Skip to main content
Fig. 5 | BMC Plant Biology

Fig. 5

From: Genotyping-by-sequencing and SNP-arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies

Fig. 5

Complementarity of QTLs detection between the 600 K array and the GBS for two regions (QTL 32/QTL95). a Manhattan plot of the -log10(p-value) along the genome. Dotted red lines correspond to QTL32 and QTL95 located on chromosome 1 and 3, respectively, for the flowering time in one environment (Ner13R). b Local manhattan plot of the -log10(p-value) (top) and linkage disequilibrium corrected by the kinship (r2K) (bottom) of all SNPs with the strongest associated marker within QTL 32 (left) and QTL 95 (right). Colored vertical lines between manhattan plot and linkage disequilibrium plot represents the distribution of markers for different technologies. Dotted lines between panels b and c linked the first marker, the most associated marker, and the last marker of each QTL (c) Local haplotypes displayed by all SNPs within the QTLs 32 (left) and 95 (right) with MAF > 5%. Inbred lines are in rows and SNPs are in columns. Inbred lines were ordered by hierarchical clustering based on local dissimilarity estimated by all SNPs within each QTL. Genotyping matrix is colored according to their allelic dose at each SNP. Red and black represent homozygotes and gray represent heterozygotes. The associated peaks (red vertical lines) and other associated SNPs with -log10(p-value) > 5 (orange vertical lines) are indicated above the genotyping matrix. H1, H2, H3, H4, H5 represent the 5 and 3 haplotypes obtained by cutting the dendograms with the most 5 and 3 dissimilar clusters within QTL32 and QTL95, respectively

Back to article page