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Frequent polyploidization events in plants have led to the establishment of many lineage-specific traits representing each species. Little is known about the genetic bases for these specific traits in polyploids, presumably due to plant genomic complexity and their difficulties of applying genetic approaches. Hexaploid Oriental persimmon (Diospyros kaki) has evolved specific fruit characters, including wide variations in fruit shapes and astringency. In this study, using whole-genome diploidized/quantitative genotypes from ddRAD-Seq data of 173 persimmon cultivars, we examined their population structures and potential correlations between their structural transitions and variations in nine fruit traits. The population structures of persimmon cultivars were highly randomized and not substantially correlated with the representative fruit traits focused on in this study, except for fruit astringency. With genome-wide association analytic tools considering polyploid alleles, we identified the loci associated with the nine fruit traits; we mainly focused on fruit-shape variations, which have been numerically characterized by principal component analysis of elliptic Fourier descriptors. The genomic regions that putatively underwent selective sweep exhibited no overlap with the loci associated with these persimmon-specific fruit traits. These insights will contribute to understanding of the genetic mechanisms by which fruit traits are independently established, possibly due to polyploidization events.

Citrus peel degreening is promoted by low temperature via modulation of multiple genes associated with chlorophyll degradation, carotenoid biosynthesis, photosystem disassembly, phytohormones, and transcription factors without involving ethylene signalling., Peel degreening is an important aspect of fruit ripening in many citrus fruit, and previous studies have shown that it can be advanced by ethylene treatment or by low-temperature storage. However, the important regulators and pathways involved in natural peel degreening remain largely unknown. To determine how natural peel degreening is regulated in lemon fruit (Citrus limon), we studied transcriptome and physiochemical changes in the flavedo in response to ethylene treatment and low temperatures. Treatment with ethylene induced rapid peel degreening, which was strongly inhibited by the ethylene antagonist, 1-methylcyclopropene (1-MCP). Compared with 25 ºC, moderately low storage temperatures of 5–20 °C also triggered peel degreening. Surprisingly, repeated 1-MCP treatments failed to inhibit the peel degreening induced by low temperature. Transcriptome analysis revealed that low temperature and ethylene independently regulated genes associated with chlorophyll degradation, carotenoid metabolism, photosystem proteins, phytohormone biosynthesis and signalling, and transcription factors. Peel degreening of fruit on trees occurred in association with drops in ambient temperature, and it coincided with the differential expression of low temperature-regulated genes. In contrast, genes that were uniquely regulated by ethylene showed no significant expression changes during on-tree peel degreening. Based on these findings, we hypothesize that low temperature plays a prominent role in regulating natural peel degreening independently of ethylene in citrus fruit.

In contrast to the progress in the research on physiological disorders relating to shelf life in fruit crops, it has been difficult to non-destructively predict their occurrence. Recent high-tech instruments have gradually enabled non-destructive predictions for various disorders in some crops, while there are still issues in terms of efficiency and costs. Here, we propose application of a deep neural network (or simply deep learning) to simple RGB images to predict a severe fruit disorder in persimmon, rapid over-softening. With 1,080 RGB images of ‘Soshu’ persimmon fruits, three convolutional neural networks (CNN) were examined to predict rapid over-softened fruits with a binary classification and the date to fruit softening. All of the examined CNN models worked successfully for binary classification of the rapid over-softened fruits and the controls with > 80% accuracy using multiple criteria. Furthermore, the prediction values (or confidence) in the binary classification were correlated to the date to fruit softening. Although the features for classification by deep learning have been thought to be in a black box by conventional standards, recent feature visualization methods (or “explainable” deep learning) has allowed identification of the relevant regions in the original images. We applied Grad-CAM, Guided backpropagation, and layer-wise relevance propagation (LRP), to find early symptoms for CNNs classification of rapid over-softened fruits. The focus on the relevant regions tended to be on color unevenness on the surface of the fruit, especially in the peripheral regions. These results suggest that deep learning frameworks could potentially provide new insights into early physiological symptoms of which researchers are unaware.

