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Despite myriad examples of local adaptation, the phenotypes and genetic variants underlying such adaptive differentiation are seldom known. Recent work on freezing tolerance and local adaptation in ecotypes ofArabidopsis thalianafrom Italy and Sweden provides an essential foundation for uncovering the genotype–phenotype–fitness map for an adaptive response to a key environmental stress.

We examined the consequences of a naturally occurring loss‐of‐function (LOF) mutation in an Italian allele of the gene that encodes the transcription factorCBF2,which underlies a major freezing‐tolerance locus. We used four lines with a Swedish genetic background, each containing aLOFCBF2allele. Two lines had introgression segments containing the ItalianCBF2allele, and two contained deletions created usingCRISPR‐Cas9. We used a growth chamber experiment to quantify freezing tolerance and gene expression before and after cold acclimation.

Freezing tolerance was lower in the Italian (11%) compared to the Swedish (72%) ecotype, and all four experimentalCBF2LOFlines had reduced freezing tolerance compared to the Swedish ecotype. Differential expression analyses identified 10 genes for which allCBF2LOFlines, and theITecotype had similar patterns of reduced cold responsive expression compared to theSWecotype.

We identified 10 genes that are at least partially regulated byCBF2that may contribute to the differences in cold‐acclimated freezing tolerance between the Italian and Swedish ecotypes. These results provide novel insight into the molecular and physiological mechanisms connecting a naturally occurring sequence polymorphism to an adaptive response to freezing conditions.