Expression profiling of cell cycle genes reveals key facilitators of cell production during carpel development, fruit set, and fruit growth in apple (Malusxdomestica Borkh.)

Genetic variations in MdSAUR36 participate in the negative regulation of mesocarp cell division and fruit size in Malus species

Final fruit size of apple (Malus domestica) cultivars is related to both mesocarp cell division and cell expansion during fruit growth, but it is unclear whether the cell division and/or cell enlargement determine most of the differences in fruit size between Malus species. In this study, by using an interspecific hybrid population between Malus asiatica "Zisai Pearl" and Malus domestica cultivar "Red Fuji," we found that the mesocarp cell number was the main causal factor of diversity in fruit size between Malus species. Rapid increase in mesocarp cell number occurred prior to 28 days after anthesis (DAA), while cell size increased gradually after 28 DAA until fruit ripening. Six candidate genes related to auxin signaling or cell cycle were predicted by combining the RNA-seq data and previous QTL data for fruit weight. Two InDels and 10 SNPs in the promoter of a small auxin upregulated RNA gene MdSAUR36 in Zisai Pearl led to a lower promoter activity than that of Red Fuji. One non-synonymous SNP G/T at 379 bp downstream of the ATG codon of MdSAUR36, which was heterozygous in Zisai Pearl, exerted significant genotype effects on fruit weight, length, and width. Transgenic apple calli by over-expressing or RNAi MdSAUR36 confirmed that MdSAUR36 participated in the negative regulation of mesocarp cell division and thus apple fruit size. These results could provide new insights in the molecular mechanism of small fruit size in Malus accession and be potentially used in molecular assisted breeding via interspecific hybridization.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01441-4.

Transcriptome and Metabolomics Integrated Analysis Reveals MdMYB94 Associated with Esters Biosynthesis in Apple (Malus × domestica)

Volatile esters are major aromas contributing to the organoleptic quality of apple fruit. However, the molecular mechanisms underlying the regulation of volatile ester biosynthesis in apple remain elusive. This study investigated the volatile profiles and transcriptomes of 'Qinguan' (QG) apple fruit during development and/or postharvest storage. Although the constitution of volatiles varied widely between the peel and flesh, the volatile profiles of the peel and flesh of ripening QG fruit were dominated by volatile esters. WGCNA results suggested that 19 genes belonging to ester biosynthesis pathways and 11 hub transcription factor genes potentially participated in the biosynthesis and regulation of esters. To figure out key regulators of ester biosynthesis, correlation network analysis, dual-luciferase assays, and yeast one-hybrid assay were conducted and suggested that MdMYB94 trans-activated the MdAAT2 promoter and participated in the regulation of ester biosynthesis. This study provides a framework for understanding ester biosynthesis and regulation in apple.

Fruit growth and development in apple: a molecular, genomics and epigenetics perspective

Fruit growth and development are physiological processes controlled by several internal and external factors. This complex regulatory mechanism comprises a series of events occurring in a chronological order over a growing season. Understanding the underlying mechanism of fruit development events, however, requires consideration of the events occurring prior to fruit development such as flowering, pollination, fertilization, and fruit set. Such events are interrelated and occur in a sequential order. Recent advances in high-throughput sequencing technology in conjunction with improved statistical and computational methods have empowered science to identify some of the major molecular components and mechanisms involved in the regulation of fruit growth and have supplied encouraging successes in associating genotypic differentiation with phenotypic observations. As a result, multiple approaches have been developed to dissect such complex regulatory machinery and understand the genetic basis controlling these processes. These methods include transcriptomic analysis, quantitative trait loci (QTLs) mapping, whole-genome approach, and epigenetics analyses. This review offers a comprehensive overview of the molecular, genomic and epigenetics perspective of apple fruit growth and development that defines the final fruit size and provides a detailed analysis of the mechanisms by which fruit growth and development are controlled. Though the main emphasis of this article is on the molecular, genomic and epigenetics aspects of fruit growth and development, we will also deliver a brief overview on events occurring prior to fruit growth.

Genome-Wide Identification and Expression Analysis of Kinesin Family in Barley (Hordeum vulgare)

Kinesin, as a member of the molecular motor protein superfamily, plays an essential function in various plants' developmental processes. Especially at the early stages of plant growth, including influences on plants' growth rate, yield, and quality. In this study, we did a genome-wide identification and expression profile analysis of the kinesin family in barley. Forty-two HvKINs were identified and screened from the barley genome, and a generated phylogenetic tree was used to compare the evolutionary relationships between Rice and Arabidopsis. The protein structure prediction, physicochemical properties, and bioinformatics of the HvKINs were also dissected. Our results reveal the important regulatory roles of HvKIN genes in barley growth. We found many cis- elements related to GA3 and ABA in homeopathic elements of the HvKIN gene and verified them by QRT-PCR, indicating their potential role in the barley kinesin family. The current study revealed the biological functions of barley kinesin genes in barley and will aid in further investigating the kinesin in other plant species.

