SNPs, GWAS associations, flowering time homologs and gene density on maize chromosome 3.

<p>In (a), the top panel shows the days-to-silk GWAS signals; blue triangles are the positive QTLs, the red are negative ones and the light blue ones at the bottom indicative of insignificant SNPs that did not pass RMIP test. SNP density along the chromosome is in grey bars in the background and significance level of RIMP scores is in the axis on the left. The gene density, calculated from the number of maize gene in every 200K bp, are in the lower panel, while the black triangles on the bottom of the density distribution mark the positions of maize flowering time homologs. Two dashed vertical lines indicate the positions of the examples in two top enriched flowering time maize homologs. (b) The enrichment of maize flowering time priori candidate: GRMZM2G115960. In this case, the co-localizing significant QTLs found in GWAS are all within the linkage block of the <i>a priori</i> candidate. (c) The enrichment of maize flowering time priori candidate: GRMZM2G365688. Three (solid red dots) of 6 significantly QTLs reside within linkage block of <i>a priori</i> candidate; the 3 unfilled red dots outside of the dashed red lines are significant, but unlinked, GWAS associations, while black dots being maize Hapmap 1 SNPs.