Figure 1.
Enrichment analysis pipeline, and the data that is required in the procedure.
Figure 2.
The distribution of allelic effects in maize days-to-silk associations. The unit of allelic effect is in day(s).
Figure 3.
The distribution of association QTLs across NAM families.
NAM GWAS associations identify a few cases of family specific QTL, while QTL found in previous joint-linkage analysis are mostly shared by 7 or 8 families.
Figure 4.
Averaged positive and negative allelic effects and their standard deviations in tropical versus temperate NAM populations.
Figure 5.
Maize flowering time related homologs, resulted from the comparison between Arabidopsis and maize genes by Compara pipeline.
Figure 6.
The comparison of estimated linkage block sizes with perfect linkage (r2 = 1), high linkage (1>r2≥0.8), intermediate linkage (1>r2≥0.6 and 0.4) and low linkage (1>r2≥0.2).
Figure 7.
Maize flowering time priori candidate genes.
Maize flowering time priori candidate genes are identified via enrichment of GWAS associations; and, the annotations are taken from their orthologous relationship to Arabidopsis genes.
Figure 8.
SNPs, GWAS associations, flowering time homologs and gene density on maize chromosome 3.
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 a priori candidate. (c) The enrichment of maize flowering time priori candidate: GRMZM2G365688. Three (solid red dots) of 6 significantly QTLs reside within linkage block of a priori 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.
Figure 9.
Flowering time variation association enrichment LOD scores comparison in different curation categories.
1: maize flowering time orthologs; 2: maize leaf genes (in Feng et al. 2010); 3: maize miRNA target leaf genes; 4: biosynthetic process (GO:0009058); 5: developmental process (GO:0032502); 6: enzyme regulator activity (GO:0030234); 7: growth (GO:0040007); 8: negative regulation of response to stimulus (GO:0048585); 9: positive regulation of response to stimulus (GO:0050729) and 10: transcription regulator activity (GO:0030528). GO terms in 6 and 10 are from molecular function GO terms, while the rest of the GO terms come from biological process.