Natural variation in STAYGREEN contributes to low‐temperature tolerance in cucumber

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Low‐temperature (LT) stress threatens cucumber production globally; however, the molecular mechanisms underlying LT tolerance in cucumber remain largely unknown. Here, using a genome‐wide association study (GWAS), we found a naturally occurring single nucleotide polymorphism (SNP) in the STAYGREEN ( CsSGR ) coding region at the gLTT5.1 locus associated with LT tolerance. Knockout mutants of CsSGR generated by clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR‐associated nuclease 9 exhibit enhanced LT tolerance, in particularly, increased chlorophyll (Chl) content and reduced reactive oxygen species (ROS) accumulation in response to LT. Moreover, the C‐repeat Binding Factor 1 (CsCBF1) transcription factor can directly activate the expression of CsSGR . We demonstrate that the LT‐sensitive haplotype CsSGR HapA , but not the LT‐tolerant haplotype CsSGR HapG could interact with NON‐YELLOW COLORING 1 (CsNYC1) to mediate Chl degradation. Geographic distribution of the CsSGR haplotypes indicated that the CsSGR HapG was selected in cucumber accessions from high latitudes, potentially contributing to LT tolerance during cucumber cold‐adaptation in these regions. CsSGR mutants also showed enhanced tolerance to salinity, water deficit, and Pseudoperonospora cubensis , thus CsSGR is an elite target gene for breeding cucumber varieties with broad‐spectrum stress tolerance. Collectively, our findings provide new insights into LT tolerance and will ultimately facilitate cucumber molecular breeding.