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Xu X.,Guangdong Academy of Agricultural Sciences | Xu X.,Guangdong Key Laboratory for New Technology Research of Vegetables | Li T.,Guangdong Academy of Agricultural Sciences | Li T.,Guangdong Key Laboratory for New Technology Research of Vegetables | And 2 more authors.
Chemical Engineering Transactions | Year: 2015

DNA methylation plays an important role for regulation of gene expression in plants. Heterosis has been widely explored in Capsicum breeding to improve yield and quality, but the genetic and molecular mechanism underlying the phenomenon remains elusive. In present study, the genomic cytosine methylation of two Capsicum genotypes (the purple and green cotyledon hot pepper) and their reciprocal hybrids were analyzed using the methylation sensitive amplified polymorphism (MSAP). Results showed that the levels of DNA methylation in F1 D85×D34 (67.0%) was higher, but F1 D34×D85 (64.36%) was slightly lower, than the mid-parent value (MPV, 64.83%). Moreover, the characteristics of DNA methylation status were significant different among the reciprocal hybrids and their parental lines. Four classes of MSAP patterns, A, B, C and D, were identified. In pattern B, the de-methylation ratio, the proportion of de-methylated loci in the total polymorphic methylation loci, was 36.2% and 41.0% in F1 D85×D34 and F1 D34×D85. The hyper-methylation ratio (pattern C), the proportion of hyper-methylation loci in the total polymorphism methylation loci, was 51.1% and 41.6% in F1 D85×D34 and F1 D34×D85. This study has demonstrated that in Capsicum heterosis involves adjustment of DNA methylation, especially changes in DNA methylation patterns. Copyright © 2015, AIDIC Servizi S. r. l.,.


Wu T.,Guangdong Academy of Agricultural Sciences | Wu T.,Guangdong Key Laboratory for New Technology Research of Vegetables | Wang R.,Guangdong Academy of Agricultural Sciences | Wang R.,Guangdong Key Laboratory for New Technology Research of Vegetables | And 13 more authors.
Gene | Year: 2014

L-type lectin receptor kinase (LecRK) proteins are an important family involved in diverse biological processes such as pollen development, senescence, wounding, salinity and especially in innate immunity in model plants such as Arabidopsis and tobacco. Till date, LecRK proteins or genes of cucumber have not been reported. In this study, a total of 25 LecRK genes were identified in the cucumber genome, unequally distributed across its seven chromosomes. According to similarity comparison of their encoded proteins, the Cucumis sativus LecRK (CsLecRK) genes were classified into six major clades (from Clade I to CladeVI). Expression of CsLecRK genes were tested using QRT-PCR method and the results showed that 25 CsLecRK genes exhibited different responses to abiotic (water immersion) and biotic (Phytophthora melonis and Phytophthora capsici inoculation) stresses, as well as that between disease resistant cultivar (JSH) and disease susceptible cultivar (B80). Among the 25 CsLecRK genes, we found CsLecRK6.1 was especially induced by P. melonis and P. capsici in JSH plants. All these results suggested that CsLecRK genes may play important roles in biotic and abiotic stresses. © 2014 Elsevier B.V.


Li T.,Guangdong Academy of Agricultural Sciences | Li T.,Guangdong Key Laboratory for New Technology Research of Vegetables | Xu X.,Guangdong Academy of Agricultural Sciences | Xu X.,Guangdong Key Laboratory for New Technology Research of Vegetables | And 3 more authors.
Journal of Plant Biology | Year: 2015

Heat stress is an important agricultural problem around the world. In pepper (Capsicum annum L.), heat stress seriously affects pollination and yield. However, to date, the molecular basis of heat stress has not been extensively studied. Using the HiSeq™ 2000 sequencing platform, the seedling transcriptome of heat-susceptible C.annuum ‘S590’(CaS) and heat-tolerant ‘R597’ (CaR) under the heat stress was examined. Over five million clean reads were generated from each library, each corresponding to a coverage of >250,000 nt. About 73% of the reads were mapped to the pepper genome, and 3,799 and 4,010 differentially expressed genes (DEGs) were identified in ‘R597’ (CaR) and ‘S590’(CaS), respectively. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses determined that the identified DEGs were involved in heat shock protein, heat shock transcription factors, hormone, as well as calcium and kinase signaling. Further validation identified 35 genes that were involved in stress response, and that most of the heat shock proteins were upregulated in two genotypes, and highly expressed in susceptible S590 than in tolerant cultivar R597; the transcription factors and hormone signaling genes showed higher levels of expression in the heat-tolerant cultivar R597 than that observed in the heat-susceptible S590. These findings facilitate in better understanding of the molecular mechanism underlying heat stress in different pepper genotypes. © 2015, Korean Society of Plant Biologists and Springer-Verlag Berlin Heidelberg.


