Insights into double sigmoid pattern during Chinese cherry fruit development through comparative physiological and transcriptomic profiles

Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don] (syn. Prunus pseudocerasus Lindl), native to China, is an important fruiting cherry species belonging to the Rosaceae family. Fruit size is a key factor limiting the large-scale production of this crop. However, the regulatory mechanisms governing fruit size in Chinese cherry remain poorly understood. In this study, we analyzed comparative physiological characteristics and performed transcriptome sequencing to identify key genes regulating fruit size in Chinese cherry. The increase in fruit diameter and weight follows a typical double-sigmoid growth pattern. The final fruit size is attributed to both cell division and cell expansion, corresponding to Sigmoid I (SI) and Sigmoid II (SII), respectively. Auxin, gibberellin, cytokinin, and brassinosteroids showed a marked increase during the SI phase, followed by varying degrees of decrease during the slow-growth stage, and a slight increase during the SII phase. During SI phase, IAA, GA3, and ZR exhibited much higher levels or more rapid increases in large fruits (HF) compared to small fruits (PJHH), indicating their important roles in early fruit enlargement. Comparative transcriptomic analysis identified a total of 8,938 DEGs through pairwise comparisons across SI and SII phases between HF and PJHH. Gene Ontology (GO) enrichment analysis revealed that numerous genes associated with cell cycle and phytohormones, including auxin, gibberellin, and cytokinin, exhibited differential expression between large- and small-fruited landraces. Some candidate genes were validated by RT-qPCR analysis, including CpCDKB2;2, CpPAT14, CpRBR, CpGH3.1, CpARF6, CpIAA6like, CpYUCCA10, CpGA2oxlike, and CpARR5like, among others. These findings provide a theoretical foundation for the regulation of fruit size in Chinese cherry breeding. In the future, new Chinese cherry cultivars with larger fruits may be bred by overexpression genes that positively regulate fruit size or by knocking out genes that negatively regulate fruit size via transgenic or gene editing technologies.