In the evolutionary paths of plants, variations of the cis-regulatory elements (CREs) resulting in expression diversification have played a central role in driving the establishment of lineage-specific traits. However, it is difficult to predict expression behaviors from the CRE patterns to properly harness them, mainly because the biological processes are complex. In this study, we used cistrome datasets and explainable convolutional neural network (CNN) frameworks to predict genome-wide expression patterns in tomato fruits from the DNA sequences in gene regulatory regions. By fixing the effects of trans-elements using single cell-type spatiotemporal transcriptome data for the response variables, we developed a prediction model of a key expression pattern for the initiation of tomato fruit ripening. Feature visualization of the CNNs identified nucleotide residues critical to the objective expression pattern in each gene and their effects, were validated experimentally in ripening tomato fruits. This cis-decoding framework will not only contribute to understanding the regulatory networks derived from CREs and transcription factor interactions, but also provide a flexible way of designing alleles with optimized expression.

Kiwifruit exhibit a peculiar ripening pattern, as extensive softening is known to occur in the absence of any detectable ethylene. We previously demonstrated that this softening is regulated by low temperature independent of ethylene. However, there are no reports that provide comparisons of the ripening patterns among different kiwifruit cultivars at various storage temperatures. The purpose of this study was to compare the ripening responses and associated gene expression in ‘Sanuki Gold’ (Actinidia chinensis var. chinensis) and ‘Hayward’ ((Actinidia chinensis var. deliciosa) fruit, two kiwifruit cultivars differing in on–vine maturity dates and postharvest storability, during storage at 5 °C, 10 °C, 15 °C and 22 °C. Fruit softening, soluble solids concentration (SSC) increase and reduction of titratable acidity (TA) occurred in the absence of any detectable ethylene, and treatment with an ethylene inhibitor 1–methylcyclopropene (1–MCP) failed to suppress the changes, suggesting that they were independent of ethylene. ‘Sanuki Gold’ fruit showed a higher sensitivity to low temperature supported by accelerated fruit softening and TA reduction, and induction of several genes such as AcACO3, AcXET2, AcPG, AcEXP1, AcPMEi, AcGA2ox1, AcMADS2, AcNAC5 and AcbZIP2 at 5 °C, 10 °C and 15 °C within 28 d. By contrast, ‘Hayward’ fruit exhibited a lower sensitivity to low temperature as accelerated softening, TA reduction and induction of most ripening–associated genes were recorded only at 5 °C and 10 °C. These differences in sensitivity to low temperature, between ‘Sanuki Gold’ and ‘Hayward’ fruit, would account for the dissimilarities observed in on–vine maturity dates and postharvest storability.

Ethylene is a gaseous phytohormone involved in various physiological processes, including fruit ripening, senescence, root hair development and stress responses. Recent genomics studies have suggested that most homologous genes of ethylene biosynthesis and signaling are conserved from algae to angiosperms, whereas the function and biosynthesis of ethylene remain unknown in basal plants. Here, we examined the physiological effects of ethylene, an ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC) and an inhibitor of ethylene perception, silver thiosulfate (STS), in a basal land plant, Marchantia polymorpha. M. polymorpha plants biosynthesized ethylene, and treatment with high concentrations of ACC slightly promoted ethylene production. ACC remarkably suppressed the growth of thalli (vegetative organs) and rhizoids (root-hair-like cells), whereas exogenous ethylene slightly promoted thallus growth. STS suppressed thallus growth and induced ectopic rhizoid formation on the dorsal surface of thalli. Thus, ACC and ethylene have different effects on the vegetative growth of M. polymorpha. We generated single and double mutants of ACC synthase-like (ACSL) genes, MpACSL1 and MpACSL2. The mutants did not show obvious defects in thallus growth, ACC content and ethylene production, indicating that MpACSL genes are not essential for the vegetative growth and biosynthesis of ACC and ethylene. Gene expression analysis suggested the involvement of MpACSL1 and MpACSL2 in stress responses. Collectively, our results imply ethylene-independent function of ACC and the absence of ACC-mediated ethylene biosynthesis in M. polymorpha.

