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Fig. 2 | BMC Plant Biology

Fig. 2

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

Fig. 2

Manhattan Plot showing NCRPIS 2.7 and Goodman 2.7 GWAS results for flowering time. Data from Romay et al. [8] were used in GWAS analysis and gene discovery. Negative log10 p-values are plotted against physical position (B73_RefGen_v4) on all 10 chromosomes. Markers significant at a Benjamini-Hochberg false discovery rate of 10% are shown in red. 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. Vertical solid lines indicate positions of significant QTL and gene annotations for flowering time, as shown by Romay et al. [8]. Dotted lines indicate positions of novel genes identified. Gene identities are described in Romay et al. [8]. a Results for GWAS conducted using the 2279-member NCRPIS population and NCRPIS 2.7 marker data. b Results for GWAS conducted using the 282-member Goodman AP collection within the NCRPIS population and Goodman 2.7 marker data. c Results for GWAS conducted using the 282-member Goodman AP collection within in the NCRPIS population and the nearest neighbor of similar phenotype (564 lines) and NCRPIS 2.7 marker data. d Results for GWAS conducted using the 282-member Goodman AP collection within in the NCRPIS population and three nearest neighbors of similar phenotype (1128 lines) and NCPRIS 2.7 marker data

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