[Show abstract][Hide abstract] ABSTRACT: The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ~100 times larger than its ancestor. Furthermore, we discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions. This study outlines the accomplishments as well as the costs of historical selection and provides molecular insights toward further improvement.
[Show abstract][Hide abstract] ABSTRACT: The tomato (Solanum lycopersicum) protein MADS-RIN plays important roles in fruit ripening. In this study, the functions of two homologous tomato proteins, FUL1 and FUL2, which contain conserved MIKC domains that typify plant MADS-box proteins, and which interact with MADS-RIN, were analysed. Transgenic functional analysis showed that FUL1 and FUL2 function redundantly in fruit ripening regulation, but exhibit distinct roles in the regulation of cellular differentiation and expansion. Over-expression of FUL2 in tomato resulted in a pointed tip at the blossom end of the fruit, together with a thinner pericarp, reduced stem diameter, and smaller leaves, but no obvious phenotypes resulted from FUL1 over-expression. Dual suppression of FUL1 and FUL2 substantially inhibited fruit ripening by blocking ethylene biosynthesis and decreasing carotenoid accumulation. In addition, the levels of transcript corresponding to ACC SYNTHASE2 (ACS2), which plays a key role in ethylene biosynthesis, were significantly decreased in the FUL1/FUL2 knock-down tomato fruits. Overall, our results suggest that FUL proteins can regulate tomato fruit ripening through fine-tuning ethylene biosynthesis and the expression of ripening-related genes.
Journal of Experimental Botany 04/2014; · 5.79 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Dof (DNA binding with One Finger) family encoding single zinc finger proteins has been known as a family of plant-specific transcription factors. These transcription factors are involved in a variety of functions of importance for different biological processes in plants. In the current study, we identified 34 Dof family genes in tomato, distributed on 11 chromosomes. A complete overview of SlDof genes in tomato is presented, including the gene structures, chromosome locations, phylogeny, protein motifs and evolution pattern. Phylogenetic analysis of 34 SlDof proteins resulted in four classes constituting six clusters. In addition, a comparative analysis between these genes in tomato, Arabidopsis and rice was also performed. The tomato Dof family expansion has been dated to recent duplication events, and segmental duplication is predominant for the SlDof genes. Furthermore, the SlDof genes displayed differential expression either in their transcript abundance or in their expression patterns under normal growth conditions. This is the first step towards genome-wide analyses of the Dof genes in tomato. Our study provides a very useful reference for cloning and functional analysis of the members of this gene family in tomato and other species.
Journal of Integrative Plant Biology 03/2013; · 3.75 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: As a primary source of lycopene in the human diet, fleshy fruits synthesize this compound both de novo and via chlorophyll metabolism during ripening. SlSGR1 encodes a STAY-GREEN protein that plays a critical role in the regulation of chlorophyll degradation in tomato leaves and fruits. We report that SlSGR1 can regulate tomato (Solanum lycopersicum) lycopene accumulation through direct interaction with a key carotenoid synthetic enzyme SlPSY1, and can inhibit its activity. This interaction with SlSGR1 mediates lycopene accumulation during tomato fruit maturation. We confirmed this inhibitory activity in bacteria engineered to produce lycopene, where the introduction of SlSGR1 reduced dramatically lycopene biosynthesis. The repression of SlSGR1 in transgenic tomato fruits resulted in altered accumulation patterns of phytoene and lycopene, whilst simultaneously elevating SlPSY1 mRNA accumulation and plastid conversion at the early stages of fruit ripening, resulting in increased lycopene and β-carotene (four- and nine-fold, respectively) in red ripe fruits. SlSGR1 influences ethylene signal transduction via the altered expression of ethylene receptor genes and ethylene-induced genes. Fruit shelf-life is extended significantly in SlSGR1-repressed tomatoes. Our results indicate that SlSGR1 plays a pivotal regulatory role in color formation and fruit ripening regulation in tomato, and further suggest that SlSGR1 activity is mediated through direct interaction with PSY1.
