Pan-Genome Analysis of TIFY Gene Family and Functional Analysis of CsTIFY Genes in Cucumber.

Cucumbers are frequently affected by gray mold pathogen Botrytis cinerea, a pathogen that causes inhibited growth and reduced yield. Jasmonic acid (JA) plays a primary role in plant responses to biotic stresses, and the jasmonate-ZIM-Domain (JAZ) proteins are key regulators of the JA signaling pathway. In this study, we used the pan-genome of twelve cucumber varieties to identify cucumber TIFY genes. Our findings revealed that two CsTIFY genes were present in all twelve cucumber varieties and showed no differences in protein sequence, gene structure, and motif composition. This suggests their evolutionary conservation across different cucumber varieties and implies that they may play a crucial role in cucumber growth. On the other hand, the other fourteen CsTIFY genes exhibited variations in protein sequence and gene structure or conserved motifs, which could be the result of divergent evolution, as these genes adapt to different cultivation and environmental conditions. Analysis of the expression profiles of the CsTIFY genes showed differential regulation by B. cinerea. Transient transfection plants overexpressing CsJAZ2, CsJAZ6, or CsZML2 were found to be more susceptible to B. cinerea infection compared to control plants. Furthermore, these plants infected by the pathogen showed lower levels of the enzymatic activities of POD, SOD and CAT. Importantly, after B. cinerea infection, the content of JA was upregulated in the plants, and cucumber cotyledons pretreated with exogenous MeJA displayed increased resistance to B. cinerea infection compared to those pretreated with water. Therefore, this study explored key TIFY genes in the regulation of cucumber growth and adaptability to different cultivation environments based on bioinformatics analysis and demonstrated that CsJAZs negatively regulate cucumber disease resistance to gray mold via multiple signaling pathways.

Pan-genome Analysis of WOX Gene Family and Function Exploration of CsWOX9 in Cucumber.

Cucumber is an economically important vegetable crop, and the warts (composed of spines and Tubercules) of cucumber fruit are an important quality trait that influences its commercial value. WOX transcription factors are known to have pivotal roles in regulating various aspects of plant growth and development, but their studies in cucumber are limited. Here, genome-wide identification of cucumber WOX genes was performed using the pan-genome analysis of 12 cucumber varieties. Our findings revealed diverse CsWOX genes in different cucumber varieties, with variations observed in protein sequences and lengths, gene structure, and conserved protein domains, possibly resulting from the divergent evolution of CsWOX genes as they adapt to diverse cultivation and environmental conditions. Expression profiles of the CsWOX genes demonstrated that CsWOX9 was significantly expressed in unexpanded ovaries, especially in the epidermis. Additionally, analysis of the CsWOX9 promoter revealed two binding sites for the C2H2 zinc finger protein. We successfully executed a yeast one-hybrid assay (Y1H) and a dual-luciferase (LUC) transaction assay to demonstrate that CsWOX9 can be transcriptionally activated by the C2H2 zinc finger protein Tu, which is crucial for fruit Tubercule formation in cucumber. Overall, our results indicated that CsWOX9 is a key component of the molecular network that regulates wart formation in cucumber fruits, and provide further insight into the function of CsWOX genes in cucumber.

CsMYB60 Confers Enhanced Resistance to Fusarium solani by Increasing Proanthocyanidin Biosynthesis in Cucumber.

Root rot caused by Fusarium solani is one of the most common fungal diseases in cucumber (Cucumis sativus). Proanthocyanidins (PAs) are known to play important roles in inhibiting the growth of phytopathogens. In addition, CsMYB60 is a known positive regulator of flavonol and PA biosynthesis in cucumber. However, it remains unclear that whether PAs can inhibit the growth of F. solani and whether CsMYB60 serves as a target gene for increasing resistance to phytopathogens in cucumber. In this study, we demonstrated that PAs (or their building block, catechin) could increase the resistance of cucumber seedlings to F. solani both in vitro and in vivo. The addition of catechins, or crude leaf extracts treated with different concentrations of catechins in culture medium, could significantly inhibit the hyphal growth of F. solani. On the other hand, cucumber seedlings treated with catechins showed higher resistance to F. solani than the seedlings of control group. Moreover, transgenic cucumber seedlings overexpressing CsMYB60, with the observed accumulation of PAs, were more resistant to F. solani than the nontransgenic siblings. Therefore, our results suggest that PAs (or catechin) can serve as a biological control agent to protect cucumber plants from the infection of F. solani. More importantly, CsMYB60 holds great promise as a target gene to confer disease resistance during the molecular breeding in cucumber.