Transcriptomic, Hormonomic and Metabolomic Analyses Highlighted the Common Modules Related to Photosynthesis, Sugar Metabolism and Cell Division in Parthenocarpic Tomato Fruits during Early Fruit Set

Parthenocarpy, the pollination-independent fruit set, can raise the productivity of the fruit set even under adverse factors during the reproductive phase. The application of plant hormones stimulates parthenocarpy, but artificial hormones incur extra financial and labour costs to farmers and can induce the formation of deformed fruit. This study examines the performance of parthenocarpic mutants having no transcription factors of SlIAA9 and SlTAP3 and sldella that do not have the protein-coding gene, SlDELLA, in tomato (cv. Micro-Tom). At 0 day after the flowering (DAF) stage and DAFs after pollination, the sliaa9 mutant demonstrated increased pistil development compared to the other two mutants and wild type (WT). In contrast to WT and the other mutants, the sliaa9 mutant with pollination efficiently stimulated the build-up of auxin and GAs after flowering. Alterations in both transcript and metabolite profiles existed for WT with and without pollination, while the three mutants without pollination demonstrated the comparable metabolomic status of pollinated WT. Network analysis showed key modules linked to photosynthesis, sugar metabolism and cell proliferation. Equivalent modules were noticed in the famous parthenocarpic cultivars ‘Severianin’, particularly for emasculated samples. Our discovery indicates that controlling the genes and metabolites proffers future breeding policies for tomatoes.

Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages

Background

MicroRNA172 (miR172) has been proven to be critical for fruit growth, since elevated miR172 activity blocks the growth of apple (Malus x domestica Borkh.) fruit. However, it is not clear how overexpression of miR172 affects apple fruit developmental processes.

Methods

To answer this question, the present study, analyzed global transcriptional changes in miR172-overexpressing (miR172OX) and nongenetically modified wild-type (WT) apple fruit at two developmental stages and in different fruit tissues via RNA-seq. In addition, two cultivars, ‘Hanfu’ and ‘M9’, which have naturally fruit size variation, were included to identify miR172-dependent DEGs. qRT–PCRwas used to verify the reliability of our RNA-seq data.

Results

Overexpression of miR172 altered the expression levels of many cell proliferation- and cell expansion-related genes. Twenty-four libraries were generated, and 10,338 differentially expressed genes (DEGs) were detected between miR172OX and WT fruit tissues. ‘Hanfu’ and ‘M9’ are two common cultivars that bear fruit of different sizes (250 g and 75 g, respectively). Six libraries were generated, and 3,627 DEGs were detected between ‘Hanfu’ and ‘M9’. After merging the two datasets, 6,888 candidate miR172-specific DEGs were identified. The potential networks associated with fruit size triggered traits were defined among genes belonging to the families of hormone synthesis, signaling pathways, and transcription factors. Our comparative transcriptome analysis provides insights into transcriptome responses to miR172 overexpression in apple fruit and a valuable database for future studies to validate functional genes and elucidate the fruit developmental mechanisms in apple.

Integrative Morphological, Physiological, Proteomics Analyses of Jujube Fruit Development Provide Insights Into Fruit Quality Domestication From Wild Jujube to Cultivated Jujube

Jujube (Ziziphus jujuba) was domesticated from wild jujube (Z. jujuba var. spinosa). Here, integrative physiological, metabolomic, and comparative proteomic analyses were performed to investigate the fruit expansion and fruit taste components in a jujube cultivar 'Junzao' and a wild jujube 'Qingjiansuanzao' with contrasting fruit size and taste. We revealed that the duration of cell division and expansion largely determined the final fruit size, while the intercellular space in the mesocarp dictated the ratio of mesocarp volume in mature fruits. The high levels of endogenous gibbereline3 (GA) and zeatin in the growing fruit of 'Junzao' were associated with their increased fruit expansion. Compared with 'Junzao,' wild jujube accumulated lower sugars and higher organic acids. Furthermore, several protein co-expression modules and important member proteins correlated with fruit expansion, sugar synthesis, and ascorbic acid metabolism were identified. Among them, GA20OX involved in GA biosynthesis was identified as a key protein regulating fruit expansion, whereas sucrose-6-phosphate synthase (SPS) and neutral invertase (NINV) were considered as key enzymes promoting sugar accumulation and as major factors regulating the ratio of sucrose to hexose in jujube fruits, respectively. Moreover, the increase of Nicotinamide adenine dinucleotide-Malate dehydrogenase (NAD-MDH) activity and protein abundance were associated with the malic acid accumulation, and the high accumulation of ascorbic acid in wild jujube was correlated with the elevated abundance of GalDH, ZjAPXs, and MDHAR1, which are involved in the ascorbic acid biosynthesis and recycling pathways. Overall, these results deepened the understanding of mechanisms regulating fruit expansion and sugar/acids metabolisms in jujube fruit.