[Show abstract][Hide abstract] ABSTRACT: Cyclins play important roles in cell division and cell expansion. They also interact with cyclin-dependent kinases to control cell cycle progression in plants. Our genome-wide analysis identified 52 expressed cyclin genes in tomato. Phylogenetic analysis of the deduced amino sequences of tomato and Arabidopsis cyclin genes divided them into 10 types, A-, B-, C-, D-, H-, L-, T-, U-, SDS- and J18. Pfam analysis indicated that most tomato cyclins contain a cyclin-N domain. C-, H- and J18 types only contain a cyclin-C domain, and U-type cyclins contain another potential cyclin domain. All of the cyclin genes are distributed throughout the tomato genome except for chromosome 8, and 30 of them were found to be segmentally duplicated; they are found on the duplicate segments of chromosome 1, 2, 3, 4, 5, 6, 10, 11 and 12, suggesting that tomato cyclin genes experienced a mass of segmental duplication. Quantitative real-time polymerase chain reaction analysis indicates that the expression patterns of tomato cyclin genes were significantly different in vegetative and reproductive stages. Transcription of most cyclin genes can be enhanced or repressed by exogenous application of gibberellin, which implies that gibberellin maybe a direct regulator of cyclin genes. The study presented here may be useful as a guide for further functional research on tomato cyclins.
International Journal of Molecular Sciences 01/2013; 15(1):120-40. · 2.46 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: As a vital antioxidant, L-ascorbic acid (AsA) affects diverse biological processes in higher plants. Lack of AsA in cell impairs plant development. In the present study, we manipulated a gene of GDP-mannose pyrophosphorylase which catalyzes the conversion of D-mannose-1-P to GDP-D-mannose in AsA biosynthetic pathway and found out the phenotype alteration of tomato. In the tomato genome, there are four members of GMP gene family and they constitutively expressed in various tissues in distinct expression patterns. As expected, over-expression of SlGMP3 increased total AsA contents and enhanced the tolerance to oxidative stress in tomato. On the contrary, knock-down of SlGMP3 significantly decreased AsA contents below the threshold level and altered the phenotype of tomato plants with lesions and further senescence. Further analysis indicated the causes for this symptom could result from failing to instantly deplete the reactive oxygen species (ROS) as decline of free radical scavenging activity. More ROS accumulated in the leaves and then triggered expressions of defence-related genes and mimic symptom occurred on the leaves similar to hypersensitive responses against pathogens. Consequently, the photosynthesis of leaves was dramatically fallen. These results suggested the vital roles of AsA as an antioxidant in leaf function and defence response of tomato.
PLoS ONE 01/2013; 8(4):e61987. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The plant-specific NAC (NAM, ATAF1,2, CUC2) transcription factors play significant roles in diverse physiological processes. In this study, we determined the regulation of a stress-related tomato (Solanum lycopersicum) NAC1 (SlNAC1) transcription factor at both the transcriptional and the post-translational level. The SlNAC1 protein was found to be stable in the presence of proteasome-specific inhibitor MG132 or MG115 and ubiquitinated in plant cells, suggesting that the SlNAC1 is subject to the ubiquitin-proteasome system-mediated degradation. Deletion analysis identified a short segment of 10 amino acids (aa261-270) that was required for ubiquitin-proteasome system-mediated degradation, among which two leucine residues (L268 and L269) were critical for the protein instability of SlNAC1. Fusion of the degron (SlNAC1(191-270) ) containing these 10 amino acids to green fluorescent protein was found to be sufficient to trigger the degradation of the fusion protein. In addition, the SlNAC1 gene is strongly upregulated during Pseudomonas infection, while repression of the NAC1 ortholog in Nicotiana benthamiana resulted in enhanced susceptibility to Pseudomonas bacteria. These results suggest that rapid upregulation of the NAC1 gene resulting in more protein production is likely one of the strategies plants use to defend themselves against pathogen infection.
[Show abstract][Hide abstract] ABSTRACT: Universal stress protein (USP) appears to play an active role in the abiotic stress response, but their functions remain largely unknown in plants. A USP gene (SpUSP) was cloned from wild tomato (Solanum pennellii) and functionally characterized in cultivated tomato in the present study. The SpUSP transcript is abundantly accumulated in leaf stomata and its expression varied with the circadian rhythm. SpUSP was remarkably induced by dehydration, salt stress, oxidative stress, and the phytohormone abscisic acid (ABA) etc. This protein was predominantly localized in the nucleus and cell membrane. Overexpressing SpUSP increased drought tolerance of tomato in the seedling and adult stages. Under drought stress, the ABA content significantly increased in the SpUSP-overexpressing plants, which induced stomatal closure and reduced water loss, leading to the enhancement of drought tolerance. Based on the microarray data, a large number of chlorophyll a/b-binding proteins and photosystem-related genes were up-regulated in the SpUSP-overexpressing plants under drought conditions, which possibly enhanced the stomatal sensivitity to ABA and maintained the photosynthetic function. SpUSP overexpression also alleviated the oxidative damage accompanied by oxidative stress-responsive gene activation and osmolyte accumulation. Annexin (SGN-U314161) was found to interacte with SpUSP in the yeast two-hybrid method. This interaction was further confirmed by the bimolecular fluorescence complementation assay. The present study demonstrated that the annexin-interacting SpUSP plays important roles in the drought tolerance of tomato by influencing ABA-induced stomatal movement, increasing photosynthesis, and alleviating oxidative stress.