Ectopic Expression of CsSUN in Tomato Results in Elongated Fruit Shape via Regulation of Longitudinal Cell Division.

Fruit shape, an important agronomic trait of cucumber (Cucumis sativus L.), is tightly controlled by a series of genes such as CsSUN, a homologue of SlSUN that is responsible for the tomato (Solanum lycopersicum) fruit shape via the modulation of cell division. However, the direct genetic evidence about the CsSUN-mediated regulation of fruit shape is still scarce, limiting our mechanistic understanding of the biological functions of CsSUN. Here, we introduced CsSUN into the round-fruited tomato inbred line 'SN1' (wild type, WT) via the Agrobacterium tumefaciens-mediated method. The high and constitutive expression of CsSUN was revealed by real-time PCR in all the tested tissues of the transgenic plants, especially in the fruits and ovaries. Phenotypic analyses showed that the ectopic expression of CsSUN increased fruit length while it decreased fruit diameter, thus leading to the enhanced fruit shape index in the transgenic tomato lines relative to the WT. Additionally, the reduction in the seed size and seed-setting rate and the stimulation of seed germination were observed in the CsSUN-expressed tomato. A histological survey demonstrated that the elongated fruits were mainly derived from the significant increasing of the longitudinal cell number, which compensated for the negative effects of decreased cell area in the central columellae. These observations are different from action mode of SlSUN, thus shedding new insights into the SUN-mediated regulation of fruit shape.

Morphological Characterization and Integrated Transcriptome and Proteome Analysis of Organ Development Defective 1 (odd1) Mutant in Cucumis sativus L.

Cucumber (Cucumis sativus L.) is an economically important vegetable crop with the unique growth habit and typical trailing shoot architecture of Cucurbitaceae. Elucidating the regulatory mechanisms of growth and development is significant for improving quality and productivity in cucumber. Here we isolated a spontaneous cucumber mutant organ development defective 1 (odd1) with multiple morphological changes including root, plant stature, stem, leaf, male and female flowers, as well as fruit. Anatomical and cytological analyses demonstrated that both cell size and number decreased, and the shoot apical meristem (SAM) was smaller in odd1 compared with WT. Pollen vigor and germination assays and cross tests revealed that odd1 is female sterile, which may be caused by the absence of ovules. Genetic analysis showed that odd1 is a recessive single gene mutant. Using the MutMap strategy, the odd1 gene was found to be located on chromosome 5. Integrated profiling of transcriptome and proteome indicated that the different expression genes related to hormones and SAM maintenance might be the reason for the phenotypic changes of odd1. These results expanded the insight into the molecular regulation of organ growth and development and provided a comprehensive reference map for further studies in cucumber.

[Effect of circ-SFMBT2 on the biological behavior of non-small cell lung cancer cells by targeting the miR-7-5p/ADAM10 axis].

OBJECTIVE: To explore the effect of circ-SFMBT2 on the biological behavior of non-small cell lung cancer (NSCLC) cells and its regulatory role on the miR-7-5p/ADAM10 axis. METHODS: qRT-PCR and Western blotting were used to determine the expression of circ-SFMBT2, miR-7-5p, and ADAM10 in NSCLC tissues and adjacent tissues. Pearson analysis was used to analyze the correlation between circ-SFMBT2 and miR-7-5p, and between miR-7-5p and ADAM10. In vitro cultured human bronchial epithelial-like cells (HBE) and lung cancer cell lines H1650, H460, A549, H1299. CCK-8 and EdU methods were used to assess the ability of cell proliferation. Plate experiment was used to detect the clone formation ability. Flow cytometry was used to detect the apoptosis rate. Transwell experiment was used to detect cell invasion ability. Dual luciferase reporter experiment detects the targeting relationship between circ-SFMBT2 and miR-7-5p, and between miR-7-5p and ADAM10. Transplanted tumor experiment in nude mice assessed the effect of knocking down circ-SFMBT2 on the growth of transplanted tumor. Immunohistochemical experiments were performed to detect the positive rates of ADAM10 and Ki67 proteins in transplanted tumor tissues. RESULTS: The expression levels of circ-SFMBT2 and ADAM10 were increased in NSCLC tissues and cell lines, while decreased the expression of miR-7-5p. circ-SFMBT2 was negatively correlated with miR-7-5p, while miR-7-5p was negatively correlated with ADAM10. Silencing the overexpression of circ-SFMBT2 and miR-7-5p could inhibit cell proliferation, clone formation and invasion, and also promote apoptosis. circ-SFMBT2 could target miR-7-5p, and ADAM10 was the target gene of miR-7-5p. The combined effect of silencing circ-SFMBT2 and inhibition of miR-7-5p, as well as miR-7-5p overexpression and ADAM10 overexpression could promote cell proliferation, clone formation and invasion, and also suppress cell apoptosis. Silencing circ-SFMBT2 could inhibit the growth of transplanted tumors. CONCLUSION: Silencing circ-SFMBT2 can suppress the proliferation, clone formation, invasion ability and induce apoptosis of NSCLC cells by regulating the miR-7-5p/ADAM10 axis.