Xu X.,Guangdong Academy of Agricultural Sciences | Xu X.,Guangdong Key Laboratory for New Technology Research of Vegetables | Wang R.,Guangdong Academy of Agricultural Sciences | Wang R.,Guangdong Key Laboratory for New Technology Research of Vegetables | And 11 more authors.
Canadian Journal of Plant Science | Year: 2015

Based on RNA-seq, we analyzed expression patterns of 55 CsWRKYs in the disease-resistant cultivar (JSH) and the disease-susceptible cucumber cultivar (B80) at 0 and 40 h post-inoculation with Phytophthoramelonis. After inoculation with P. melonis, in JSH and B80, the number of up-regulated CsWRKY genes was both 25 with 22 commonly up-regulated genes, and there were 22 CsWRKY genes down-regulated in JSH and 23 in B80 with 18 commonly down-regulated genes, and there were eight CsWRKY genes with no or little change in transcript expression in JSH and seven in B80 with four common genes. Among the 55 CsWRKY genes, 17 genes showed significant differences (differences-twofold) in the degree of change of gene transcription level between JSH and B80 from RNA-seq data analysis, and the results validated using real-time PCR showed that there were only six genes (CsWRKY2, 20, 26, 35, 44, 52) out of the 17 that exhibited significant differences (differences-twofold) with four genes (CsWRKY2, 20, 26, 52) consistent with the data from RNA-seq and two genes (CsWRKY 35, 44) inconsistent with the data from RNA-seq. In addition, the six genes were strongly up-regulated after salicylic acid (SA) treatment with five genes (CsWRKY2, 20, 26, 35, 44) up to peak at 12 h and one gene (CsWRKY52) up to peak at 24 h in expression and that four CsWRKY genes (CsWRKY2, 20, 44, 52) out of six were strongly up-regulated with three genes (CsWRKY2, 20, 44) up to the highest point at 24 h and one gene (CsWRKY52) up after methyl jasmonate (MeJA) treatment. Based on the results above, we predicted CsWRKY2, 20, 26, 35, 44 and 52 may be involved in disease resistance of JSH against Phytophthoramelonis by SA and (or) JA signaling pathway(s). © 2015, Agricultural Institute of Canada. All rights reserved.


Xu X.,Guangdong Academy of Agricultural Sciences | Xu X.,Guangdong Key Laboratory for New Technology Research of Vegetables | Chao J.,Guangdong Academy of Agricultural Sciences | Chao J.,Guangdong Key Laboratory for New Technology Research of Vegetables | And 12 more authors.
PLoS ONE | Year: 2016

Phytophthora root rot caused by Phytophthora capsici (P. capsici) is a serious limitation to pepper production in Southern China, with high temperature and humidity. Mapping PRR resistance genes can provide linked DNA markers for breeding PRR resistant varieties by molecular marker-assisted selection (MAS). Two BC1 populations and an F2 population derived from a cross between P. capsici-resistant accession, Criollo de Morelos 334 (CM334) and P. capsici-susceptible accession, New Mexico Capsicum Accession 10399 (NMCA10399) were used to investigate the genetic characteristics of PRR resistance. PRR resistance to isolate Byl4 (race 3) was controlled by a single dominant gene, PhR10, that was mapped to an interval of 16.39Mb at the end of the long arm of chromosome 10. Integration of bulked segregant analysis (BSA) and Specific Length Amplified Fragment sequencing (SLAF-seq) provided an efficient genetic mapping strategy. Ten polymorphic Simple Sequence Repeat (SSR) markers were found within this region and used to screen the genotypes of 636 BC1 plants, delimiting PhR10 to a 2.57 Mb interval between markers P52-11-21 (1.5 cM away) and P52-11-41 (1.1 cM). A total of 163 genes were annotated within this region and 31 were predicted to be associated with disease resistance. PhR10 is a novel race specific gene for PRR, and this paper describes linked SSR markers suitable for marker-assisted selection of PRR resistant varieties, also laying a foundation for cloning the resistance gene. © 2016 Xu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Wang R.,Guangdong Academy of Agricultural Sciences | Wang R.,Guangdong Key Laboratory for New Technology Research of Vegetables | Huang H.,Guangdong Academy of Agricultural Sciences | Lin Y.,Guangdong Academy of Agricultural Sciences | And 4 more authors.
Canadian Journal of Plant Science | Year: 2014