Staying in touch: how highly specialised moth pollinators track host plant phenology in unpredictable climates

Background

For specialised pollinators, the synchrony of plant and pollinator life history is critical to the persistence of pollinator populations. This is even more critical in nursery pollination, where pollinators are obligately dependant on female host plant flowers for oviposition sites. Epicephala moths (Gracillariidae) form highly specialised nursery pollination mutualisms with Phyllanthaceae plants. Several hundred Phyllanthaceae are estimated to be exclusively pollinated by highly specific Epicephala moths, making these mutualisms an outstanding example of plant–insect coevolution. However, there have been no studies of how Epicephala moths synchronise their activity with host plant flowering or persist through periods when flowers are absent. Such knowledge is critical to understanding the ecology and evolutionary stability of these mutualisms. We surveyed multiple populations of both Breynia oblongifolia (Phyllanthaceae) and it’s Epicephala pollinators for over two years to determine their phenology and modelled the environmental factors that underpin their interactions.

Results

The abundance of flowers and fruits was highly variable and strongly linked to local rainfall and photoperiod. Unlike male flowers and fruits, female flowers were present throughout the entire year, including winter. Fruit abundance was a significant predictor of adult Epicephala activity, suggesting that eggs or early instar larvae diapause within dormant female flowers and emerge as fruits mature. Searches of overwintering female flowers confirmed that many contained pollen and diapausing pollinators. We also observed diapause in Epicephala prior to pupation, finding that 12% (9/78) of larvae emerging from fruits in the autumn entered an extended diapause for 38–48 weeks. The remaining autumn emerging larvae pupated directly without diapause, suggesting a possible bet-hedging strategy.

Conclusions

Epicephala appear to use diapause at multiple stages in their lifecycle to survive variable host plant phenology. Furthermore, moth abundance was predicted by the same environmental variables as male flowers, suggesting that moths track flowering through temperature. These adaptations may thereby mitigate against unpredictability in the timing of fruiting and flowering because of variable rainfall. It remains to be seen how widespread egg diapause and pre-pupal diapause may be within Epicephala moths, and, furthermore, to what degree these traits may have facilitated the evolution of these highly diverse mutualisms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01889-4.

Genome wide analysis of kinesin gene family in Citrullus lanatus reveals an essential role in early fruit development

BACKGROUND

Kinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon, a valued and nutritious fruit, and yet their functions have not been characterized. Especially, their involvement in early fruit development, which directly determines the size, shape, yield and quality of the watermelon fruit, remains unclear.

RESULTS

In this study, we performed a whole-genome investigation and comprehensive analysis of kinesin genes in C. lanatus. In total, 48 kinesins were identified and categorized into 10 kinesin subfamilies groups based on phylogenetic analysis. Their uneven distribution on 11 chromosomes was revealed by distribution analysis. Conserved motif analysis showed that the ATP-binding motif of kinesins was conserved within all subfamilies, but not the microtubule-binding motif. 10 segmental duplication pairs genes were detected by the syntenic and phylogenetic approaches, which showed the expansion of the kinesin gene family in C. lanatus genome during evolution. Moreover, 5 ClKINs genes are specifically and abundantly expressed in early fruit developmental stages according to comprehensive expression profile analysis, implying their critical regulatory roles during early fruit development. Our data also demonstrated that the majority of kinesin genes were responsive to plant hormones, revealing their potential involvement in the signaling pathways of plant hormones.

CONCLUSIONS

Kinesin gene family in watermelon was comprehensively analyzed in this study, which establishes a foundation for further functional investigation of C. lanatus kinesin genes and provides novel insights into their biological functions. In addition, these results also provide useful information for understanding the relationship between plant hormone and kinesin genes in C. lanatus.

Exogenous 6-benzyladenine application affects root morphology by altering hormone status and gene expression of developing lateral roots in Malus hupehensis

Malus hupehensis is an extensively used apple rootstock in China. In the current study, M. hupehensis seedlings were treated with exogenous 2.2 µm 6-benzyladenine (6-BA) so as to investigate the mechanism by which 6-BA affects lateral root development. The results indicate that 6-BA treatment promotes elongation and thickening of both root and shoot in M. hupehensis, but reduces the number of lateral roots, as well as reducing the auxin level after 6-BA treatment. Moreover, MhAHK4, MhRR1 and MhRR2 were also significantly up-regulated in response to 6-BA treatment. Expression levels of auxin synthesis- and transport-related genes, such as MhYUCCA6, MhYUCCA10, MhPIN1 and MhPIN2, were down-regulated, which corresponds with lower auxin levels in the 6-BA-treated seedlings. A negative regulator of auxin, MhIAA3, was induced by 6-BA treatment, leading to reduced expression of MhARF7 and MhARF19 in 6-BA-treated seedlings. As a result, expression of MhWOX11, MhWOX5, MhLBD16 and MhLBD29 was blocked, which in turn inhibited lateral root initiation. In addition, a lower auxin level decreased expression of MhRR7 and MhRR15, which repressed expression of key transcription factors associated with root development, thus inhibiting lateral root development. In contrast, 6-BA treatment promoted secondary growth (thickening) of the root by inducing expression of MhCYCD3;1 and MhCYCD3;2. Collectively, the changes in hormone levels and gene expression resulted in a reduced number of lateral roots and thicker roots in 6-BA-treated plants.