Transcriptome profiling reveals response genes for downy mildew resistance in cucumber.

MAIN CONCLUSION: We discovered a potential defense pathway of cucumber to downy mildew. The signaling that activates the pathways of ROS and lignin accumulation may play an important role in the defense response. Many resistance genes were identified by transcriptome analysis. Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the most destructive diseases and causes severe yield losses of cucumber. However, the genes and pathways involved in regulating DM resistance were still poorly understood. In our study, we observed that the highly sensitive inbred line 53 (IL53) exhibited more severe disease symptoms than the highly resistant inbred line 51 (IL51) under P. cubensis infection. Furthermore, lignin, limiting the germination and extension of P. cubensis, and H2O2, as a signaling molecule during the resistant process, were both shown to increase, indicating that the signaling that activates these pathways might be responsible for the resistance divergence between IL51 and IL53. Transcriptome analysis, using the resistant and susceptible pools in F2 populations with IL51 and IL53 as parents, showed that a series of differentially expressed genes was involved in multiple functions of defense response: pathogen-associated molecular pattern recognition, signal transduction, reactive oxygen species and lignin accumulation, and transcription regulators. Combining physiological data with transcriptomes, we predicted a potential molecular mechanism of cucumber resistance to DM. Our research provided a foundation for further studies on the mechanism of cucumber resistance to DM.

Genome-wide identification and characterization of WOX genes in Cucumis sativus.

WUSCHEL-related homeobox (WOX) proteins are plant-specific transcription factors that are profoundly involved in regulation of plant development and stress responses. In this study, we totally identified 11 WOX transcription factor family members in cucumber (Cucumis sativus, CsWOX) genome and classified them into three clades with nine subclades based on phylogenetic analysis results. Alignment of amino acid sequences revealed that all WOX members in cucumber contained the typical homeodomain, which consists of 60-66 amino acids and is folded into a helix-turn-helix structure. Gene duplication event analysis indicated that CsWOX1a and CsWOX1b were a segment duplication pair, which might affect the number of WOX members in cucumber genome. The expression profiles of CsWOX genes in different tissues demonstrated that the members sorted into the ancient clade (CsWOX13a and CsWOX13b) were constitutively expressed at higher levels in comparison to the others. Cis-element analysis in promoter regions suggested that the expression of CsWOX genes was associated with phytohormone pathways and stress responses, which was further supported by RNA-seq data. Taken together, our results provide new insights into the evolution of cucumber WOX genes and improve our understanding about the biological functions of the CsWOX gene family.

Overexpression of SlMYB75 enhances resistance to Botrytis cinerea and prolongs fruit storage life in tomato.

KEY MESSAGE: SlMYB75 increased the accumulation of JA and improved the scavenging of excess H2O2 to resist B. cinerea. Overexpression of SlMYB75 greatly prolongs tomato fruit storage life. Botrytis cinerea (B. cinerea) is a major threat to the production and storage life of tomato (Solanum lycopersicum) fruit around the world. SlMYB75 is an R2R3MYB transcription factor associated with the biosynthesis of anthocyanidin, but little is known about its function in the resistance of tomato to B. cinerea. In this study, we found that the overexpression of SlMYB75 regulated the accumulation of jasmonic acid (JA) and promoted the JA-mediated signaling pathway to resist B. cinerea infection. Moreover, the activities of peroxidase and superoxide dismutase, which were activated to scavenge hydrogen peroxide produced as a result of the B. cinerea infection, were enhanced in the transgenic tomato plants. Scanning electron microscopy images showed that the wax on the fruit skin surface was significantly decreased in the transgenic tomatoes compared with the wild type. However, SlMYB75 prolonged fruit storage life by both enhancing resistance to B. cinerea and directly downregulating the fruit shelf life-related gene SlFSR. Collectively, this study provides a good candidate gene for breeding high-quality tomatoes with a long storage life and high disease resistance.