Dm1, a dwarf mutant from Cucurbita maxima (Duch. ex Lam) by natural mutation, showed distinct dwarf phenotypes such as shorter vines and fewer and shorter internodes. Genetic analysis indicated that the dm1 mutation was recessive, and the dwarfing character was controlled by a single locus. DNA-AFLP analysis showed that a fragment (MCAG/ETT) was linked with the dwarfing character of dm1 and that the fragment contained 152 base pairs (bp). It was investigated in F2 populations of dm1 and vine plants, and the genetic distance between the MCAG/ETT fragment and dwarf gene in dm1 was 11.2 cM, calculated by JoinMap 3.0 software. In addition, the result of cDNA-AFLP analysis showed that there were 52 differential transcript derived fragments (TDFs) found between dm1 and vine plants. Only four TDFs, A16T12, A16T9, A6T14 and A6T16, were expressed stably and specifically in dm1 plants in subsequent investigation. The four fragments share 71, 79, 87 and 79% nucleic acid sequence similarity with the complete coding sequence of Arabidopsis thaliana histidine kinase 3 (AHK3) mRNA, nucleic acid sequence of Vitis vinifera dihydroflavonol-4-reductase-like (DFRL), nucleic acid sequence of Glycine max histone-lysine N-methyltransferase ATX4-like and nucleic acid sequence of Arabidopsis thaliana histidinol dehydrogenase (HDH), respectively. Bioinformatics analysis indicated that AHK3, DFRL and HDH were respectively related to Cytokinin signaling, indole acetic acid signaling and Ni accumulation, which played important roles in plant growth, so the expression of the four TDFs may contribute to form dwarfism in dm1.


Li T.,Guangdong Academy of Agricultural Sciences | Li T.,Guangdong Key Laboratory for New Technology Research of Vegetables | Shao X.-X.,Guangdong Academy of Agricultural Sciences | Shao X.-X.,Guangdong Key Laboratory for New Technology Research of Vegetables | And 5 more authors.
International Journal Bioautomation | Year: 2015

Activity of bc1 complex (ABC1K) is a protein kinase commonly found in eukaryotes and prokaryotes. It plays an important role in various developmental and physiological processes, especially critical for plant response to diverse biotic and abiotic stresses. In this study, a genome analysis was carried out and 18 genes of ABC1K family were identified in tomato. Phylogenetic results showed that these members could be classified into three groups ? ancestral clade, mitochondrial clade and photosyntheticspecific clade, with several subgroups based on subcellular location prediction by WoLF PSORT and all the SlABC1K proteins contained an ABC1K conserved kinase motifs-VAIK (VAVK, VAMK) and DFG (DEG). Conserved motifs analyzed by MEME program indicated that all ABC1K protein contains motif 2, 5, 6 and 8. Predictably, the SlABC1K proteins were localized in chloroplasts or mitochondria; in our analysis of expression patterns, SlABC1K genes could be detected in all tomato organs, and eight genes were specifically expressed in tomato leaf, which implied that the SlABC1Ks might be involved in energy metabolism in tomato. The expression of several genes was significantly changed under abiotic stress, implying their probability of performing various roles in abiotic stresses (NaCl, high temperature, cold, abscisic acid and salicylic acid).