Higher growth of the apple (Malus × domestica Borkh.) fruit cortex is supported by resource intensive metabolism during early development

BACKGROUND

The major fleshy tissues of the apple fruit are spatially separable into cortex and pith. These tissues display differential growth during development. Key features of such differential growth, and sink metabolic programs supporting it have not been investigated previously. We hypothesized that differential growth between these fruit tissues is supported by differential sink metabolic programs, particularly during early development. Growth, metabolite concentrations, and transcript abundance of metabolism-related genes were measured to determine characteristics of differential growth and their underlying metabolic programs.

RESULTS

The cortex displayed > 5-fold higher growth than the pith during early fruit development, indicating that differential growth was established during this period. Further, when resource availability was increased through sink-removal, cortex growth was preferentially enhanced. Greatest diversity in metabolic programs between these tissues was evident during early fruit development. Higher cortex growth during early development was facilitated by increased catabolism of imported carbon (C) resources, sorbitol and sucrose, and the nitrogen (N) resource, asparagine. It was also associated with enhanced primary C metabolism, and C storage as malate and quinate. The pith metabolic program during this period involved limited allocation of C and N to growth, but greater allocation to storage, and enhanced sucrose-sucrose cycling.

CONCLUSIONS

Together, these data indicate that the fruit cortex tissue displays a resource intensive metabolic program during early fruit development. This provides the C backbones, proteins, energy and osmolytes to support its higher growth.

Gibberellic acid induced parthenocarpic 'Honeycrisp' apples (Malus domestica) exhibit reduced ovary width and lower acidity

Fruit set and development are dependent on auxin, gibberellin, and cytokinin, which cause parthenocarpic development in many species when applied ectopically. Commercial sprays containing these hormones are used to improve apple fruit set, size, and shape, but have been implicated negatively in other aspects of fruit quality. We applied gibberellic acid (GA₃), synthetic auxin (NAA), and the auxin-transport inhibitor NPA to 'Honeycrisp' apple flowers. Fruit retention and size were quantified throughout development, and seed number and fruit quality parameters were measured at maturity. GA₃ alone caused the development of seedless parthenocarpic apples. At maturity, GA₃-treated apples were narrower due to reduced ovary width, indicating that GA₃ induced normal growth of the hypanthium, but not the ovary. GA₃-treated fruits were also less acidic than hand-pollinated controls, but had similar firmness, starch, and sugar content. To further understand the regulation of parthenocarpy, we performed tissue-specific transcriptome analysis on GA₃-treated, NAA-treated, and control fruits, at 18 days after treatment and again at maturity. Overall, transcriptome analysis showed GA₃-treated and hand-pollinated fruits were highly similar in RNA expression profiles. Early expression differences in putative cell division, cytokinin degradation, and cell wall modification genes in GA₃-treated ovaries correlated with the observed shape differences, while early expression differences in the acidity gene Ma1 may be responsible for the changes in pH. Taken together, our results indicate that GA₃ triggers the development of parthenocarpic apple fruit with morphological deviations that correlate with a number of candidate gene expression differences.

Transcription profiles reveal the regulatory mechanisms of spur bud changes and flower induction in response to shoot bending in apple (Malus domestica Borkh.)

Shoot bending, as an effective agronomic measure, has been widely used to promote flowering in 'Fuji' apple trees. Here, we examined the transcriptional responses of genes in 'Fuji' apple buds at different flowering stages under a shoot-bending treatment using RNA sequencing. A complex genetic crosstalk-regulated network, involving abscisic acid-related genes, starch metabolism and circadian rhythm-related genes, as well as stress response-related genes, was up-regulated by shoot bending, in which were contrbuted to apple flower bud formation in response to shoot-bending conditions. Flower induction plays an important role in the apple tree life cycle, but young trees produce fewer and inferior flower buds. Shoot bending, as an effective agronomic measure, has been widely used to promote flowering in 'Fuji' apple trees. However, little is known about the gene expression network patterns and molecular regulatory mechanisms caused by shoot bending during the induced flowering. Here, we examined the transcriptional responses of genes in 'Fuji' apple buds at different flowering stages under a shoot-bending treatment using RNA sequencing. A steady up-regulation of carbon metabolism-related genes led to relatively high levels of sucrose in early induced flowering stages and starch accumulation during shoot bending. Additionally, global gene expression profiling determined that cytokinin, indole-3-acetic acid, gibberellin synthesis and signalling-related genes were significantly regulated by shoot bending, contributing to cell division and differentiation, bud growth and flower induction. A complex genetic crosstalk-regulated network, involving abscisic acid-related genes, starch metabolism- and circadian rhythm-related genes, as well as stress response-related genes, was up-regulated by shoot bending. Additionally, some transcription factor family genes that were involved in sugar, abscisic acid and stress response signalling were significantly induced by shoot bending. These important flowering genes, which were mainly involved in photoperiod, age and autonomous pathways, were up-regulated by shoot bending. Thus, a complex genetic network of regulatory mechanisms involved in sugar, hormone and stress response signalling pathways may mediate the induction of apple tree flowering in response to shoot-bending conditions.