Sex expression in plants is often flexible and contributes to the maintenance of genetic diversity within a species. In diploid persimmons (the genus Diospyros), the sexuality is controlled by the Y chromosome-encoded small-RNA gene, OGI, and its autosomal counterpart, MeGI. Hexaploid Oriental persimmon (Diospyros kaki) evolved more flexible sex expression, where genetically male individuals carrying OGI can produce both male and female flowers (monoecy). This is due to (semi-)inactivation of OGI by the Kali-SINE retrotransposon insertion on the promoter region and the resultant DNA methylations. Instead, flower sex determination in Oriental persimmon is also dependent on DNA methylation states of MeGI. Here, we focused on a cultivar, Kumemaru, which shows stable male flower production. Our results demonstrated that cv. Kumemaru carries OGI with Kali-SINE, which was highly methylated as well as in other monoecious cultivars; nevertheless, OGI gene could have a basal expression level. Transcriptomic analysis between cv. Kumemaru and 14 cultivars that predominantly produce female flowers showed differentially expressed genes (DEGs) specific to cv. Kumemaru, which is mainly involved in stress responses. Co-expression gene networks focusing on the DEGs also suggested the involvement of stress signals, mainly via gibberellin (GA), salicylic acid (SA), and especially jasmonic acid (JA) signal pathways. We also identified potential regulators of this co-expression module, represented by the TCP4 transcription factor. Furthermore, we attempted to identify cv. Kumemaru-specific transcript polymorphisms potentially contributing to derepressed OGI expression by cataloging subsequences (k-mers) in the transcriptomic reads from cv. Kumemaru and the other 14 female cultivars. Overall, although the direct genetic factor to activate OGI remains to be solved, our results implied the involvement of stress signals in the release of silenced OGI and the resultant continuous male production.

Aluminum (Al)-tolerant tobacco cell line ALT301 derived from SL (wild-type) hardly exhibits Al-triggered reactive oxygen species (ROS) compared with SL. Molecular mechanism leading to this phenotype was investigated comparatively with SL. Under normal growth condition, metabolome data suggested the activation of glycolysis and lactate fermentation but the repression of the tricarboxylic acid (TCA) cycle in ALT301, namely aerobic fermentation, which seemed to be transcriptionally controlled partly by higher expression of genes encoding lactate dehydrogenase and pyruvate dehydrogenase kinase. Microarray and gene ontology analyses revealed the upregulation of the gene encoding related to APETALA2.3 (RAP2.3)-like protein, one of the group VII ethylene response factors (ERFVIIs), in ALT301. ERFVII transcription factors are known to be key regulators for hypoxia response that promotes substrate-level ATP production by glycolysis and fermentation. ERFVIIs are degraded under normoxia by the N-end rule pathway of proteolysis depending on both oxygen and nitric oxide (NO), and NO is produced mainly by nitrate reductase (NR) in plants. In ALT301, levels of the NR gene expression (NIA2), NR activity and NO production were all lower compared with SL. Consistently, the known effects of NO on respiratory pathways were also repressed in ALT301. Under Al-treatment condition, NO level increased in both lines but was lower in ALT301. These results suggest that the upregulation of the RAP2.3-like gene and the downregulation of the NIA2 gene and resultant NO depletion in ALT301 coordinately enhance aerobic fermentation, which seems to be related to a higher capacity to prevent ROS production in mitochondria under Al stress.

Sexuality is one of the fundamental mechanisms that work towards maintaining genetic diversity within a species. In diploid persimmons (Diospyros spp.), separated sexuality, the presence of separate male and female individuals (dioecy), is controlled by the Y chromosome-encoded small-RNA gene, OGI. On the other hand, sexuality in hexaploid Oriental persimmon (Diospyros kaki) is more plastic, with OGI-bearing genetically male individuals, able to produce both male and female flowers (monoecy). This is thought to be linked to the partial inactivation of OGI by a retrotransposon insertion, resulting in DNA methylation of the OGI promoter region. To identify the genetic factors regulating branch sexual conversion, genome-wide correlation/association analyses were conducted using ddRAD-Seq data from an F1 segregating population, and using both quantitative and diploidized genotypes, respectively. We found that allelic ratio at the Y-chromosomal region, including OGI, was correlated with male conversion based on quantitative genotypes, suggesting that OGI can be activated in cis in a dosage-dependent manner. Genome-wide association analysis based on diploidized genotypes, normalized for the effect of OGI allele dosage, detected three fundamental loci associated with male conversion. These loci underlie candidate genes, which could potentially act epigenetically for the activation of OGI expression.

