Artificial Intelligence, or AI, is becoming increasingly prevalent in a wide variety of scientific fields. The recent progress in deep neural networks, or simply “deep learning”, in particular, has been remarkable, which is leading to the development of valuable technologies for various biological applications. Nevertheless, the application of these AI technologies in the field of horticultural science has not progressed. In the horticultural field, there is often a tendency to compare/compete with the accuracy (or ability) of AI and experts with long experience or existing systems, which may prevent the widespread adoption of AI technology in horticulture. The current evolving AI technologies go beyond mere prediction and diagnosis; through the application of “explainable AI” techniques, which can allow novel interpretations from a scientific perspective. It extends not only to conventional image analysis, but also to various data formats, including genetic sequences or any other numerical array data. Here, we introduce recent developments and evolution of AI technologies, mainly deep learning, in plant biology and horticultural science. Recent applications of convolutional neural networks (CNN) in image analyses allowed prediction/diagnosis of various invisible traits. Further combined application of explainable AI techniques and physiological assessments may spot features that potentially reveal the mechanisms of objective traits from a novel viewpoint. We also examined prospects for new applications of deep learning in horticultural science, such as for genetic factors or with new algorithms represented by Transformer.

Malformed flowers similar to super-double-flowers were observed in potted ‘Cherie’ carnation (Dianthus caryophyllus L.) plants. In the malformed flower (mlf) lines, most flowers were malformed at 15°C, but not at 20°C. Thus, we hypothesized that the malformation was due to a mutation associated with morphological responses to temperature. In this study, RNA-sequencing analysis of young flower buds and whole-genome re-sequencing of leaves were performed using wild-type (WT) and mlf plants to identify malformation-related candidate genes. The RNA-sequencing analysis revealed 691 significant differentially expressed genes (DEGs) between WT flower buds at 15 or 20°C and mlf flower buds at 15°C. The Gene Ontology (GO) analysis indicated that metal ion binding, transmembrane transport, and anaphase-promoting complex enriched GO terms in mlf, whereas translation and ribosome enriched GO in terms of WT. The Kyoto Encyclopedia of Genes and Genomes analysis revealed an increase in the expression of 9-cis-epoxycarotenoid dioxygenase (NCED), Pyrabactin Resistance 1-Like (PYL), and Calmodulin (CAM), but a decrease in the expression of Histone H4, in mlf. The fragments per kilobase per million reads (FPKM) values were used to select candidate malformation-related DEGs. Transcription factor genes, including WUSCHEL (WUS) and STERILE APETALA, were upregulated in mlf, whereas PISTILLATA-like protein, MADS-box protein CMB2, and F-box UNUSUAL FLORAL ORGANS were downregulated. Heat Shock Cognate 70 kDa (HSC70) and Temperature-induced lipocalin-1 were upregulated in mlf, but genes encoding histones and ribosomal proteins were downregulated. Moreover, NCED1, PYL8 and 9, and cytokinin-related genes were upregulated in mlf. Using whole-genome re-sequencing data, sequence variants were detected in the upstream regions and exons of WUS, HSC70-1 and 2, CAM7, and ribosomal protein-encoding genes. Furthermore, examination of the F₁ progeny derived from WT and mlf crosses with cultivars producing fertile pollen revealed a significant difference in the proportion of malformed flower phenotypes between WT and mlf regardless of temperature, suggesting that the malformed flower phenotypes of mlf can be inherited. Candidate genes associated with the temperature-dependent super-double-flower phenotypes were examined.