Histological, hormonal and transcriptomic reveal the changes upon gibberellin-induced parthenocarpy in pear fruit

Phytohormones play crucial roles in fruit set regulation and development. Here, gibberellins (GA₄₊₇), but not GA₃, induced pear parthenocarpy. To systematically investigate the changes upon GA₄₊₇ induced pear parthenocarpy, dynamic changes in histology, hormone and transcript levels were observed and identified in unpollinated, pollinated and GA₄₊₇-treated ovaries. Mesocarp cells continued developing in both GA₄₊₇-treated and pollinated ovaries. In unpollinated ovaries, mesocarp cells stopped developing 14 days after anthesis. During fruit set process, GA₄₊₇, but not GA₁₊₃, increased after pollination. Abscisic acid (ABA) accumulation was significantly repressed by GA₄₊₇ or pollination, but under unpollinated conditions, ABA was produced in large quantities. Moreover, indole-3-acetic acid biosynthesis was not induced by GA₄₊₇ or pollination treatments. Details of this GA-auxin-ABA cross-linked gene network were determined by a comparative transcriptome analysis. The indole-3-acetic acid transport-related genes, mainly auxin efflux carrier component genes, were induced in both GA₄₊₇-treated and pollinated ovaries. ABA biosynthetic genes of the 9-cis-epoxycarotenoid dioxygenase family were repressed by GA₄₊₇ and pollination. Moreover, directly related genes in the downstream parthenocarpy network involved in cell division and expansion (upregulated), and MADS-box family genes (downregulated), were also identified. Thus, a model of GA-induced hormonal balance and its effects on parthenocarpy were established.

Comparative Transcriptome and Microscopy Analyses Provide Insights into Flat Shape Formation in Peach (Prunus persica)

Fruit shape is an important external characteristic that consumers use to select preferred fruit cultivars. In peach, the flat fruit cultivars have become more and more popular worldwide. Genetic markers closely linking to the flat fruit trait have been identified and are useful for marker-assisted breeding. However, the cellular and genetic mechanisms underpinning flat fruit formation are still poorly understood. In this study, we have revealed the differences in fruit cell number, cell size, and in gene expression pattern between the traditional round fruit and modern flat fruit cultivars. Flat peach cultivars possessed significantly lower number of cells in the vertical axis because cell division in the vertical direction stopped early in the flat fruit cultivars at 15 DAFB (day after full bloom) than in round fruit cultivars at 35 DAFB. This resulted in the reduction in vertical development in the flat fruit. Significant linear relationship was observed between fruit vertical diameter and cell number in vertical axis for the four examined peach cultivars (R² = 0.9964) at maturation stage, and was also observed between fruit vertical diameter and fruit weight (R² = 0.9605), which indicated that cell number in vertical direction contributed to the flat shape formation. Furthermore, in RNA-seq analysis, 4165 differentially expressed genes (DEGs) were detected by comparing RNA-seq data between flat and round peach cultivars at different fruit development stages. In contrast to previous studies, we discovered 28 candidate genes potentially responsible for the flat shape formation, including 19 located in the mapping site and 9 downstream genes. Our study indicates that flat and round fruit shape in peach is primarily determined by the regulation of cell production in the vertical direction during early fruit development.

Proteomic analysis reveals dynamic regulation of fruit development and sugar and acid accumulation in apple

Understanding the fruit developmental process is critical for fruit quality improvement. Here, we report a comprehensive proteomic analysis of apple fruit development over five growth stages, from young fruit to maturity, coupled with metabolomic profiling. A tandem mass tag (TMT)-based comparative proteomics approach led to the identification and quantification of 7098 and 6247 proteins, respectively. This large-scale proteomic dataset presents a global view of the critical pathways involved in fruit development and metabolism. When linked with metabolomics data, these results provide new insights into the modulation of fruit development, the metabolism and storage of sugars and organic acids (mainly malate), and events within the energy-related pathways for respiration and glycolysis. We suggest that the key steps identified here (e.g. those involving the FK2, TST, EDR6, SPS, mtME and mtMDH switches), can be further targeted to confirm their roles in accumulation and balance of fructose, sucrose and malate. Moreover, our findings imply that the primary reason for decreases in amino acid concentrations during fruit development is related to a reduction in substrate flux via glycolysis, which is mainly regulated by fructose-bisphosphate aldolase and bisphosphoglycerate mutase.