Kiwifruit is considered a climacteric fruit since exogenous ethylene induces ripening-associated changes. However, we previously reported that low temperature modulated ripening in kiwifruit since ripening occurred faster during storage at 5°C compared to 20°C, in the absence of any detectable ethylene. It is therefore not clear which temperature is suitable for long-term storage of kiwifruit. The purpose of this study was to determine the optimum temperature for long-term storage, and analysis of ripening-related genes in 'Rainbow Red' kiwifruit. Kiwifruit were harvested at commercial maturity, and stored at either 0, 2, 5 or 22°C in ethylene-free chambers. During storage, incidence of fruit deterioration and changes in fruit firmness, soluble solids concentration (SSC) and titratable acidity (TA) were monitored at 4-week intervals. Real-time PCR was also conducted to analyze the changes in expression of selected ripening-related genes. Incidence of fruit fast senescence and deterioration was high at 22°C, so kiwifruit could only be stored for a maximum of 8 weeks. Nevertheless, healthy fruit at 22°C remained firm and maintained high TA for 8 weeks. The incidence of ethylene-producing fruit, and consequent fast senescence, was greatly reduced at 5°C, while it was completely suppressed at 0 and 2°C. Fruit at 5°C decreased in firmness and TA faster, attaining eating-ripe quality within 8 weeks. At 2°C, fruit decreased in firmness and TA gradually, achieving eating-ripe quality after 12 weeks. Conversely, fruit at 0°C maintained higher firmness and TA, and did not attain eating-ripe quality even after 12 weeks. SSC increased at all storage temperatures, although the lowest levels were observed in fruit at 0°C. Real-Time PCR analysis revealed that cell-wall-modifying genes (AcPG, AcPL2, AcEXP1 and AcXET2) and carbohydrate-metabolism-associated genes (Acβ-AMY1 and Acβ-AMY2) were markedly induced in fruit at 5°C. Overall, these results indicate that 0°C is the suitable temperature for long-term storage of kiwifruit, while 2°C is suitable for medium-term storage. For short-term storage, 5°C can be recommended.

Aluminum (Al)-tolerant tobacco cell line ALT301 derived from SL (wild-type) hardly exhibits Al-triggered reactive oxygen species (ROS) compared with SL. Molecular mechanism leading to this phenotype was investigated comparatively with SL. Under normal growth condition, metabolome data suggested the activation of glycolysis and lactate fermentation but the repression of the tricarboxylic acid (TCA) cycle in ALT301, namely aerobic fermentation, which seemed to be transcriptionally controlled partly by higher expression of genes encoding lactate dehydrogenase and pyruvate dehydrogenase kinase. Microarray and gene ontology analyses revealed the upregulation of the gene encoding related to APETALA2.3 (RAP2.3)-like protein, one of the group VII ethylene response factors (ERFVIIs), in ALT301. ERFVII transcription factors are known to be key regulators for hypoxia response that promotes substrate-level ATP production by glycolysis and fermentation. ERFVIIs are degraded under normoxia by the N-end rule pathway of proteolysis depending on both oxygen and nitric oxide (NO), and NO is produced mainly by nitrate reductase (NR) in plants. In ALT301, levels of the NR gene expression (NIA2), NR activity and NO production were all lower compared with SL. Consistently, the known effects of NO on respiratory pathways were also repressed in ALT301. Under Al-treatment condition, NO level increased in both lines but was lower in ALT301. These results suggest that the upregulation of the RAP2.3-like gene and the downregulation of the NIA2 gene and resultant NO depletion in ALT301 coordinately enhance aerobic fermentation, which seems to be related to a higher capacity to prevent ROS production in mitochondria under Al stress.

Peel degreening is an important aspect of fruit ripening in many citrus fruit, and earlier studies have shown that it can be advanced either by ethylene treatment or during low temperature storage. However, the important regulators and pathways involved in natural peel degreening remain largely unknown. To understand how natural peel degreening is regulated in lemon (Citrus limon L.) fruit, flavedo transcriptome and physiochemical changes in response to either ethylene treatment or low temperature were studied. Ethylene treatment induced rapid peel degreening which was strongly inhibited by the ethylene antagonist, 1-methylcyclopropene (1-MCP). Compared with 25°C, moderately low temperatures (5°C, 10°C, 15°C and 20°C) also triggered peel degreening. Surprisingly, repeated 1-MCP treatments failed to inhibit the peel degreening induced by low temperature. Transcriptome analysis revealed that low temperature and ethylene independently regulated genes associated with chlorophyll degradation, carotenoid metabolism, photosystem proteins, phytohormone biosynthesis and signalling, and transcription factors. On-tree peel degreening occurred along with environmental temperature drops, and it coincided with the differential expression of low temperature-regulated genes. In contrast, genes that were uniquely regulated by ethylene showed no significant expression changes during on-tree peel degreening. Based on these findings, we hypothesize that low temperature plays a prominent role in regulating natural peel degreening independently of ethylene in citrus fruit.HighlightCitrus peel degreening is promoted by low temperature via modulation of multiple genes associated with chlorophyll degradation, carotenoid biosynthesis, photosystem disassembly, phytohormones and transcription factors without involving ethylene signalling.

