Figure 1.
Phenotypic distribution of iron deficiency chlorosis (IDC).
The rating of IDC (1–5) is on x-axis and the number of genotypes having the IDC score (represented as density) are presented as y-axis. The curve over the histogram represents the normal distribution of the IDC scores in the population.
Figure 2.
A graph of the first two principal components obtained from all the 34,428 polymorphic SNPs.
This graph explains the similarities between the two independent populations and the overall population structure.
Figure 3.
Heatmap of Gower’s similarity distance among the individuals of the population.
Based on the colors distribution, it is evident that relatedness can have a major effect on identifying associations to IDC in the population.
Figure 4.
QQ plot for the six models tested.
P-value observed is plotted on the y-axis and P-expected is plotted on the x-axis. Each color represents a model of regression used. The best model is the one that is close to the diagonal line.
Figure 5.
Manhattan plots with significant QTL that are associated with IDC.
Chromosomes (1–20) ordered on x-axis and each chromosome is represented by a different color. The –log10(p-value) is presented on the y-axis. The cutoff horizontal lines indicate 0.01 and 0.1 percentile tails of the empirical distribution obtained using 10,000 bootstraps. Vertical grey blocks indicate QTL regions that have major effect on IDC trait identified by stepwise regression. The boundaries of the QTL region (based on the position of markers) and significant candidate genes are represented on the top of QTL.
Table 1.
Significant markers associated with IDC in the population of soybean.
Figure 6.
QTL that has known candidate gene are only represented. Only significant markers at the 0.1 percentile bootstrapped empirical distribution were included in the figure. Significance of the markers is indicated as *** if fall in the 0.01 percentile tail and ** if fall in the 0.1 percentile tail of the bootstrapped empirical distribution. The stepwise included markers are marked in blue. r2 values are represented in different colors. Marker pairs with r2 values>0.6 are considered to be in linkage disequilibrium. a) is the QTL on Gm03 (44.798 Mbp–47.140 Mbp), b) is the QTL on Gm05 (7.837 Mbp–10.627 Mbp), c) is the QTL on Gm07 (6.074 Mbp–7.101 Mbp), d) is the QTL on Gm16 (26.914 Mbp–27.597 Mbp) and e) is QTL region on Gm19 (39.832 Mbp–41.320 Mbp).
Table 2.
Significant QTL regions associated with IDC that have Candidate iron genes.
Table 3.
Allelic combinations and IDC means for the allele combinations that have a mean<2.5 (Tolerant) and>3.5 (Susceptible).