Differential response of cell-cycle and cell-expansion regulators to heat stress in apple (Malus domestica) fruitlets

Temperature is one of the most significant factors affecting physiological and biochemical aspects of fruit development. Current and progressing global warming is expected to change climate in the traditional deciduous fruit tree cultivation regions. In this study, 'Golden Delicious' trees, grown in a controlled environment or commercial orchard, were exposed to different periods of heat treatment. Early fruitlet development was documented by evaluating cell number, cell size and fruit diameter for 5-70 days after full bloom. Normal activities of molecular developmental and growth processes in apple fruitlets were disrupted under daytime air temperatures of 29°C and higher as a result of significant temporary declines in cell-production and cell-expansion rates, respectively. Expression screening of selected cell cycle and cell expansion genes revealed the influence of high temperature on genetic regulation of apple fruitlet development. Several core cell-cycle and cell-expansion genes were differentially expressed under high temperatures. While expression levels of B-type cyclin-dependent kinases and A- and B-type cyclins declined moderately in response to elevated temperatures, expression of several cell-cycle inhibitors, such as Mdwee1, Mdrbr and Mdkrps was sharply enhanced as the temperature rose, blocking the cell-cycle cascade at the G1/S and G2/M transition points. Moreover, expression of several expansin genes was associated with high temperatures, making them potentially useful as molecular platforms to enhance cell-expansion processes under high-temperature regimes. Understanding the molecular mechanisms of heat tolerance associated with genes controlling cell cycle and cell expansion may lead to the development of novel strategies for improving apple fruit productivity under global warming.

Down-regulation of multiple CDK inhibitor ICK/KRP genes promotes cell proliferation, callus induction and plant regeneration in Arabidopsis

The ICK/KRP cyclin-dependent kinase (CDK) inhibitors are important plant cell cycle regulators sharing only limited similarity with the metazoan CIP/KIP family of CDK inhibitors. Information is still limited regarding the specific functions of different ICK/KRP genes in planta. We have shown previously that down-regulation of multiple CDK inhibitor ICK/KRP genes up-regulates the E2F pathway and increases cell proliferation, and organ and seed sizes in Arabidopsis. In this study, we observed that the quintuple ick1/2/5/6/7 mutant had more cells in the cortical layer of the root apical meristem (RAM) than the wild type (Wt) while its RAM length was similar to that of the Wt, suggesting a faster cell cycle rate in the quintuple mutant. We further investigated the effects of down-regulating ICK genes on tissue culture responses. The cotyledon explants of ick1/2/5/6/7 could form callus efficiently in the absence of cytokinin and also required a lower concentration of 2,4-D for callus induction compared to the Wt plants, suggesting increased competence for callus induction in the mutant. In addition, the quintuple ick mutant showed enhanced abilities to regenerate shoots and roots, suggesting that increased competence to enter the cell cycle in the quintuple mutant might make it possible for more cells to become proliferative and be utilized to form shoots or roots. These findings indicate that CDK activity is a major factor underlying callus induction and increased cell proliferation can enhance in vitro organogenesis.

PaKRP, a cyclin-dependent kinase inhibitor from avocado, may facilitate exit from the cell cycle during fruit growth

Previous studies using 'Hass' avocado cultivar showed that its small-fruit (SF) phenotype is limited by cell number. To explore the molecular components affecting avocado cell production, we isolated four cDNAs encoding: an ICK/KRP protein, known to play cell cycle-regulating roles through modulation of CDK function; two CDK proteins and a D-type cyclin, and monitored their expression patterns, comparing NF (normal fruit) versus SF profiles. The accumulation of PaKRP gradually deceased during growth in both fruit populations. Despite these similarities, SF exhibited higher levels of PaKRP accumulation at early stages of growth. Moreover, in NF, augmented PaKRP expression coincided with a decrease in CDK and PaCYCD1 levels, whereas in SF, enhanced PaKPR expression was coupled with an earlier decline of CDK and PaCYCD1 levels. For both NF and SF, enhanced mesocarp PaKRP transcript accumulation, was associated with elevated abscisic acid (ABA) and ABA catabolites content. Nevertheless, the collective ABA levels, including catabolites, were substantially higher in SF tissues, as compared with NF tissues. Finally, additional expression analysis revealed that in cultured cells, PaKRP could be induced by ABA. Together, our data links PaKRP with exit from the fruit cell cycle and suggest a role for ABA in controlling its expression.

Characterization and expression profiling of cucumber kinesin genes during early fruit development: revealing the roles of kinesins in exponential cell production and enlargement in cucumber fruit

Rapid cell division and expansion in early fruit development are important phases for cucumber fruit yield and quality. Kinesin proteins are microtubule-based motors responsible for modulating cell division and enlargement. In this work, the candidate kinesin genes involved in rapid cell division and expansion during cucumber fruit development were investigated. The morphological and cellular changes during early fruit development were compared in four cucumber genotypes with varied fruit size. The correlation between the expression profiles of cucumber kinesin genes and cellular changes in fruit was investigated. Finally, the biochemical characteristics and subcellular localizations of three candidate kinesins were studied. The results clarified the morphological and cellular changes during early cucumber fruit development. This study found that CsKF2-CsKF6 were positively correlated with rapid cell production; CsKF1 and CsKF7 showed a strongly positive correlation with rapid cell expansion. The results also indicated that CsKF1 localized to the plasma membrane of fast-expanding fruit cells, that CsKF2 might play a role in fruit chloroplast division, and that CsKF3 is involved in the function or formation of phragmoplasts in fruit telophase cells. The results strongly suggest that specific fruit-enriched kinesins are specialized in their functions in rapid cell division and expansion during cucumber fruit development.