A 57-year-old man with high-risk myelodysplastic syndrome underwent umbilical cord blood transplantation. He began receiving steroids on day 14 for acute graft-versus-host disease, and experienced dizziness on day 75 during gradual dose reduction. Multiple hemorrhages were observed in the cerebrum, cerebellum, and brainstem. His bleeding increased, and he underwent a brain biopsy on day 91. Subsequently, he was diagnosed with central nervous system vasculitis (CNSV) on the basis of the observed aggregation of mature CD3

During ripening, European pear (Pyrus communis L. cv. ‘La France’) fruit undergo dramatic softening in response to increased ethylene production, whereas Chinese pear (Pyrus bretschneideri Rehd. cv. ‘Yali’) fruit remain firm, despite producing large amounts of ethylene. The molecular basis of this differential softening behavior is not well understood. In this study, we combined a yeast-based signal sequence trap (YSST) and macroarray gene expression analysis to identify putative genes encoding secreted proteins that control pear fruit softening. We identified 22 cDNAs annotated as encoding proteins with diverse cell wall-associated functions that were up- or down-regulated during fruit ripening in ‘La France’. Gene expression analysis in fruit that were treated with the ethylene perception inhibitor 1-methylcyclopropene (1-MCP) at 4 d after the onset of ripening revealed that 16 of the targeted genes are ethylene-regulated, while the others appear to be ethylene independent. Comparative gene expression analyses of ‘La France’ and ‘Yali’ fruit during ripening suggested that four ethylene-regulated cDNAs encoding cell wall modifying proteins, contig 2 (polygalacturonase 3), contig 15 (expansin), contig 19 (expansin) and contig 55 (pectate lyase) contribute to the different softening behaviors of ‘La France’ and ‘Yali’ fruit. Additionally, one ethylene-independent cell wall related gene, contig 36 (expansin), and three genes encoding proteins of unknown function, contigs 1, 13 and contig 75 showed differential expression between ‘La France’ and ‘Yali’ fruit during ripening. The results presented herein represent promising candidates for future functional analysis and elucidation of softening mechanisms.

European pear fruit (Pyrus communis L.) respond to low temperature (LT) treatments by inducing ethylene production and fruit ripening. However, it is unclear to what extent this response is the result of LT alone or LT-induced ethylene production. In this study, we followed the physiological and molecular responses of ‘Passe Crassane’ pears to LT and the ethylene analogue, propylene, at various storage temperatures. Fruit at 20 °C treated with propylene softened to eating firmness (13–21 N) within 9–10 d, with little changes in endogenous ethylene production (

Parthenocarpy, a process in which fruit set occurs without fertilization, leads to the production of seedless fruit. A number of floral homeotic mutants with abnormal stamen development exhibit parthenocarpic fruit set. Flower development is thought to repress ovary growth before anthesis. However, the mechanism of parthenocarpic fruit development caused by aberrant flower formation is poorly understood. To investigate the molecular mechanism of parthenocarpic fruit development in floral homeotic mutants, we performed functional analysis of Tomato APETALA3 (TAP3) by loss-of-function approaches. Organ-specific promoter was used to induce organ-specific loss of function in stamen and ovary/fruit. We observed increased cell expansion in tap3 mutants and TAP3-RNAi lines during parthenocarpic fruit growth. These were predominantly accompanied by the up-regulation of GA biosynthesis genes, including SlGA20ox1, SlGA20ox2, and SlGA20ox3, as well as reduced expression of the GA-inactivating gene SlGA2ox1 and the auxin signaling gene SlARF7 involved in a crosstalk between GA and auxin. These transcriptional profiles are in agreement with the GA levels in these lines. These results suggest that stamen development negatively regulates fruit set by repressing the GA biosynthesis.

