Fig. 3.

The phenotypic effects of ELF3-TR variation are strongly background-dependent. (A) PCA of developmental traits of all ELF3-TR alleles in Ws and Col genetic backgrounds. Shared color indicates a given ELF3-TR allele in both genetic backgrounds. A. thaliana images are as in Fig. 1A. The contributions of phenotypes to principal components are similar to Fig. 1A, except that PC2 is inverted (no effect on interpretation, loadings in Fig. S5C). Representative TR copy number alleles are shown from an analysis including all alleles (for all alleles see Fig. S5; for Col-background specific PCA, see Fig. S6). (B) Days to flower under SD and hypocotyl length under LD differ for particular TR alleles between Ws (Upper) and Col (Lower) backgrounds. ELF3-TR alleles are indicated with the number of Qs encoded, Ws and Col-0 are wild-type, elf3-4 and elf3-200 are respective vector controls (VC). Error bars represent SEM. Genotypes labeled with different letters differed significantly in phenotype by Tukey-HSD test with α = 0.05. For all Col-background phenotype data, see Fig. S6 A–G. Data are from multiple independently generated expression-matched (Fig. S1 C and D) T3 and T4 lines for each TR copy number allele (Table S4). These experiments were repeated at least once with similar results.