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Fig. 1 | BMC Plant Biology

Fig. 1

From: COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

Fig. 1

Manhattan Plot showing GWAS results for ratio of α-tocopherol to γ-tocopherol conversion. Data from Lipka et al. [16] were input into COMPILE for GWAS analysis and gene discovery. Negative log10 p-values are plotted against physical position (B73_RefGen_v4) on all 10 chromosomes. Values in red are significant at Benjamini-Hochberg false discovery rate of 5%. A visual marker for the Bonferroni threshold (averaged from the individual threshold y-values of each chromosome) at (α = 0.1) is indicated by the blue horizontal line. The vertical line marks the position of the maize tocopherol O-methyltransferase (ZmVTE4). Dotted lines indicate the positions of genes identified by COMPILE not identified in the original study: a MADS-box 36 transcription factor (Zm00001d043589), a putative glycosyl transferase gene (Zm00001d019057), and a the long non-coding RNA occurred very early in embryo development, and only between 84 and 96 h post-pollination in the nucellus [17]

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