We investigated the physiological effects of short-term postharvest near infrared (NIR) radiation on relative transpiration rates, stomatal apertures, and reactive oxygen species (ROS) levels in guard cells on excised young lettuce leaves and on transpiration of leaf lettuce at commercial maturity. When the young leaves were radiated by NIR of wavelengths longer than 850 nm at 100 μmol m−2 s−1 for short duration (10–60) min, relative transpiration rates during subsequent storage were reduced, but not by visible light radiation and by longer radiation (180 min) of NIR. The reduction in transpiration rates by the short-term NIR radiation was greater at 10 °C than at 25 °C under both dark and light conditions during subsequent storage. The short-term NIR radiation enhanced stomatal closure and ROS accumulation in guard cells of young lettuce leaves. These results indicate that the suppression of transpiration by short-term NIR radiation is likely to be mediated through stomatal closure due to NIR-induced ROS accumulation. The reduction of transpiration by short-term NIR radiation was obtained not only in excised young leaves but also in leaf lettuce at commercial maturity, resulting in keeping freshness. The short-term NIR radiation could be an additional means to extend shelf life of leaf vegetables.

Double flowers induced by virus-induced gene silencing (VIGS) of two C-class MADS-box genes, pMADS3 and FBP6, were investigated in four cultivars of Petunia hybrida. In flowers induced by either pMADS3-VIGS or FBP6-VIGS, only small changes in commercial appearance were recognized regardless of cultivar, whereas in those induced by pMADS3/FBP6-VIGS, complete conversion of stamens into petaloid tissues and marked enlargement of upper limb-like tissues were observed, resulting in a decorative appearance in all the four cultivars. In whorl 4, cultivar-dependent conversion of carpels into new flowers was noted in pMADS3/FBP6-VIGS flowers. Of the four cultivars, only ‘Mambo Purple’ exhibited the development of new flowers instead of carpels and the emergence of ectopic new flowers from the axil of whorl 3 organs, which created an ornamental appearance with a high commercial value. Investigation of large and small petaloid stamens induced by pMADS3/FBP6-VIGS and pMADS3-VIGS, respectively, revealed only small differences in cell size compared to the large difference in total surface area. Quantitative RT-PCR analysis of SQUAMOSA/AP1/FRU type A-class genes, FBP29, PFG, and FBP26, showed no close relationship between the expression of those genes and petaloid stamen size. The suppressed C-class gene function at the late stage of flower development has little influence on the final size of petaloid tissue.

Using a tomato ( Solanum lycopersicum ) DNA macroarray consisting of 11,520 genes, we identified 419 ripening-associated genes (224 upregulated, 195 downregulated). Treatment with 1-methylcyclopropene (1-MCP) at the turning stage restored expression to levels of the mature green (MG) stage in 159 upregulated and 45 downregulated genes, suggesting a strong dependence on ethylene signaling during ripening. Among 194 ethylene-upregulated genes, 143 genes in ripening inhibitor ( rin ) fruit and 140 genes in non-ripening ( nor ) fruit responded poorly to exogenous ethylene, suggesting the necessity of RIN and NOR signals for their expression. In contrast, 36 and 70 genes responded to ethylene in rin and nor fruit, respectively, to a similar extent as in wild-type fruit, suggesting a clear independence of RIN and NOR signals for their response to ethylene. Ripening-associated expression of number of genes involved in respiratory, lipid and energy metabolism, and ethylene were upregulated during ripening under strong control of an ethylene signal. Large number of photosynthesis-related genes were downregulated during ripening in an ethylene-independent manner, whereas decreased expression of a few genes such as chloroplast thiazole biosynthetic protein and phosphoenolpyruvate carboxylase, was overturned by 1-MCP treatment, suggesting ethylene dependent regulation. Ripening-associated expression of several transcription and signal transduction factors, such as TDR4 , GRAS , S-adenosyl- l -homocysteine hydrolase, BNK1 , bZip , and BTB showed clear ethylene dependency, suggesting their involvement in regulation of fruit ripening downstream of ethylene signaling.

Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.

