Tandem repeats (TRs) have extremely high mutation rates and are often considered to be neutrally evolving DNA. However, in coding regions, TR copy number mutations can significantly affect phenotype and may facilitate rapid adaptation to new environments. In several human genes, TR copy number mutations that expand polyglutamine (polyQ) tracts beyond a certain threshold cause incurable neurodegenerative diseases. PolyQ-containing proteins exist at a considerable frequency in eukaryotes, yet the phenotypic consequences of natural variation in polyQ tracts that are not associated with disease remain largely unknown. Here, we use
Arabidopsis thaliana
to dissect the phenotypic consequences of natural variation in the polyQ tract encoded by
EARLY FLOWERING 3
(
ELF3
), a key developmental gene. Changing ELF3 polyQ tract length affected complex ELF3-dependent phenotypes in a striking and nonlinear manner. Some natural
ELF3
polyQ variants phenocopied
elf3
loss-of-function mutants in a common reference background, although they are functional in their native genetic backgrounds. To test the existence of background-specific modifiers, we compared the phenotypic effects of
ELF3
polyQ variants between two divergent backgrounds, Col and Ws, and found dramatic differences. In fact, the Col-
ELF3
allele, encoding the shortest known ELF3 polyQ tract, was haploinsufficient in Ws × Col F
1
hybrids. Our data support a model in which variable polyQ tracts drive adaptation to internal genetic environments.