Identification of PpTHE1, a cell wall integrity sensor regulating the increased duration of harvest window in slow-melting flesh peach, through the assembly of a chromosome-level reference genome of Prunus persica.

Slow-melting flesh (SMF) in peaches offers many advantages, including easy transportation, maintaining flavour after ripening, an extended harvest window, and reduced losses caused by fruit softening. However, the underlying molecular mechanism remains elusive. A high-quality genome of the SMF cultivar Chunrui was sequenced, assembled and annotated. The assembled genome was 249.6 Mb in size and characterized by a contig N50 of 12.35 Mb and a scaffold N50 of 30.27 Mb. Analysis of a segregating population indicated that a single dominant gene or major gene controlled the SMF trait. This trait was mapped to chromosome 4, which had a total length of 1.39 Mb. Fine mapping and gene expression analyses identified the receptor protein kinase THESEUS 1 (PpTHE1) as a candidate SMF gene. A Gypsy LTR-retrotransposon inserted downstream of PpTHE1 inhibited its expression. Functional analyses in peach and tomato fruits showed PpTHE1 played a positive role in maintaining fruit firmness. Screening of a yeast library using the kinase domain of PpTHE1 as the bait identified an ERF-type transcription factor PpERF61 and pectinlyase PpPL15. Luciferase complementation imaging, bimolecular fluorescence complementation and co-immunoprecipitation assays showed that PpTHE1 could interact with PpERF61 and PpPL15 in planta. Furthermore, our experimental data revealed that PpTHE1 significantly attenuates the DNA-binding capacity of PpERF61 to its target genes. These findings reveal the regulatory mechanism underlying the SMF fruit quality trait and thus provide theoretical support for breeding programmes to develop high-quality, storage-tolerant peach genotypes.