The aluminum-activated malate transporter (ALMT) family of proteins transports malate and/or inorganic anions across plant membranes. To demonstrate the possible role of ALMT genes in tomato fruit development, we focused on SlALMT4 and SlALMT5, the two major genes expressed during fruit development. Predicted proteins were classified into clade 2 of the family, many members of which localize to endomembranes. Tissue-specific gene expression was determined using transgenic tomato expressing the β-glucuronidase reporter gene controlled by their own promoters. Both the genes were expressed in vascular bundles connecting to developing seeds in fruit and in the embryo of mature seeds. Further, SlALMT5 was expressed in embryo in developing seeds in fruit. Subcellular localization of both proteins to the endoplasmic reticulum (ER) was established by transiently expressing the green fluorescent protein fusions in plant protoplasts. SlALMT5 probably localized to other endomembranes as well. Localization of SlALMT5 to the ER was also confirmed by immunoblot analysis. The transport function of both SlALMT proteins was investigated electrophysiologically in Xenopus oocytes. SlALMT5 transported malate and inorganic anions such as nitrate and chloride, but not citrate. SlALMT4 also transported malate, but the results were less consistent perhaps because it did not localize strongly to the plasma membrane. To elucidate the physiological role of SlALMT5 further, we overexpressed SlALMT5 in tomato. Compared with the wild type, overexpressors exhibited higher malate and citrate contents in mature seeds, but not in fruit. We conclude that the malate transport function of SlALMT5 expressed in developing fruit influences the organic acid contents in mature seeds.

Fruit ripening in response to treatments with propylene, 1-methycyclopropene (1-MCP), and low temperature was characterized in 'Sanuki Gold' kiwifruit, Actinidia chinensis Planch. Propylene treatment immediately induced rapid fruit softening, increased AC-PG (polygalacturonase) and AC-EXP (expansin) mRNA accumulation, and stimulated an increase in the soluble solid concentration (SSC) and a decrease in titratable acidity (TA). After 3 d exposure to propylene, ethylene production and AC-PL (pectate lyase) mRNA accumulation were observed. 1-MCP treatment after 24 h exposure to propylene eliminated AC-PG mRNA accumulation and suppressed continued changes in SSC and TA. Application of 1-MCP at the start of the treatment, followed by continuous propylene exposure, markedly delayed fruit softening, and the expression of the cell wall-modifying genes, and changes in the SSC and TA, indicating that kiwifruit become insensitive to ethylene at least for 3 d following 1-MCP exposure. Surprisingly, significant fruit softening, mRNA accumulation of AC-PG, AC-PL, and AC-EXP, and decreased TA were observed without ethylene production in intact fruit stored at low temperature for 1 month, but not in fruit stored at room temperature. Repeated 1-MCP treatments (twice a week) failed to inhibit the changes that occurred in low temperature storage. These observations indicate that low temperature modulates the ripening of kiwifruit in an ethylene-independent manner, suggesting that kiwifruit ripening is inducible by either ethylene or low temperature signals.

Heterostylous species have two types of flowers, thrum and pin morphs, and these are controlled by a single diallelic locus designated the 'S locus'; fertilization between these two types of flowers is successful. The S gene and the molecular mechanism by which it operates remain to be uncovered, although heterostyly has been studied since the time of Darwin. We compared transcripts and proteins of the thrum and pin flowers of heterostylous flax (Linum grandiflorum) to characterize the molecular differences between them and to elucidate the molecular machinery of heterostyly. Twelve floral morph-related genes were eventually isolated by an integrated study of subtraction and 2D-PAGE analyses, and four genes, TSS1, LgAP1, LgMYB21 and LgSKS1, were predicted to be related to heterostyly. TSS1, a thrum style-specific gene, showed some features suitable for the S gene. Although its biological function is unclear, TSS1 was expressed only in the thrum style and is probably linked to the S locus. LgMYB21, another thrum style gene, would be involved in floral morphogenesis. LgMYB21 was highly expressed in the thrum style, which is shorter than the pin style, and its overexpression in Arabidopsis reduced pistil length. Furthermore, a comparison of transcript and protein accumulations showed no differences in the mRNA accumulation of some thrum-specific proteins, including LgSKS1, suggesting that these are regulated by floral morph-specific post-transcriptional regulation. The Linum S locus regulates not only S specificity but also many floral phenotypes. Dynamic regulation of transcripts and proteins would be necessary for the pleiotropic function of the Linum S locus.