Dahlia (Dahlia variabilis) flower colors are diverse and are determined by the accumulation of flavonoids. Cultivars with dark red flowers accumulate more anthocyanins in their petals. Flower color changes such as color fading often occur in some cultivars. In this study, low minimum temperature regulated flower color fading and flavonoid synthesis in dahlia ‘Nessho’ were investigated. The pigment contents and expression levels of flavonoid biosynthesis genes were investigated in detail under several growing environments in which color fading occurs. Flavones accumulate more in color-faded orange flowers than in dark red ray florets. The expression analysis of the anthocyanin synthesis pathway genes indicated that the upregulation of flavone synthase (DvFNS) gene expression correlated with the high accumulation of flavones in color-faded petals. DvFNS expression was also detected in young leaves, and the expression level was higher in winter than in summer. Seasonal changes in DvFNS expression in young leaves significantly correlated with color fading in petals. The change in DvFNS expression in young unexpanded leaves of relatively high-sensitive plants was significantly higher than that of low-sensitive plants before and after treatment under inductive conditions. In conclusion, low-temperature-inducible changes in the flavonoid accumulation in petals was suggested to reflect a change in DvFNS expression occurring in the meristem prior to flower bud formation. This temporal DvFNS expression in young unexpanded leaves of ‘Nessho’ dahlia could be an insight for the selection and breeding of non-color fading plants.

The selection of appropriate pollinizer cultivars is essential for stable fruit production of Japanese apricot because this species has many self-incompatible cultivars. In this study, the chilling responses of flower buds during endodormancy and the heat responses of flower buds during ecodormancy were quantified as development rates (DVRs) in ‘Kotsubu-nanko’, ‘Hakuo’, and ‘NK14’, three pollinizer cultivars of the leading cultivar ‘Nanko’ in Wakayama Prefecture. Approximating functions of DVRs for both endodormancy release and ecodormancy release were obtained on the basis of chilling and heat exposure tests on young trees with various combinations of temperatures and periods. These analyses demonstrated that temperatures over 15°C were only effective for endodormancy release of ‘Hakuo’ buds. Compared with the buds of ‘Kotsubu-nanko’ and ‘Hakuo’, those of ‘NK14’ were less sensitive to 15–20°C during the ecodormancy stage. Blooming date prediction models for these cultivars were constructed using the DVR values. Then, the applicability of the three cultivars as pollinizers for ‘Nanko’ was evaluated based on whether their predicted blooming times overlapped with that of ‘Nanko’. The models were optimized by adjusting the threshold of blooming percentages and initial points of heat accumulation during ecodormancy release to achieve the smallest differences between predicted and observed blooming dates (root mean squared error = 3.72–5.90). Simulations under different temperatures revealed the most suitable pollinizer cultivar for ‘Nanko’ going forward. Our predictions indicate that, in the simulated warmer conditions, the blooming date of ‘Kotsubu-nanko’ will be delayed 10 or more days compared with that of ‘Nanko’, and larger differences between the blooming dates of ‘Hakuo’ and ‘Nanko’ will occur under lower and higher temperatures. The blooming period of ‘NK14’ was predicted to remain stably synchronized with that of ‘Nanko’ under a range of simulated warmer and colder temperature conditions. These results showed that ‘NK14’ is an appropriate pollinizer for stable fruit production of ‘Nanko’ in the future, and highlight the importance of blooming time assessments based on the temperature responses of flower buds.

Many horticultural trees, including apple (Malus × domestica Borkh.), exhibit alternative fruit bearing. Despite many observations suggesting that bearing tendency is a genetic trait, genetic factors related to bearing tendency have rarely been investigated, as most previous studies have focused on comparing phytohormone and gene expression levels between ON- and OFF-years within a cultivar. Therefore, to gain insights into the genetic factors related to the strength of biennial bearing, we compared gene expression levels between the regular bearing cultivar ‘McIntosh’ and the alternative bearing cultivar ‘Wijcik’ (the bud mutant of ‘McIntosh’). Over a three-year period, the flowering rate of ‘McIntosh’ remained relatively stable, ranging from 89% to 95%, whereas that of ‘Wijcik’ showed significant variation from 83% to 24% before returning to 89%. Comparative transcriptome analysis of terminal buds during the floral induction period revealed 7,200 genes that were differentially expressed between the two cultivars, with 1,423 genes showing annual variation only in ‘Wijcik’. Gene Ontology enrichment analysis revealed upregulation of many genes related to photosynthesis and response to high light intensity in the OFF-year in ‘Wijcik’. Moreover, the relative expression levels of flowering repressors, such as MdTFL1-1, MdTFL1-2, MdRAP2.7, and MdJMJ13, at 75 days after full bloom were significantly higher in the ON-year than in the OFF-year for ‘Wijcik’. Our findings suggest that the high biennial bearing tendency of columnar apples may be attributed, in part, to greater annual variation in the expression of MdTFL1 and light-related genes.