Genome-wide identification and characterization of cucumber bHLH family genes and the functional characterization of CsbHLH041 in NaCl and ABA tolerance in Arabidopsis and cucumber.

BACKGROUND: The basic/helix-loop-helix (bHLH) transcription factor family exists in all three eukaryotic kingdoms as important participants in biological growth and development. To date, the comprehensive genomic and functional analyses of bHLH genes has not been reported in cucumber (Cucumis sativus L.). RESULTS: Here, a total of 142 bHLH genes were identified and classified into 32 subfamilies according to the conserved motifs, phylogenetic analysis and gene structures in cucumber. The sequences of CsbHLH proteins were highly conserved based on the results of multiple sequence alignment analyses. The chromosomal distribution, synteny analysis, and gene duplications of these 142 CsbHLHs were further analysed. Many elements related to stress responsiveness and plant hormones were present in the promoter regions of CsbHLH genes based on a cis-element analysis. By comparing the phylogeny of cucumber and Arabidopsis bHLH proteins, we found that cucumber bHLH proteins were clustered into different functional clades of Arabidopsis bHLH proteins. The expression analysis of selected CsbHLHs under abiotic stresses (NaCl, ABA and low-temperature treatments) identified five CsbHLH genes that could simultaneously respond to the three abiotic stresses. Tissue-specific expression profiles of these five genes were also analysed. In addition, 35S:CsbHLH041 enhanced the tolerance to salt and ABA in transgenic Arabidopsis and in cucumber seedlings, suggesting CsbHLH041 is an important regulator in response to abiotic stresses. Lastly, the functional interoperability network among the CsbHLH proteins was analysed. CONCLUSION: This study provided a good foundation for further research into the functions and regulatory mechanisms of CsbHLH proteins and identified candidate genes for stress resistance in cucumber.

Genome-wide analysis of the WRKY gene family in the cucumber genome and transcriptome-wide identification of WRKY transcription factors that respond to biotic and abiotic stresses.

BACKGROUND: Cucumber (Cucumis sativus L.) is an economically important vegetable crop species. However, it is susceptible to various abiotic and biotic stresses. WRKY transcription factors play important roles in plant growth and development, particularly in the plant response to biotic and abiotic stresses. However, little is known about the expression pattern of WRKY genes under different stresses in cucumber. RESULTS: In the present study, an analysis of the new assembly of the cucumber genome (v3.0) allowed the identification of 61 cucumber WRKY genes. Phylogenetic and synteny analyses were performed using related species to investigate the evolution of the cucumber WRKY genes. The 61 CsWRKYs were classified into three main groups, within which the gene structure and motif compositions were conserved. Tissue expression profiles of the WRKY genes demonstrated that 24 CsWRKY genes showed constitutive expression (FPKM > 1 in all samples), and some WRKY genes showed organ-specific expression, suggesting that these WRKYs might be important for plant growth and organ development in cucumber. Importantly, analysis of the CsWRKY gene expression patterns revealed that five CsWRKY genes strongly responded to both salt and heat stresses, 12 genes were observed to be expressed in response to infection from downy mildew and powdery mildew, and three CsWRKY genes simultaneously responded to all treatments analysed. Some CsWRKY genes were observed to be induced/repressed at different times after abiotic or biotic stress treatment, demonstrating that cucumber WRKY genes might play different roles during different stress responses and that their expression patterns vary in response to stresses. CONCLUSIONS: Sixty-one WRKY genes were identified in cucumber, and insight into their classification, evolution, and expression patterns was gained in this study. Responses to different abiotic and biotic stresses in cucumber were also investigated. Our results provide a better understanding of the function of CsWRKY genes in improving abiotic and biotic stress resistance in cucumber.

Comprehensive analysis of multiprotein bridging factor 1 family genes and SlMBF1c negatively regulate the resistance to Botrytis cinerea in tomato.