De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading

BACKGROUND

Litchi (Litchi chinensis Sonn.) is one of the most important fruit trees cultivated in tropical and subtropical areas. However, a lack of transcriptomic and genomic information hinders our understanding of the molecular mechanisms underlying fruit set and fruit development in litchi. Shading during early fruit development decreases fruit growth and induces fruit abscission. Here, high-throughput RNA sequencing (RNA-Seq) was employed for the de novo assembly and characterization of the fruit transcriptome in litchi, and differentially regulated genes, which are responsive to shading, were also investigated using digital transcript abundance(DTA)profiling.

RESULTS

More than 53 million paired-end reads were generated and assembled into 57,050 unigenes with an average length of 601 bp. These unigenes were annotated by querying against various public databases, with 34,029 unigenes found to be homologous to genes in the NCBI GenBank database and 22,945 unigenes annotated based on known proteins in the Swiss-Prot database. In further orthologous analyses, 5,885 unigenes were assigned with one or more Gene Ontology terms, 10,234 hits were aligned to the 24 Clusters of Orthologous Groups classifications and 15,330 unigenes were classified into 266 Kyoto Encyclopedia of Genes and Genomes pathways. Based on the newly assembled transcriptome, the DTA profiling approach was applied to investigate the differentially expressed genes related to shading stress. A total of 3.6 million and 3.5 million high-quality tags were generated from shaded and non-shaded libraries, respectively. As many as 1,039 unigenes were shown to be significantly differentially regulated. Eleven of the 14 differentially regulated unigenes, which were randomly selected for more detailed expression comparison during the course of shading treatment, were identified as being likely to be involved in the process of fruitlet abscission in litchi.

CONCLUSIONS

The assembled transcriptome of litchi fruit provides a global description of expressed genes in litchi fruit development, and could serve as an ideal repository for future functional characterization of specific genes. The DTA analysis revealed that more than 1000 differentially regulated unigenes respond to the shading signal, some of which might be involved in the fruitlet abscission process in litchi, shedding new light on the molecular mechanisms underlying organ abscission.

Callose and cellulose synthase gene expression analysis from the tight cluster to the full bloom stage and during early fruit development in Malus × domestica

Apple (Malus × domestica) is an economically important temperate fruit-bearing crop which belongs to the family of Rosaceae and its pomaceous fruit is one of the most commonly cultivated. Several studies have demonstrated that the cell wall plays a pivotal role during flower and fruit development. It takes active part in pollen tube growth and contributes to determine the fruit firmness trait through the action of cell wall-related enzymes (i.e. polygalacturonase and pectinmethylesterase). We have investigated the expression of callose and cellulose synthase genes during flowering from tight cluster to anthesis and during early fruit development in domesticated apple. We also link the changes observed in gene expression to the profile of soluble non-structural carbohydrates at different developmental stages of flowers/fruitlets and to the qualitative results linked to wall polysaccharides' composition obtained through near-infrared spectroscopy. This work represents an important addition to the study of tree physiology with respect to the analysis of the expression of callose and cellulose synthase genes during flower and early fruit development in domesticated apple.

Cell division and endoreduplication play important roles in stem swelling of tuber mustard (Brassica juncea Coss. var. tumida Tsen et Lee)

We investigated spatio-temporal variations in cell division and the occurrence of endoreduplication in cells of tuber mustard stems during development. Cells in the stem had 8C nuclei (C represents DNA content of a two haploid genome), since it is an allotetraploid species derived from diploid Brassica rapa (AA) and B. nigra (BB), thus indicating the occurrence of endoreduplication. Additionally, we observed a dynamic change of cell ploidy in different regions of the swollen stems, with a decrease in 4C proportion in P4-1 and a sharp increase in 8C cells that became the dominant cell type (86.33% at most) in the inner pith cells. Furthermore, cDNAs of 14 cell cycle genes and four cell expansion genes were cloned and their spatial transcripts analysed in order to understand their roles in stem development. The expression of most cell cycle genes peaked in regions of the outer pith (P2 or P3), some genes regulating S/G2 and G2/M (BjCDKB1;2, BjCYCB1;1 and BjCYCB1;2) significantly decrease in P5 and P6, while G1/S regulators (BjE2Fa, BjE2Fb and BjE2Fc) showed a relative high expression level in the inner pith (P5) where cells were undergoing endoreduplication. Coincidentally, BjXTH1and BjXTH2 were exclusively expressed in the endoreduplicated cells. Our results suggest that cells of outer pith regions (P2 and P3) mainly divide for cell proliferation, while cells of the inner pith expand through endoreduplication. Endoreduplication could trigger expression of BjXTH1 and BjXTH2 and thus function in cell expansion of the pith tissue.

Transcriptome analyses of early cucumber fruit growth identifies distinct gene modules associated with phases of development

ABBACKGROUND: Early stages of fruit development from initial set through exponential growth are critical determinants of size and yield, however, there has been little detailed analysis of this phase of development. In this study we combined morphological analysis with 454 pyrosequencing to study transcript level changes occurring in young cucumber fruit at five ages from anthesis through the end of exponential growth.