Journal of Experimental Botany 08/2012; 63(15):5593-606. · 5.79 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
[Show abstract][Hide abstract] ABSTRACT: Annexins have been suggested to play pivotal roles in stress resistance and plant development. However, related studies on fruit-bearing plants, especially on fruit development, are very limited. In the present study, we provide a comprehensive overview of the annexin family in tomato, describing the gene structure, promoter cis-regulatory elements, organ expression profile, and gene expression patterns under hormone and stress treatments. Bioinformatic analysis revealed that the nine tomato annexins were structurally different from their animal counterparts, but highly conserved annexin domains were still found in most of them. Cis-regulatory element prediction showed that there were important elements in the 2kb upstream promoter regions, including stress- and hormone-responsive-related elements. The expression patterns of these genes were investigated, and the results revealed that they were regulated under developmental processes and environmental stimuli. Among them, AnnSl1.1 and AnnSl2 were highly expressed in most of the tested organs. Genes preferentially or specifically expressed in organs, such as stigma or ovary (AnnSl6), stamen (AnnSl8), and fruit pericarp (AnnSl1.2 and AnnSl9), were identified. Some annexin genes were induced by plant hormones including abscisic acid (AnnSl3, AnnSl6, AnnSl8, and AnnSl9) and gibberellic acid (AnnSl1.1, AnnSl1.2, AnnSl4, and AnnSl7). Most of these annexin genes were induced by salt, drought, wounding, and heat or cold stresses. The present study provides significant information for understanding the diverse roles of annexins in tomato growth and development.
[Show abstract][Hide abstract] ABSTRACT: The wild species Solanum habrochaites is more cold tolerant than the cultivated tomato (S. lycopersicum). To explore the mechanisms underlying cold tolerance of S. habrochaites, seedlings of S. habrochaites LA1777 introgression lines (ILs), as well as the two parents, were evaluated under low temperature (4°C). The IL LA3969 and its donor parent LA1777 were found to be more cold tolerant than the recurrent parent S. lycopersicum LA4024. The differences in physiology and global gene expression between cold-tolerant (LA1777 and LA3969) and -sensitive (LA4024) genotypes under cold stress were further investigated. Comparative transcriptome analysis identified 1613, 1456, and 1523 cold-responsive genes in LA1777, LA3969, and LA4024, respectively. Gene ontology (GO) term enrichment analysis revealed that more GO biological process terms were significantly enriched among the up-regulated genes in the two tolerant genotypes, whereas more biological processes were significantly repressed by cold stress in the sensitive one. A total of 92 genes with significant differential expression between tolerant and sensitive genotypes under cold stress were identified. Among these, many stress-related GO terms were significantly enriched, such as 'response to stimulus' and 'response to stress'. Moreover, GO terms 'response to hormone stimulus', 'response to reactive oxygen species (ROS)', and 'calcium-mediated signaling' were also overrepresented. Several transcripts involved in hormone or ROS homeostasis were also differentially expressed. ROS, hormones, and calcium as signaling molecules may play important roles in regulating gene expression in response to cold stress. Moreover, the expression of various transcription factors, post-translational proteins, metabolic enzymes, and photosynthesis-related genes was also specifically modulated. These specific modifications may play pivotal roles in conferring cold tolerance in tomato. These results not only provide new insights into the molecular mechanisms of cold tolerance in tomato, but also provide potential candidate genes for genetic improvement.
PLoS ONE 01/2012; 7(11):e50785. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Trichomes are universal biological structures originating from the aerial epidermis, which serve as an excellent model to study plant differentiation at the cell level. Although the pathway regulating trichome formation in the Rosids has been well characterized, only very recently a few genes were identified for trichome initiation in the Asterids. In this study, we cloned Woolly (Wo), essential for trichome formation in tomato. Transgenic experiments revealed that the woolly phenotype is caused by the mutation in Wo which encodes a homeodomain protein containing a bZIP motif and a START domain. We identified three alleles of Wo and found that each allele contains a missense mutation, which respectively results in an amino acid substitution at the C terminus. Microarray and expression analysis showed that the expression of a B-type cyclin gene, SlCycB2, is possibly regulated by Wo, which also participates in trichome formation. Suppression of Wo or SlCycB2 expression by RNAi decreased the number of type I trichomes, and direct protein-protein interaction was detected between them, implying that both proteins may work together in the regulation of this type of trichome formation. Cytological observation and Wo transcript analysis in the developing seeds showed that embryo development was also correlated with Wo.
