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Fig. 3 | BMC Genetics

Fig. 3

From: Genome-wide association study of Gossypium arboreum resistance to reniform nematode

Fig. 3

Marker-trait associations for reniform nematode resistance evaluated for the 246Ā Gossypium arboreum germplasm accessions. a Genome wide Manhattan plot of association from compressed mixed linear model; x-axis showed the SNPs along each chromosome; y-axis was the ā€“log10 (P-value) for the association. S1_842793872 and S1_842793960 on chromosome 7, S1_634724647 and S1_634724595 on chromosome 12 are physically close to each other with nearly the same P-values (Additional file 4), so they overlapped as one dot in the figure. The alternate orange and blue dots represent SNPs mapped to different chromosomes, with the blue dots on the most right of the Manhattan plot located on scaffolds, which could not be assembled onto the 13 chromosomes of the G. arboreum reference genome. Dots above the blue horizontal line are SNPs with P-value <ā€‰0.001, whereas the one dot above the red line is the SNP with P-value <ā€‰0.0001. b Quantile-quantile (Q-Q) plot for the compressed mixed linear model

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