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Gao C.,China Agricultural University | Ju Z.,China Agricultural University | Li S.,China Agricultural University | Zuo J.,National Engineering Research Center for Vegetables | And 4 more authors.
Journal of Integrative Plant Biology | Year: 2013

Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important information about the gene function and regulatory mechanism. L-Ascorbic acid (AsA), which is an essential nutrient component for human health and plant metabolism, plays key roles in diverse biological processes such as cell cycle, cell expansion, stress resistance, hormone synthesis, and signaling. Here, we applied a weighted gene correlation network analysis approach based on gene expression values and AsA content data in ripening tomato (Solanum lycopersicum L.) fruit with different AsA content levels, which leads to identification of AsA relevant modules and vital genes in AsA regulatory pathways. Twenty-four modules were compartmentalized according to gene expression profiling. Among these modules, one negatively related module containing genes involved in redox processes and one positively related module enriched with genes involved in AsA biosynthetic and recycling pathways were further analyzed. The present work herein indicates that redox pathways as well as hormone-signal pathways are closely correlated with AsA accumulation in ripening tomato fruit, and allowed us to prioritize candidate genes for follow-up studies to dissect this interplay at the biochemical and molecular level. © 2013 Institute of Botany, Chinese Academy of Sciences.

Zhang X.,Beijing Institute of Technology | Zhang J.,Beijing Institute of Technology | Zhang Y.,Beijing Institute of Technology | Xin Y.,CAS Institute of Microbiology | He H.,National Engineering Research Center for Vegetables
International Journal of Systematic and Evolutionary Microbiology | Year: 2013

A novel actinomycete, strain W6T, was isolated from a soil sample of Yunnan Province, China. The bacterium was aerobic, non-motile, non-spore-forming and Gram-stain-positive. Genetic, phenotypic and chemical properties of the isolate were studied. 16S rRNA gene sequence data suggested that the novel isolate belonged to the genus Friedmanniella and shared 98.6 % sequence similarity with Friedmanniella antarctica DSM 11053T and Friedmanniella okinawensis DSM 21744T, the most closely related species. The cell-wall peptidoglycan contained LL-diaminopimelic acid, and mycolic acids were absent. The main menaquinone was MK-9(H4) and the predominant fatty acids were anteiso-C15:0 and iso-C15:0. The phospholipid profile contained phosphatidylglycerol, phosphatidylinositol, phosphatidylcholine and diphosphatidylglycerol. The DNA G+C content of strain W6T was 72 mol%. Strain W6T showed 30.0 % and 28.5 % DNA-DNA relatedness, respectively, to F. antarctica DSM 11053T and F. okinawensis DSM 21744T. The combined genotypic and phenotypic data showed that strain W6T should be assigned to the genus Friedmanniella as a representative of a novel species, for which the name Friedmanniella flava sp. nov. is proposed. The type strain is W6T (= CGMCC 4.6856T = JCM 17701T). © 2013 IUMS.

Zhang L.-Y.,Huazhong Agricultural University | Zhang L.-Y.,National Engineering Research Center for Vegetables | Zhang Y.-Y.,Huazhong Agricultural University | Chen R.-G.,Huazhong Agricultural University | And 4 more authors.
Plant Molecular Biology Reporter | Year: 2010

The full genomic region of the root knot nematode (Meloidogyne spp.) resistance gene Mi-1 was cloned from tomato and transformed into lettuce to investigate its function in a heterologous system. Transgenic lettuce lines containing the Mi-1 gene were developed using Agrobacterium-mediated transformation. Ectopic expression of the Mi-1 gene was observed in transgenic lines, and resistance to root knot nematode was improved. © Springer-Verlag 2009.

Guo S.,National Engineering Research Center for Vegetables | Guo S.,Cornell University | Zheng Y.,Cornell University | Zheng Y.,China Agricultural University | And 9 more authors.
BMC Genomics | Year: 2010

Background: Cucumber, Cucumis sativus L., is an economically and nutritionally important crop of the Cucurbitaceae family and has long served as a primary model system for sex determination studies. Recently, the sequencing of its whole genome has been completed. However, transcriptome information of this species is still scarce, with a total of around 8,000 Expressed Sequence Tag (EST) and mRNA sequences currently available in GenBank. In order to gain more insights into molecular mechanisms of plant sex determination and provide the community a functional genomics resource that will facilitate cucurbit research and breeding, we performed transcriptome sequencing of cucumber flower buds of two near-isogenic lines, WI1983G, a gynoecious plant which bears only pistillate flowers, and WI1983H, a hermaphroditic plant which bears only bisexual flowers.Result: Using Roche-454 massive parallel pyrosequencing technology, we generated a total of 353,941 high quality EST sequences with an average length of 175bp, among which 188,255 were from gynoecious flowers and 165,686 from hermaphroditic flowers. These EST sequences, together with ~5,600 high quality cucumber EST and mRNA sequences available in GenBank, were clustered and assembled into 81,401 unigenes, of which 28,452 were contigs and 52,949 were singletons. The unigenes and ESTs were further mapped to the cucumber genome and more than 500 alternative splicing events were identified in 443 cucumber genes. The unigenes were further functionally annotated by comparing their sequences to different protein and functional domain databases and assigned with Gene Ontology (GO) terms. A biochemical pathway database containing 343 predicted pathways was also created based on the annotations of the unigenes. Digital expression analysis identified ~200 differentially expressed genes between flowers of WI1983G and WI1983H and provided novel insights into molecular mechanisms of plant sex determination process. Furthermore, a set of SSR motifs and high confidence SNPs between WI1983G and WI1983H were identified from the ESTs, which provided the material basis for future genetic linkage and QTL analysis.Conclusion: A large set of EST sequences were generated from cucumber flower buds of two different sex types. Differentially expressed genes between these two different sex-type flowers, as well as putative SSR and SNP markers, were identified. These EST sequences provide valuable information to further understand molecular mechanisms of plant sex determination process and forms a rich resource for future functional genomics analysis, marker development and cucumber breeding. © 2010 Guo et al; licensee BioMed Central Ltd.

He X.,China Agricultural University | He H.,National Engineering Research Center for Vegetables | Fan Z.,China Agricultural University | Zhao X.,National Engineering Research Center for Vegetables
Journal of Chinese Institute of Food Science and Technology | Year: 2013

The effect of three domestic cooking methods (boiling, micro waving, steaming of different time duration) on the changes in glucosinolates (GS) in three cruciferous vegetables (baby Chinese cabbage, cabbage mustard, Chinese kale) was investigated with high performance liquid chromatography (HPLC). The GS contents in Chinese kale and cabbage mustard was approximately four times of that in baby Chinese cabbage, while the composition of GS is varied among the three vegetables. The retention of total GS showed a clear tendency of decrease, with retention rates of GS of 42.5%, 38.5% and 70.0% in baby Chinese cabbage, cabbage mustard and Chinese kale, respectively, after 2 min treatment. The GS content retentions of the three cruciferous vegetables are all above 98% at 3 min treatment under steaming.

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