BACKGROUND: Multiprotein bridging factor 1 s (MBF1s) are members of the transcriptional co-activator family that have involved in plant growth, development and stress responses. However, little is known about the Solanum lycopersicum MBF1 (SlMBF1) gene family. RESULTS: In total, five SlMBF1 genes were identified based on the tomato reference genome, and these genes were mapped to five chromosomes. All of the SlMBF1 proteins were highly conserved, with a typical MBF1 domain and helix-turn-helix_3 domain. In addition, the promoter regions of the SlMBF1 genes have various stress and hormone responsive cis-regulatory elements. Encouragingly, the SlMBF1 genes were expressed with different expression profiles in different tissues and responded to various stress and hormone treatments. The biological function of SlMBF1c was further identified through its overexpression in tomato, and the transgenic tomato lines showed increased susceptibility to Botrytis cinerea (B. cinerea). Additionally, the expression patterns of salicylic acid (SA)-, jasmonic acid (JA)- and ethylene (ET)- mediated defense related genes were altered in the transgenic plants. CONCLUSIONS: Our comprehensive analysis provides valuable information for clarifying the evolutionary relationship of the SlMBF1 members and their expression patterns in different tissues and under different stresses. The overexpression of SlMBF1c decreased the resistance of tomato to B. cinerea through enhancing the gene expression of the SA-mediated signaling pathway and depressing JA/ET-mediated signaling pathways. These results will facilitate future functional studies of the transcriptional co-activator family.

CsMYB60 is a key regulator of flavonols and proanthocyanidans that determine the colour of fruit spines in cucumber.

Spine colour is an important fruit quality trait that influences the commercial value of cucumber (Cucumis sativus). However, little is known about the metabolites and the regulatory mechanisms of their biosynthesis in black spine varieties. In this study, we determined that the pigments of black spines are flavonoids, including flavonols and proanthocyanidins (PAs). We identified CsMYB60 as the best candidate for the previously identified B (Black spine) locus. Expression levels of CsMYB60 and the key genes involved in flavonoid biosynthesis were higher in black-spine inbred lines than that in white-spine lines at different developmental stages. The insertion of a Mutator-like element (CsMULE) in the second intron of CsMYB60 decreased its expression in a white-spine line. Transient overexpression assays indicated that CsMYB60 is a key regulatory gene and Cs4CL is a key structural gene in the pigmentation of black spines. In addition, the DNA methylation level in the CsMYB60 promoter was much lower in the black-spine line compared with white-spine line. The CsMULE insert may decrease the expression level of CsMYB60, causing hindered synthesis of flavonols and PAs in cucumber fruit spines.

Comprehensive Analysis of Cucumber Gibberellin Oxidase Family Genes and Functional Characterization of CsGA20ox1 in Root Development in Arabidopsis.

Cucumber (Cucumis sativus L.) is an important vegetable crop worldwide and gibberellins (GAs) play important roles in the regulation of cucumber developmental and growth processes. GA oxidases (GAoxs), which are encoded by different gene subfamilies, are particularly important in regulating bioactive GA levels by catalyzing the later steps in the biosynthetic pathway. Although GAoxs are critical enzymes in GA synthesis pathway, little is known about GAox genes in cucumber, in particular about their evolutionary relationships, expression profiles and biological function. In this study, we identified 17 GAox genes in cucumber genome and classified them into five subfamilies based on a phylogenetic tree, gene structures, and conserved motifs. Synteny analysis indicated that the tandem duplication or segmental duplication events played a minor role in the expansion of cucumber GA2ox, GA3ox and GA7ox gene families. Comparative syntenic analysis combined with phylogenetic analysis provided deep insight into the phylogenetic relationships of CsGAox genes and suggested that protein homology CsGAox are closer to AtGAox than OsGAox. In addition, candidate transcription factors BBR/BPC (BARLEY B RECOMBINANT/BASIC PENTACYSTEINE) and GRAS (GIBBERELLIC ACID-INSENSITIVE, REPRESSOR of GAI, and SCARECROW) which may directly bind promoters of CsGAox genes were predicted. Expression profiles derived from transcriptome data indicated that some CsGAox genes, especially CsGA20ox1, are highly expressed in seedling roots and were down-regulated under GA3 treatment. Ectopic over-expression of CsGA20ox1 in Arabidopsis significantly increased primary root length and lateral root number. Taken together, comprehensive analysis of CsGAoxs would provide a basis for understanding the evolution and function of the CsGAox family.

