Species-wide gene editing of a flowering regulator reveals hidden phenotypic variation
Fig 2
Quantitative genetic analysis of FLC-independent flowering.
(A) Distribution of flowering time (DTF) of F2 individuals, including the mean value of the respective flc mutant parent lines. The numbers of F2 individuals per population are shown on top. The arrow indicates a single outlier of population C3-090, which was excluded in the correlation shown in C. (B) Correlation between the phenotypic range of the parents and of the F2 populations (range = F2(max) − F2(min)). Simple linear model, DTF, excluding a single outlier of population C3-090 (see panel A): r2adj = 0.65, p = 0.0006; including the outlier: r2adj = 0.37, p = 0.016; RLN, r2adj = 0.52, p = 0.0033; CLN, r2adj = 0.15, p = 0.109. (C) Flowering trait correlations in F2 populations. Range of Pearson’s r: RLN versus DTF 0.41 to 0.85; RLN versus CLN 0.31 to 0.80; DTF versus CLN 0.13 to 0.68; all p < 0.0001. (D) Summary of QTL analysis. On top, schematic representation of chromosomes, with black dots representing centromeres. The physical position of genes with a known role in flowering is shown below (S6 Table), with color indicating the published classification [33,34]. LOD scores were summed over a non-overlapping moving window of size 100 kb and are shown at the center of the window. The detected QTL clusters 1–4 are indicated on top, the widths of the gray boxes indicate the size of each cluster. Cluster 1 is a 2 Mb region (±1 Mb from QTL LOD peak at 24.675 Mb). Cluster 2 is a 7 Mb region (0–7 Mb) on chromosome 5. Clusters 3 and 4 are smaller and contain fewer QTL. The QTL intervals (95% Bayes interval) are shown as horizontal lines, and the physical positions of a priori flowering candidate genes are indicated as dashed vertical green lines. (E) Proportional explained additive variation (PEV) of QTL co-localizing with FT. (F) Correlation of FT expression levels with flowering traits. Mutants on the lower and wild types on the upper triangle. Pearson’s r, mutants, −0.57 to −0.45, p < 0.001, 109 d.f.; wild types, DTF: r = −0.34, p < 0.01, RLN r = −0.51, p < 0.001, 59 d.f. The significance of the correlations is indicated by *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; n.s., not significant. The data underlying this figure can be found in S1 Data and https://doi.org/10.5281/zenodo.15403194.