Fig. 3. Manhattan and Q-Q plots for GWAS of five LN traits. Manhattan and Q-Q plots for SPAD (a, f), shoot length (SL) (b, g), root length (RL) (c, h), shoot fresh weight (SFW) (d, i), and root fresh weight (RFW) (e, j) using the FarmCPU model on rMVP. The horizontal red line represents the threshold (-log10 (P)=5.934) for identifying significant SNPs associated with the low-N response. Candidate genes, including both known and novel ones, are highlighted in red and black above the lead SNPs. In the Q-Q plots, the horizontal axis shows the expected –log10 (P), while the vertical axis indicates the observed -log10 (P) for each SNP.
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