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In widely cultivated tomato (\n                      <jats:italic>Solanum lycopersicum<\/jats:italic>\n                      ) varieties, the\n                      <jats:italic>uniform ripening<\/jats:italic>\n                      (\n                      <jats:italic>u<\/jats:italic>\n                      ) mutation, a loss-of-function allele of the\n                      <jats:italic>Solanum lycopersicum Golden2-like 2<\/jats:italic>\n                      (\n                      <jats:italic>SlGLK2<\/jats:italic>\n                      ), has been selected to improve fruit appearance. However, this selection is associated with reduced fruit nutritional quality, lowering the levels of sugars and tocopherols due to impaired plastid development. In this study, the function of\n                      <jats:italic>SlGLK2<\/jats:italic>\n                      was restored by introducing an additional mutation using the temperature-tolerant\n                      <jats:italic>Lachnospiraceae bacterium<\/jats:italic>\n                      ND 2006 Cas12a (\n                      <jats:italic>Lb<\/jats:italic>\n                      Cas12a) genome editing system. A 13-bp deletion in the linker region of SlGLK2 protein in the\n                      <jats:italic>CR-Slglk2-4<\/jats:italic>\n                      line restored the reading frame and led to enhanced chlorophyll accumulation and plastid development, particularly in the stem end region of the fruit. The edited line also showed increased total soluble solids and tocopherol content in ripe fruit. Biochemical, transcriptomic, and transcriptional activity analyses confirmed the functional restoration of\n                      <jats:italic>SlGLK2<\/jats:italic>\n                      in the\n                      <jats:italic>CR-Slglk2-4<\/jats:italic>\n                      line. This study not only provides a useful Micro-Tom line for investigating plastid biogenesis in tomato fruit but also demonstrates the potential of genome editing to restore the latent functions of pseudogenized genes in modern crops, offering a new approach for recovering traits lost during plant domestication or crop improvement.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s00299-026-04024-z","type":"journal-article","created":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T17:44:47Z","timestamp":1792086287000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Reactivation of a loss-of-function SlGLK2 allele by frame-restoring genome editing in tomato"],"prefix":"10.1007","volume":"45","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2303-3396","authenticated-orcid":false,"given":"Kentaro","family":"Ezura","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheolwoo","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,15]]},"reference":[{"key":"4024_CR74","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","volume":"630","author":"J Abramson","year":"2024","unstructured":"Abramson J, Adler J, Dunger J et al (2024) Accurate structure prediction of biomolecular interactions with AlphaFold 3. 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