RESULTS

The fruit samples produced 1.13 million ESTs which were assembled into 27,859 contigs with a mean length of 834 base pairs and a mean of 67 reads per contig. All contigs were mapped to the cucumber genome. Principal component analysis separated the fruit ages into three groups corresponding with cell division/pre-exponential growth (0 and 4 days post pollination (dpp)), peak exponential expansion (8dpp), and late/post-exponential expansion stages of growth (12 and 16 dpp). Transcripts predominantly expressed at 0 and 4 dpp included homologs of histones, cyclins, and plastid and photosynthesis related genes. The group of genes with peak transcript levels at 8dpp included cytoskeleton, cell wall, lipid metabolism and phloem related proteins. This group was also dominated by genes with unknown function or without known homologs outside of cucurbits. A second shift in transcript profile was observed at 12-16dpp, which was characterized by abiotic and biotic stress related genes and significant enrichment for transcription factor gene homologs, including many associated with stress response and development.

CONCLUSIONS

The transcriptome data coupled with morphological analyses provide an informative picture of early fruit development. Progressive waves of transcript abundance were associated with cell division, development of photosynthetic capacity, cell expansion and fruit growth, phloem activity, protection of the fruit surface, and finally transition away from fruit growth toward a stage of enhanced stress responses. These results suggest that the interval between expansive growth and ripening includes further developmental differentiation with an emphasis on defense. The increased transcript levels of cucurbit-specific genes during the exponential growth stage may indicate unique factors contributing to rapid growth in cucurbits.

The AINTEGUMENTA genes, MdANT1 and MdANT2, are associated with the regulation of cell production during fruit growth in apple (Malus × domestica Borkh.)

BACKGROUND

Fruit growth in apple (Malus × domestica Borkh.) is mediated by cell production and expansion. Genes involved in regulating these processes and thereby fruit growth, are not well characterized. We hypothesized that the apple homolog(s) of AINTEGUMENTA (ANT), an APETALA2-repeat containing transcription factor, regulates cell production during fruit growth in apple.

RESULTS

Two ANT genes, MdANT1 and MdANT2, were isolated from apple and their expression was studied during multiple stages of fruit development. MdANT1 and MdANT2 expression was high during early fruit growth coincident with the period of cell production, rapidly declined during exit from cell production, and remained low during the rest of fruit development. The effects of increase in carbohydrate availability during fruit growth were characterized. Increase in carbohydrate availability enhanced fruit growth largely through an increase in cell production. Expression of MdANT1 and MdANT2 increased sharply by up to around 5-fold in response to an increase in carbohydrate availability. Expression of the ANT genes was compared across two apple genotypes, 'Gala' and 'Golden Delicious Smoothee' (GS), which differ in the extent of fruit growth, largely due to differences in cell production. In comparison to 'Gala', the larger fruit-size genotype, GS, displayed higher levels and a longer duration of MdANT1 and MdANT2 expression. Expression of the ANTs and cell cycle genes in the fruit core and cortex tissues isolated using laser capture microdissection was studied. During early fruit growth, expression of the MdANTs was higher within the cortex, the tissue that constitutes the majority of the fruit. Additionally, MdANT1 and MdANT2 expression was positively correlated with that of A- and B-type CYCLINS, B-type CYCLIN-DEPENDENT-KINASES (CDKBs) and MdDEL1.

CONCLUSIONS

Multiple lines of evidence from this study suggest that MdANT1 and MdANT2 regulate cell production during fruit growth in apple. ANTs may coordinate the expression of cell proliferation genes and thereby affect the competence of cells for cell production during fruit growth. Together, data from this study implicate MdANT1 and MdANT2 in the regulation of fruit growth in apple.

A commentary on the G₂/M transition of the plant cell cycle

BACKGROUND

The complex events of mitosis rely on precise timing and on immaculate preparation for their success, but the G₂/M transition in the plant cell cycle is currently steeped in controversy and alternative models.

SCOPE

In this brief review, the regulation of the G₂/M transition in plants is commented on. The extent to which the G₂/M transition is phosphoregulated by WEE1 kinase and CDC25 phosphatase, as exemplified in yeasts and animals, is discussed together with an alternative model that excludes these proteins from this transition. Arabidopsis T-DNA insertional lines for WEE1 and CDC25 that develop normally prompted the latter model. An argument is then presented that environmental stress is the norm for higher plants in temperate conditions. If so, the repressive role that WEE1 has under checkpoint conditions might be part of the normal cell cycle for many proliferative plant cells. Arabidopsis CDC25 can function as either a phosphatase or an arsenate reductase and recent evidence suggests that cdc25 knockouts are hypersensitive to hydroxyurea, a drug that induces the DNA-replication checkpoint. That other data show a null response of these knockouts to hydroxyurea leads to an airing of the controversy surrounding the enigmatic plant CDC25 at the G₂/M transition.