A fragment substitution in the promoter of CsHDZIV11/CsGL3 is responsible for fruit spine density in cucumber (Cucumis sativus L.).

KEY MESSAGE: The indel in the promoter of CsHDZIV11 co-segregates with fruit spine density and could be used for molecular breeding in cucumber. Fruit spine density is an important quality trait for marketing in cucumber (Cucumis sativus L.). However, the molecular basis of fruit spine density in cucumber remains unclear. In this study, we isolated a mutant, few spines 1 (fs1), from CNS2 (wild type, WT), a North China-type cucumber with a high density of fruit spines. Genetic analysis showed that fs1 was controlled by a single recessive Mendelian factor. Bulked segregant analysis combined with genome resequencing were used for mapping fs1 in the F2 population derived from a cross between the fs1 mutant and WT, and it was located on chromosome 6 through association analysis. To develop more polymorphic markers to locate fs1, another F2 population was constructed from the cross between fs1 and 'Chinese long' 9930. Then, fs1 was narrowed down to a 110.4-kb genomic region containing 25 annotated genes. A fragment substitution was identified in the promoter region of Csa6M514870 between fs1 and WT. This fragment in fs1 was also present in wild cucumber. Csa6M514870 encodes a PDF2-related protein, a homeodomain-leucine zipper IV transcription factor (CsHDZIV11/CsGL3) sharing high identity and similarity with proteins related to trichome formation or epidermal cell differentiation. Quantitative reverse-transcription PCR revealed a higher expression level of CsHDZIV11 in young fruits from fs1 compared to WT. A molecular marker based on this indel co-segregated with the spine density. This work provides a solid foundation not only for understanding the molecular mechanism of fruit spine density, but also for molecular breeding in cucumber.

The identification of Cucumis sativus Glabrous 1 (CsGL1) required for the formation of trichomes uncovers a novel function for the homeodomain-leucine zipper I gene.

The spines and bloom of cucumber (Cucumis sativus L.) fruit are two important quality traits related to fruit market value. However, until now, none of the genes involved in the formation of cucumber fruit spines and bloom trichomes has been identified. Here, the characterization of trichome development in wild-type (WT) cucumber and a spontaneous mutant, glabrous 1 (csgl1) controlled by a single recessive nuclear gene, with glabrous aerial organs, is reported. Via map-based cloning, CsGL1 was isolated and it was found that it encoded a member of the homeodomain-leucine zipper I (HD-Zip I) proteins previously identified to function mainly in the abiotic stress responses of plants. Tissue-specific expression analysis indicated that CsGL1 was strongly expressed in trichomes and fruit spines. In addition, CsGL1 was a nuclear protein with weak transcriptional activation activity in yeast. A comparative analysis of the digital gene expression (DGE) profile between csgl1 and WT leaves revealed that CsGL1 had a significant influence on the gene expression profile in cucumber, especially on genes related to cellular process, which is consistent with the phenotypic difference between csgl1 and the WT. Moreover, two genes, CsMYB6 and CsGA20ox1, possibly involved in the formation of cucumber trichomes and fruit spines, were characterized. Overall, the findings reveal a new function for the HD-Zip I gene subfamily, and provide some candidate genes for genetic engineering approaches to improve cucumber fruit external quality.

Genome-wide identification and characterization of R2R3MYB family in Solanum lycopersicum.

The R2R3MYB proteins comprise one of the largest families of transcription factors and play regulatory roles in developmental processes and defense responses in plants. However, there has been relatively little effort to systematically carry out comprehensive genomic and functional analyses of these genes in tomato (Solanum lycopersicum L.), a reference species for Solanaceae plants, and the model plant for fruit development. In this study, a total of 121 R2R3MYB genes were identified in the tomato genome released recently and further classified into 29 subgroups based on the phylogenetic analysis of the complete protein sequences. Phylogenetic comparison of the members of this superfamily among tomato, Arabidopsis, grape, rice, poplar, soybean, cucumber and apple revealed that the putative functions of some tomato R2R3MYB proteins were clustered into the Arabidopsis functional clades. The chromosome distribution pattern revealed that tomato R2R3MYB genes were enriched on several chromosomes and 52 % of the family members were tandemly duplicated genes. Tissue specificity or different expression levels of SlR2R3MYBs in different tissues suggested differential regulation of tissue development as well as metabolic regulation. The transcript abundance level analysis during abiotic conditions identified a group of R2R3MYB genes that responded to one or more treatments suggesting that the SlR2R3MYBs played major roles in the plant response to abiotic conditions and involved in signal transduction pathways. This study not only provides a solid foundation for further functional dissection of tomato R2R3MYB family genes, but may also be profitable for, in the future, the improvement of tomato stress tolerance and fruit quality.

