Soichiro Nishiyama

Persimmon fruit accumulates high levels of proanthocyanidins (PAs), causing extreme astringency. In pollination-constant and non-astringent (PCNA) cultivars, PA accumulation ceases early in fruit development. Although the PCNA trait is recessively controlled by the ASTRINGENCY ( AST ) locus, its causal gene has remained unknown. Using haplotype-resolved forward genetics in a hexaploid genetic background, we identified the previously uncharacterized TANNIN ( TAN ) as the causal gene. Long-read sequencing revealed that PCNA originated through the accumulation of independently derived ast alleles that cause transcriptional deficiency of TAN . These findings resolve the complex genetic basis of natural astringency loss in persimmon and provide a framework for molecular breeding. Further investigation of TAN function would uncover mechanisms underlying massive accumulation of PAs in persimmon fruit and insight into specialized metabolite sequestration.

Fruit size and shape, which influence horticultural quality, are determined by the number and the size of the cells in the local region. In fruit trees, however, the difficulty of applying molecular genetic approaches has hindered a detailed understanding of the localization and orientation of cell division in developing fruit tissues. In this study, we established a novel framework to visualize cell division in pre-anthesis ovaries of drupe crops, providing clear insight into the spatial distribution and orientation of dividing cells. We systematically optimized a 5-ethynyl-2′-deoxyuridine (EdU) labeling protocol for thick ovary tissues by adjusting infiltration conditions and fixation methods. In addition, electron microscopy combined with wide-view tiling visualization was applied to directly identify dividing cells, including those undergoing chromosome segregation and cell plate formation. By combining with machine learning–based detection, we efficiently and objectively identified dividing cells. Using these complementary approaches, we found that cell division activity was broadly distributed throughout pre-anthesis ovaries in several drupe crops analyzed, without pronounced spatial restriction. In contrast, analysis of division orientation revealed region-specific patterns: cells in the outermost exocarp divided predominantly anticlinally, whereas cells in the mesocarp divided largely periclinally, consistent with subsequent ovary (fruit) enlargement. The integrated framework presented here provides a foundation for understanding the spatial and three-dimensional regulation of cell division during pre-anthesis ovary development and may be extended in future studies to later stages of fruit development.

In Prunus, self-incompatibility (SI) is controlled by S-RNases and pollen-expressed F-box proteins, whereas the molecular processes governing S-RNase regul

Fruit size and shape, which influence horticultural quality, are determined by the number and the size of the cells in the local region. In fruit trees, however, the difficulty of applying molecular genetic approaches has hindered a detailed understanding of the localization and orientation of cell division in developing fruit tissues. In this study, we established a novel framework to visualize cell division in pre-anthesis ovaries of three drupe crops, peach ( Prunus persica ), Japanese apricot ( P. mume ) and the interspecific hybrid Japanese apricot ( P. salicina x P. mume ), providing clear insight into the spatial distribution and orientation of dividing cells. We systematically optimized a 5-ethynyl-2′-deoxyuridine (EdU) labeling protocol for thick ovary tissues by adjusting infiltration conditions and fixation methods. In addition, electron microscopy combined with wide-view tiling visualization was applied to directly identify dividing cells, including those undergoing chromosome segregation and cell plate formation. By combining with machine learning-based detection, we efficiently and objectively identified dividing cells. Using these complementary approaches, we found that cell division activity was broadly distributed throughout pre-anthesis ovaries in all three crops, without pronounced spatial restriction. In contrast, analysis of division orientation revealed region-specific patterns: cells in the outermost exocarp divided predominantly anticlinally, whereas cells in the mesocarp divided largely periclinally, consistent with subsequent ovary (fruit) enlargement. The integrated framework presented here provides a foundation for understanding the spatial and three-dimensional regulation of fruit development and for future studies in fruit morphogenesis and horticulture.

Spatial gene expression and 2D/3D ultrastructural analyses reveal a unique intercellular sequestration mechanism underlying massive proanthocyanidin accumulation in persimmon fruit.