In the production of seedless table grapes, it is conventional to use plant growth regulators including gibberellins. Little is known about the differences in aroma volatiles between seedless-treated grapes and nontreated (seeded) grapes. Therefore, in this study, the aroma volatile profiles of seedless-treated and nontreated ‘Shine Muscat’ grape berries during ripening were compared using gas chromatography-mass spectrometry. Measurements of volatiles during ripening showed 202 peaks in the seedless-treated and nontreated whole grape berries. According to two-way analysis of variance, the number of volatiles with differences between seedless-treated and nontreated berries and/or between ripening stages was 123, whereas those with no differences between treatments and between ripening stages was 79. Two-way hierarchical clustering analysis for the 123 volatiles showed that seedless-treated berries at the early ripening stages were separated from the other berries, and the seedless-treated and nontreated berries at the post-ripening stage were classified into the same cluster. At the early ripening stage, more lipoxygenase-pathway volatiles were produced in the seedless-treated berries than in the non-treated ones. Linalool compounds increased in both seedless-treated and nontreated berries with ripening. Gene expression profile comparisons using principal component analysis of RNA-sequencing data showed that the seedless-treated berries ripened earlier than the nontreated berries at the early ripening stage. The number of differentially expressed genes in the seedless-treated berries decreased during ripening. Using weighted gene co-expression network analyses, 12 modules and 24 modules were detected in berry skin and flesh, respectively. The correlation analysis revealed that 33 volatiles correlated with four modules in the skin and 50 volatiles correlated with nine modules in the flesh. Most of the volatiles correlated with these modules were those that showed significant differences between treatments and/or ripening stages by two-way analysis of variance. The differences in the aroma volatile profiles between seedless-treated and nontreated berries decreased as harvest was delayed, suggesting that delaying the harvest may make it possible to bring the aroma of seedless-treated ‘Shine Muscat’ berries closer to the original aroma of the seeded berries.

To develop novel humidification technology for strawberry production to achieve higher yields and improve fruit quality, four Japanese June-bearing strawberry cultivars were grown in a greenhouse with or without humidification treatment (HT) based on vapor pressure deficit (VPD). HT reduced VPD from transplanting to March, but did not affect the VPD condition from April to May. Soon after transplanting, HT enhanced plant growth and the daily leaf-emergence rate, and significantly advanced flower-bud emergence and first-fruit harvest for the first inflorescence for ‘Koiminori’, ‘Kaorino’, and ‘Saga i9’. However, HT significantly delayed flower-bud differentiation and first-fruit harvest of the second inflorescence of ‘Kaorino’ and ‘Yumenoka’. HT significantly increased the total weight of marketable fruit for ‘Koiminori’, ‘Kaorino’, and ‘Saga i9’. In addition, HT significantly increased the total fresh weight of marketable fruit harvested until December for ‘Koiminori’ and ‘Saga i9’. HT did not significantly affect the firmness of fruit skin (FFS), soluble-solid content (SSC), fruit acidity (FA), or SSC/acidity of ‘Koiminori’, ‘Kaorino’, and ‘Yumenoka’.

In Japan, greenhouse cucumber production is generally conducted as either a long-term, one cropping system or a short-term, two cropping system; short-term cultivation requires time for crop replacement, which may result in lower yields. It is important to increase plants’ intercepted light to increase yield, which requires maintaining a high leaf area index. In this study, a new training method (separating method), in which the sink and source are separated, was developed for the short-term cultivation of cucumber (Cucumis sativus L.) under greenhouse conditions. In the separating method, the main stem had only leaves and the lateral branch had only fruits. The main stem was trained vertically and pinched when it reached a 1.8 m high training wire, while the lateral branch continued to grow horizontally at approximately 40 cm above the floor. A hydroponic system was used from October 2020 to February 2021. During this period, we assessed the yield productivity of the new training method and compared it with that of the lowering method (training method for growing the main stem without pinching) based on yield components. We observed that the fresh yield of the separating method was lower than that of the lowering method owing to a decrease in the number of fruits as result of fruit picking from the main stem. Conversely, total dry matter under the separating method was higher than that under the lowering method, and this could be attributed to the greater increase in leaf area index under the separating method. In terms of photosynthetic rate, values for the upper leaves were lower than those for the lowering method in the separating method approximately one month after pinching. These results suggested that the separating method could produce yields comparable to those of the lowering method in short-term cultivation. In addition, this method may contribute to mechanical harvesting because the fruit is always in a fixed location.