Genome-wide analysis of the WD-repeat protein family in cucumber and Arabidopsis.

The WD-repeat (WDR) proteins comprise an astonishingly diverse superfamily of regulatory proteins. To date, genome-wide characterization of this family has only been conducted in Arabidopsis and little is known about WDR genes in cucumber (Cucumis sativus L.). This study identified 191 cucumber WDR genes in the latest cucumber genome and the CsWDR family contained a smaller number of identified genes compared to Arabidopsis. The results of this study were also supported by genome distribution and gene duplication analysis. Phylogenetic analysis showed that the WDR proteins could be classified into 21 subgroups. Moreover, an additional 12 AtWDR proteins were also identified and a complete overview of this gene family in Arabidopsis is presented, including the phylogeny, chromosome locations and duplication events. In addition, a comparative analysis between these genes in cucumber and Arabidopsis was performed and it suggested that there was strong gene conservation and that there was an expansion of particular functional genes during the evolution of the two species. The transcript abundance level analysis during abiotic stress (NaCl, ABA and low temperature treatments) identified six CsWDR genes that responded to one or more treatments. Tissue-specific expression profiles of these six genes were also analyzed. This study has produced a comparative genomics analysis of the WDR gene family in cucumber and Arabidopsis and provides the first steps towards the selection of CsWDR genes for cloning and functional dissection that can be used in further studies into their roles in cucumber stress resistance.

A rice quantitative trait locus for salt tolerance encodes a sodium transporter.

Many important agronomic traits in crop plants, including stress tolerance, are complex traits controlled by quantitative trait loci (QTLs). Isolation of these QTLs holds great promise to improve world agriculture but is a challenging task. We previously mapped a rice QTL, SKC1, that maintained K(+) homeostasis in the salt-tolerant variety under salt stress, consistent with the earlier finding that K(+) homeostasis is important in salt tolerance. To understand the molecular basis of this QTL, we isolated the SKC1 gene by map-based cloning and found that it encoded a member of HKT-type transporters. SKC1 is preferentially expressed in the parenchyma cells surrounding the xylem vessels. Voltage-clamp analysis showed that SKC1 protein functions as a Na(+)-selective transporter. Physiological analysis suggested that SKC1 is involved in regulating K(+)/Na(+) homeostasis under salt stress, providing a potential tool for improving salt tolerance in crops.

The phosphatidylcholine diacylglycerol cholinephosphotransferase is required for efficient hydroxy fatty acid accumulation in transgenic Arabidopsis.

We previously identified an enzyme, phosphatidylcholine diacylglycerol cholinephosphotransferase (PDCT), that plays an important role in directing fatty acyl fluxes during triacylglycerol (TAG) biosynthesis. The PDCT mediates a symmetrical interconversion between phosphatidylcholine (PC) and diacylglycerol (DAG), thus enriching PC-modified fatty acids in the DAG pool prior to forming TAG. We show here that PDCT is required for the efficient metabolism of engineered hydroxy fatty acids in Arabidopsis (Arabidopsis thaliana) seeds. When a fatty acid hydroxylase (FAH12) from castor (Ricinus communis) was expressed in Arabidopsis seeds, the PDCT-deficient mutant accumulated only about half the amount of hydroxy fatty acids compared with that in the wild-type seeds. We also isolated a PDCT from castor encoded by the RcROD1 (Reduced Oleate Desaturation1) gene. Seed-specific coexpression of this enzyme significantly increased hydroxy fatty acid accumulation in wild type-FAH12 and in a previously produced transgenic Arabidopsis line coexpressing a castor diacylglycerol acyltransferase 2. Analyzing the TAG molecular species and regiochemistry, along with analysis of fatty acid composition in TAG and PC during seed development, indicate that PDCT acts in planta to enhance the fluxes of fatty acids through PC and enrich the hydroxy fatty acids in DAG, and thus in TAG. In addition, PDCT partially restores the oil content that is decreased in FAH12-expressing seeds. Our results add a new gene in the genetic toolbox for efficiently engineering unusual fatty acids in transgenic oilseeds.