Proceedings of the National Academy of Sciences 07/2011; 108(29):11836-41. · 9.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Trichomes are small hairs that originate from the epidermal cells of nearly all land plants, and they exist in unicellular and multicellular forms. The regulatory pathway of unicellular trichomes in Arabidopsis is well characterized. However, little is known about the multicellular trichome formation in tomato (Solanum lycopersicum). The woolly (Wo) gene controls multicellular trichome initiation and leads to embryonic lethality when homozygous in tomato. To clone and characterize Wo, the gene was fine-mapped to a DNA fragment of ~200 kb using the map-based cloning strategy. A series of sequence-based molecular markers, including simple sequence repeat, sequence characterized amplified region, and cleaved amplified polymorphic sequence were utilized in this study. Analysis of the sequence indicated that this region carries 19 putative open reading frames. These results will provide not only the important information for the isolation and characterization of Wo but also the starting point for studying the regulatory pathway responsible for trichome formation and embryonic lethality in tomato.
Theoretical and Applied Genetics 06/2011; 123(4):625-33. · 3.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: NAC (for NAM, ATAF1, 2, and CUC2) family genes have been found to play an important role in diversified developmental processes and environmental responses. A new NAC-type transcription factor SlNAC3 was primarily identified and isolated from the cDNA libraries of tomato cultivar Ailsa Craig. It contains three exons and two introns within genomic DNA sequence and encodes a polypeptide of 329 amino acids. A plant-specific and conserved NAC domain is located in the N-terminus of SlNAC3. The protein SlNAC3 is subcellularly localized in the nucleus of onion epidemical cells and it has a transcriptional activation domain in the C-terminal region which shows extremely divergent among NACs. Phylogenetic analysis showed that SlNAC3 belonged to the OsNAC3 subgroup of the NAC protein family. Tissue expression profile analysis revealed that SlNAC3 was expressed mainly in flower, fruit and root. The transcription expression of SlNAC3 was inhibited by salt, drought stress and ABA treatment. These data demonstrate that SlNAC3 might interact with environmental and endogenous stimuli and probably function when plants response to salt and drought stresses through ABA signaling pathways as a transcriptional activator.
[Show abstract][Hide abstract] ABSTRACT: Expression of artificial microRNAs (amiRNAs) in plants can target and degrade the invading viral RNA, consequently conferring virus resistance. Two amiRNAs, targeting the coding sequence shared by the 2a and 2b genes and the highly conserved 3' untranslated region (UTR) of Cucumber mosaic virus (CMV), respectively, were generated and introduced into the susceptible tomato. The transgenic tomato plants expressing amiRNAs displayed effective resistance to CMV infection and CMV mixed with non-targeted viruses, including tobacco mosaic virus and tomato yellow leaf curl virus. A series of grafting assays indicate scions originated from the transgenic tomato plant maintain stable resistance to CMV infection after grafted onto a CMV-infected rootstock. However, the grafting assay also suggests that the amiRNA-mediated resistance acts in a cell-autonomous manner and the amiRNA signal cannot be transmitted over long distances through the vascular system. Moreover, transgenic plants expressing amiRNA targeting the 2a and 2b viral genes displayed slightly more effective to repress CMV RNA accumulation than transgenic plants expressing amiRNA targeting the 3' UTR of viral genome did. Our work provides new evidence of the use of amiRNAs as an effective approach to engineer viral resistance in the tomato and possibly in other crops.
Transgenic Research 06/2011; 20(3):569-81. · 2.61 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Plant microRNAs (miRNAs) are vital components of the translation control system that regulates plant development and reproduction. The biological function of sly-miR156 was investigated by over-expression in tomato plants. Transgenic tomato plants exhibited a drastically altered phenotype, with reduced height, smaller but more numerous leaves, and smaller fruit. The inflorescence structure of sly-miR156 over-expressing plants phenocopied the sft mutant. The putative targets of sly-miR156 were identified by data base search and included six SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box transcription factor genes. Their expression patterns were then determined in 35S-miR156a and wild type tomato plants. These target genes, as well as the tomato FLOWERING LOCUS T (FT) ortholog SFT, were significantly down-regulated in sly-miR156 over-expressing plants. These studies reveal novel phenotypes regulated by miR156.