Tomato fruits under salt stress exhibit growth inhibition, resulting in increased fruit firmness and decreased fruit size. In angiosperms, the ovary becomes a fruit upon pollination and the fruit develops through fruit formation and maturation. Since fruit size does not change after a green fruit reaches its maximum size, it is important to analyze the early stages of fruit development. Therefore, in this study, we focused on the control and properties of cell walls during the initial fruit formation process that determines tomato (Solanum lycopersicum cv. ‘Micro-Tom’) fruit size. As a result of analyzing mechanical properties, an increase in fruit hardness under salt stress conditions (160 mM NaCl) was observed in early tomato fruits during the initial fruit formation process. Furthermore, by observing changes in the distribution of cell wall polysaccharides, we found that during early fruit development including 5 DPA, which is a time of tissue expansion, the pericarp hardens due to the accumulation of cellulose. Meanwhile, Xyloglucan endotransglucosylase/hydrolase (XTH) and expansin, which are cell wall loosening enzymes, do not increase. Our results showed that the increase in fruit hardness under salt stress conditions occurred in early tomato fruits during the initial fruit formation process, and the reduction in fruit size due to salt stress was due to changes in cell wall properties during the early fruit formation process.

We analyzed FLOWERING LOCUS T (FT) orthologs to elucidate the regulatory mechanisms of flowering in carnations. There are six FT candidate genes in the carnation genome. Phylogenetic analysis and amino acid alignment suggested that four genes were FT-like genes involved in promoting flowering. Of these, Dca19666.1 had the all conserved amino acids necessary for florigen activity. Therefore, this gene was designated as DcFT1 and used for further analysis. DcFT1 transcript levels increased as the plants developed from the vegetative to the reproductive growth stages. DcFT1 was unevenly expressed in the leaves, and was more abundant in young leaves. A splice variant was identified; however, its relationship with flowering could not be determined. The early blooming cultivar showed an early elevation of DcFT1 compared to the late-blooming cultivar. Treatment to accelerate flowering by cooling at the end of the day also accelerated the increase in DcFT1 expression. The cloned DcFT1 was overexpressed in Arabidopsis for functional characterization. The resulting transgenic plants began to bolt earlier than the control plants transformed with the empty vector. qRT-PCR analysis of the DcFT1-overexpressor showed that several genes related to flowering were upregulated. These results suggest that DcFT1 is an important regulator of carnation flowering.

Chrysanthemums are among the most popular and economically valuable ornamental plants in the world. Herein, we investigated the effects of diamine putrescine (Put), a polyamine involved in plant cell differentiation and stress resistance, and 1-naphthaleneacetic acid (NAA), an auxin widely considered essential for root initiation, on the development of adventitious roots (ARs) and root systems in chrysanthemum cuttings. We also determined the optimal combination of concentrations of these treatments for AR developmental growth. When the cuttings were cultured with different concentrations of Put solutions, clear increases in AR length were recorded, although the number of ARs was unaffected. In addition, the number of lateral roots arising from ARs was increased by Put application. Treatment with 5-mg·L⁻¹ NAA in the first week followed by 100-mg·L⁻¹ Put in the next three weeks considerably increased the AR length compared with the use of each reagent alone. With the sequential application of 5-mg·L⁻¹ NAA and 200-mg·L⁻¹ Put, the fresh weight of the total roots that developed from the cuttings was increased by 6.05-fold compared with that without treatment. The superoxide dismutase activity and superoxide anion production rate were reduced in roots developed from Put-treated chrysanthemum cuttings. These results may indicate that Put application affected AR elongation by altering the quantitative balance among reactive oxygen species.