Article Figures & Data
Figures
- Figure 1
Phenotypic distributions of the KRN trait in GWAS and validation populations. (A) Density plots of the four GWAS populations. Embedded picture shows the typical KRN counts for B73, B73xMo17 (BxM), Mo17xB73 (MxB) and Mo17 lines. (B) Density plots of two validation populations, elite inbred lines and extreme KRN accessions. Embedded pictures shows examples of an extreme low KRN accession and an extreme high KRN accession. (C) Density plots of cycle 30 long ear (C30 LE) and cycle 30 short ear (C30 SE) in the BSLE population. Embedded pictures indicate the ear length and KRN variation after 30 generations of selection. Blue and red dashed lines indicate the mean KRN values of B73 (KRN = 17.1) and Mo17 (KRN = 10.8).
- Figure 2
Stacked plots of GWAS and QTL results. From upper to lower panels are results from the Bayesian-based multi-variant (A) stepwise regression (B) and single variant(C) models for GWAS and the joint QTL mapping result (D). The red dashed line in the QTL plot indicates the 1,000 permutation threshold and black lines show the QTL confidence intervals. Red squares in panel (A), triangles in panel (B) and circles in panel (C) indicate the kernel row number associated variants selected for further genetic validation.
- Figure 3
Genetic validation results of selected kernel row number associated variants (KAVs). (A) Transformed P values using single variant (SV) model and posterior model frequencies using Bayesian-based multi-variant (BMV) model were extracted and plotted for the 77 informative KAVs identified by at least one of the three GWAS models. KAVs detected only by the SV model are plotted in the lower right quadrant, KAVs detected only by the stepwise regression model are plotted as non-gray dots in the lower left quadrant, the KAVs detected only by the BMV model are plotted in the upper left quadrant, KAVs detected by both the SV and BMV models are plotted in the upper right quadrant and control variants are plotted as gray dots in the lower left quadrant. Validated KAVs are marked in red. A control variant is a genomic variant that is randomly chosen from a set of SNPs that were not associated with KRN in the initial GWAS. (B) Venn diagram of the validation results.