[Show abstract][Hide abstract] ABSTRACT: Plant miRNA regulates multiple developmental and physiological processes, including drought responses. We found that the accumulation of Sly-miR169 in tomato (Solanum lycopersicum) was induced by drought stress. Consequently, Sly-miR169 targets, namely, three nuclear factor Y subunit genes (SlNF-YA1/2/3) and one multidrug resistance-associated protein gene (SlMRP1), were significantly down-regulated by drought stress. Constitutive over-expression of a miR169 family member, Sly-miR169c, in tomato plant can efficiently down-regulate the transcripts of the target genes. Compared with non-transgenic plants, transgenic plants over-expressing Sly-miR169c displayed reduced stomatal opening, decreased transpiration rate, lowered leaf water loss, and enhanced drought tolerance. Our study is the first to provide evidence that the Sly-miR169c negatively regulates stomatal movement in tomato drought responses.
[Show abstract][Hide abstract] ABSTRACT: GDP-Mannose 3',5'-epimerase (GME; EC 220.127.116.11) catalyses the conversion of GDP-D-mannose to GDP-L-galactose, an important step in the ascorbic acid (AsA) biosynthesis pathway in higher plants. In this study, two members of the GME gene family were isolated from tomato (Solanum lycopersicum). Both SlGME genes encode 376 amino acids and share a 92% similarity with each other. Semi-quantitative RT-PCR indicated that SlGME1 was constantly expressed in various tissues, whereas SlGME2 was differentially expressed in different tissues. Transient expression of fused SlGME1-GFP (green fluorescent protein) and SlGME2-GFP in onion cells revealed the cytoplasmic localisation of the two proteins. Transgenic plants over-expressing SlGME1 and SlGME2 exhibited a significant increase in total ascorbic acid in leaves and red fruits compared with wild-type plants. They also showed enhanced stress tolerance based on less chlorophyll content loss and membrane-lipid peroxidation under methyl viologen (paraquat) stress, higher survival rate under cold stress, and significantly higher seed germination rate, fresh weight, and root length under salt stress. The present study demonstrates that the overexpression of two members of the GME gene family resulted in increased ascorbate accumulation in tomato and improved tolerance to abiotic stresses.
[Show abstract][Hide abstract] ABSTRACT: To unravel the molecular mechanisms of drought responses in tomato, gene expression profiles of two drought-tolerant lines identified from a population of Solanum pennellii introgression lines, and the recurrent parent S. lycopersicum cv. M82, a drought-sensitive cultivar, were investigated under drought stress using tomato microarrays. Around 400 genes identified were responsive to drought stress only in the drought-tolerant lines. These changes in genes expression are most likely caused by the two inserted chromosome segments of S. pennellii, which possibly contain drought-tolerance quantitative trait loci (QTLs). Among these genes are a number of transcription factors and signalling proteins which could be global regulators involved in the tomato responses to drought stress. Genes involved in organism growth and development processes were also specifically regulated by drought stress, including those controlling cell wall structure, wax biosynthesis, and plant height. Moreover, key enzymes in the pathways of gluconeogenesis (fructose-bisphosphate aldolase), purine and pyrimidine nucleotide biosynthesis (adenylate kinase), tryptophan degradation (aldehyde oxidase), starch degradation (beta-amylase), methionine biosynthesis (cystathionine beta-lyase), and the removal of superoxide radicals (catalase) were also specifically affected by drought stress. These results indicated that tomato plants could adapt to water-deficit conditions through decreasing energy dissipation, increasing ATP energy provision, and reducing oxidative damage. The drought-responsive genes identified in this study could provide further information for understanding the mechanisms of drought tolerance in tomato.
Journal of Experimental Botany 08/2010; 61(13):3563-75. · 5.79 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Purple flowering stalk (Brassica campestris ssp. chinensis var.purpurea Hort.) was generally regarded as a recalcitrant species for microspore culture in Brassica crops. Conditions for reliable induction of microspore embryogenesis were studied in 12 genotypes of purple flowering stalk. A treatment of short heat shock to microspore by incubating at 32 °C for 18 h was suitable for the survival of microspores, sustained cell divisions, and further induced embryogenesis. Subsequently, the reduced concentration of macro salts (1/2 NLN) provided an optimal condition for the development of embryoids. Under the optimized conditions for microspore embryoid development, 10 genotypes responded to microspore culture with the frequencies ranging from 2.7 to 70.5 embryoids per dish. However, regenerated plants were obtained from 9 genotypes, and more than 75% these regenerated plants were double haploid. This report establishes an efficient protocol for microspore culture and offers great potential for DH breeding in purple flowering stalk.
Scientia Horticulturae 01/2009; 121(4):419-424. · 1.50 Impact Factor