Fruit growth has long been described using single- or double-sigmoid curves; however, these temporal models cannot fully capture the spatial heterogeneity that ultimately shapes a fruit. Here, we present a three-dimensional analysis pipeline that non-destructively tracks spatial fruit growth dynamics from field-collected imaginary. Surface landmarks were drawn, and video recordings were taken throughout development for three pome fruits, apple ( Malus × domestica ), Japanese pear ( Pyrus pyrifolia ) and European pear ( Pyrus communis ), and two drupe fruits, peach ( Prunus persica ) and Japanese apricot ( Prunus mume ), to track their motion. Using 3D Gaussian Splatting, we successfully reconstructed 3D models of the fruits, and the landmark displacement could be measured with high accuracy, with R ² ≥ 0.98 when compared to manual recordings. We found a common spatial growth gradient in the longitudinal growth shared in the pomes and drupes of the Rosaceae; proximal (stem-end) regions exhibited more pronounced growth than the distal (stylar) end. An exception was found in European pear ‘Bartlett,’ which showed relatively vigorous growth in the distal region, explaining its distinct shape with expanded distal end. Transverse expansion varied far less than longitudinal expansion, with a possible association with initial fruit morphology. Inter-fruit growth variability peaked in the fastest-growing regions, particularly in the distal area of the European pear, highlighting the link between growth vigor and phenotypic variance. These results provide foundational insights into the developmental dynamics of both pome and drupe fruits of the Rosaceae family, contributing to the optimization of fruit size, shape, and uniformity.

Understanding fruit development patterns is essential, as they are directly linked to fruit size and shape, which ultimately determine final yield and quality. While conventional models describe fruit development based on growth parameters for the whole fruit, it remains unclear how tissue growth at different fruit portions is coordinated to promote overall fruit development. Therefore, in this study, we investigated the relationship between differences in developmental rates among fruit portions and fruit morphology in persimmon ( Diospyros kaki ), a species known for its high morphological diversity. Starting two weeks after blooming (WAB), surface landmarks were routinely drawn along the calyx-apex line on fruits of four persimmon cultivars with diverse shapes, and the landmark displacement was quantified every two weeks using 3D phenotyping. Consistent with previous studies, all cultivars exhibited active development in the regions near the calyx, with the greatest difference in growth rates between the calyx and apex occurring at 6–8 WAB. However, the extent of these spatial differences varied among cultivars. In elongated fruits, a gradual growth gradient was observed from the calyx toward the apex, with relatively high growth rates even near the apex. In contrast, in flattened fruits, growth was highly concentrated near the calyx, while development in other regions remained minimal. The findings of this study provide a foundation for future research on fruit shape regulation and the elucidation of physiological disorders in persimmon. Highlights: Spatially resolved 3D phenotyping quantified growth dynamics in persimmon fruit Growth rates varied along the fruit axis, with active growth near the calyx in all tested cultivars Growth gradients were linked to final fruit shape

Fruit quality represents the major constraints to consumer acceptance of new blueberry cultivars. However, breeding for fruit quality is challenging due to its complex inheritance and genotype × environment interaction. Despite previous efforts to detect quantitative trait loci (QTL) associated with fruit quality traits, most of the identified QTL explain only a fraction of the total variability or lack stability across multiple environments. In this study, we investigated multiple fruit quality traits and phenology-related traits of 187 diverse southern highbush blueberry germplasm over 2–4 years. Significant phenotypic variation across observation years was detected for most traits. Genome-wide association study (GWAS) failed to identify stable peaks supported by multiple observation years, indicating complex control of fruit-related traits. To elucidate factors contributing to phenotypic variation, the relationship between observed phenotypic values and the stability measure of these values was examined. Significant correlations were found between the variation of phenology-related traits and the stability of fruit-related traits; it was found that early blooming and ripening accessions tended to exhibit variable firmness over the years. Additionally, size variability was influenced by the fruit size itself: accessions producing smaller fruit tended to show more variation in size over the years. Furthermore, GWAS conducted on the stability indices identified novel marker–trait associations that were not detected using normalized phenotypic values only, and their effects on fruit-related traits were similarly dependent on environment (observation year). Collectively, these findings deepen our understanding of variability in fruit-related traits and provide insights into their genetic control, thereby advancing breeding for superior cultivars with stable phenotypic performance.