Frequency”) for identified SNPs (1st row) are identified at a given read depth (3rd row; “Read depth”). Annotated genes (4th row; “Genes”) and markers (6th row; “Markers”) are extended in size up- and downstream (“Genes extended”; “Marker extended”) to associate SNPs in the particular region to the genes / markers. By the extension, more SNPs can be annotated to a gene/marker than without (dashed lines and arrows below the 3rd row indicate relationships). Reported frequency in the last two rows of markers and genes are the calculated haplotype frequency for the wild donor parent in the population. The marker and gene-based haplotype calculation is illustrated in the methods section. The figure should only illustrate the model of SNP information aggregation and does not contain real data