The timing of flowering and fruit ripening plays a decisive role in the productivity, quality, and climate adaptability of fruit trees. In Japanese plum, these phenological traits are particularly vulnerable to shifting temperatures and unstable winter chilling. This study uncovers the genetic architecture underlying key phenological stages—flowering onset, full bloom, ripening date, fruit development period, and productivity—by identifying genomic regions that consistently regulate these traits across multiple years. Using a cost-efficient genome-wide strategy, the research pinpoints stable genetic loci and candidate genes linked to flowering behavior and fruit maturation. These findings offer practical genetic targets that can accelerate breeding for climate-resilient plum varieties.
Japanese plum is one of the world's most economically important stone fruit crops, yet its genetic improvement remains slow due to long breeding cycles, high heterozygosity, and strong sensitivity to environmental conditions. Phenological traits such as flowering time and ripening date are central to yield stability, frost avoidance, and harvest planning, but they are increasingly disrupted by climate change. In many production regions, reduced winter chilling threatens proper dormancy release and leads to irregular flowering and unstable yields. Traditional breeding approaches struggle to respond efficiently to these emerging risks. Based on these challenges, there is a pressing need to conduct in-depth research into the genetic control of key phenological traits in Japanese plum.
Researchers from the Department of Plant Breeding at CEBAS-CSIC (Spain), in collaboration with the Institute of Agricultural and Food Research and Development of Murcia (IMIDA, Spain) and the University of California, Davis (USA), report a comprehensive genetic analysis of phenological traits in Japanese plum. Published (DOI: 10.1093/hr/uhaf271) in Horticulture Researc h in 2025, the study combines high-coverage whole-genome sequencing of parental cultivars with low-coverage sequencing of offspring to map genetic regions controlling flowering, ripening, and productivity across multiple years.
The study analyzed three Japanese plum populations over three consecutive years, capturing both genetic and environmental influences on phenology. A total of 113 quantitative trait loci (QTLs) were identified, with 60 showing stable effects across years—an essential criterion for breeding reliability. Major genomic regions influencing flowering stages were repeatedly detected on linkage groups LG1, LG2, LG4, and LG6, confirming that flowering time is a complex, polygenic trait.
Ripening date and fruit development period showed particularly strong and consistent associations with regions on LG4, highlighting this chromosome as a central regulator of fruit maturation. Notably, many ripening-related QTLs overlapped spatially with those controlling fruit development length, suggesting tightly linked or pleiotropic genetic control.
Beyond trait mapping, the researchers identified biologically meaningful candidate genes within stable QTL regions. These include genes related to ethylene signaling, heat-shock transcription factors, and RNA polymerase II regulation—pathways known to integrate developmental timing with environmental cues. Importantly, the sequencing strategy achieved high resolution at a fraction of the cost of conventional genotyping platforms, making it practical for real-world breeding programs.
"Phenological timing determines whether a tree flowers too early, ripens too late, or fails to adapt to climate variability," the authors note. "By identifying stable genetic regions that consistently influence these traits across years, we provide breeders with reliable molecular entry points. This approach not only clarifies how flowering and ripening are genetically controlled, but also demonstrates that cost-efficient genome sequencing can deliver high-impact insights for perennial crop improvement."
The results offer immediate value for marker-assisted selection in Japanese plum breeding. Stable QTLs and candidate genes can be transformed into molecular markers to predict flowering and ripening behavior at the seedling stage, dramatically shortening breeding cycles. In the context of climate change, these tools enable the development of cultivars better adapted to reduced winter chilling and shifting temperature patterns. Beyond plum, the study provides a scalable genomic framework applicable to other fruit trees facing similar phenological challenges, supporting more resilient, efficient, and climate-ready horticultural production systems worldwide.