Li T.,Guangdong Academy of Agricultural Sciences | Li T.,Guangdong Key Laboratory for New Technology Research of Vegetables | Wang H.-M.,Guangdong Academy of Agricultural Sciences | Li Z.-L.,Guangdong Academy of Agricultural Sciences | And 2 more authors.
International Journal Bioautomation | Year: 2015

Heterosis has been mostly used in hot pepper breeding and production, but the molecular basis of heterosis has not been extensively studied. In this study, comparative transcriptomes analysis of parental lines (D6, D7) and F1 hybrids (D6×D7 and D7×D6) was performed. A total of 0.6 billion raw reads, and 0.44 billion high-quality reads were obtained after the filtering process. Statistical analysis of genes with presence/deletion variations showed that, there were 1068 (6.20%) and 780 (4.56%) genes in the single parent express consistent type in the direct (D6×D7) and reciprocal (D7×D6) F1 hybrids, respectively. More genes fit into the non-additive expression type in two F1 hybrids compared to the parents, and less than 8% of the genes belong to the additive expression type. 66.08% in direct and 62.96% in reciprocal F1 hybrids belong to the epistatic dominance expression pattern. There were more differentially expressed genes (DEGs) between the two parental lines (351) than between the two hybrids (17). The results of gene ontology (GO) analysis showed that there were obvious differences in electron transmission and photorespiration between two F1 hybrids. GO terms for regulating plant hypersensitive responses, and MAPK pathways were only enriched in the direct hybrid (D6×D7).


Wu T.,Guangdong Academy of Agricultural Sciences | Wu T.,Guangdong Key Laboratory for New Technology Research of Vegetables | Luo S.,Guangdong Academy of Agricultural Sciences | Luo S.,Guangdong Key Laboratory for New Technology Research of Vegetables | And 12 more authors.
Molecular Breeding | Year: 2014

Pumpkin (Cucurbita moschata Duch.) is an important vegetable crop cultivated worldwide. In this study, the pumpkin transcriptome was sequenced by RNA-seq using the Illumina Hiseq 2000. A total of 52,849,316 clean sequencing reads, 66,621 contigs and 62,480 unigenes were postulated. Based on similarity searches with known proteins, 47,899 genes (76.66 % of the unigenes) were annotated: 47,596, 34,368 and 16,700 mapped in Nr, Swissprot and COG classifications, respectively; 21,164 were annotated with 44 gene ontology functional categories; and 13,728 were annotated to 269 pathways by searching the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 7,814 simple sequence repeats (SSRs) were identified in these unigenes and 4,794 pairs of primers were designed for application of SSRs. To date, 35 SSRs have been validated in 12 pumpkin varieties and can separate the pumpkin varieties into Cucurbita maxima and Cucurbita moschata. In addition, the expression of eight photoperiod-related unigenes were studied in different pumpkin plants and it was deduced that they may contribute to late flowering and light insensitiveness. This research will provide an important platform to facilitate gene discovery for functional genome studies of pumpkin and to conduct SSR discovery for breeders for use in pumpkin breeding. © 2014, Springer Science+Business Media Dordrecht.


Xu X.-W.,Guangdong Academy of Agricultural Sciences | Xu X.-W.,Guangdong Key Laboratory for New Technology Research of Vegetables | Li T.,Guangdong Academy of Agricultural Sciences | Li T.,Guangdong Key Laboratory for New Technology Research of Vegetables | And 2 more authors.
International Journal Bioautomation | Year: 2015

MicroRNAs (miRNAs) play an important role in many developmental processes and stress responses in plants. In this study, tolerant hot pepper cultivar 'R597' (CaR) and sensitive cultivar 'S590' (CaS) were used to detected differentially expressed miRNAs under high temperatures and high air humidity. The length distribution of obtained small RNAs was significantly different between libraries. There were a total of 71 miRNA families identified in two genotypes, and 24 conserved miRNA families were detected in all four sRNA libraries. MIR166, MIR156/157, MIR167, MIR168, MIR2118, and MIR5301 were highly expressed in four libraries, and 93 miRNAs had a species-specific expression. Among them, 60 miRNAs were preferentially expressed in S590 leaves and 33 miRNAs were preferentially expressed in R597 leaves. Mostly miRNAs were less-conserved miRNAs. The most abundant miRNAs with different expressions between two pepper species was miR6149b, which exhibited a high level (read count 42,443) in CaSCK but no expressed in CaRCK. We found 650 (CaRCK), 1054 (CaRHH), 914 (CaSCK), 1045 (CaSHH) potential targets for 92 (CaRCK), 124 (CaRHH), 128 (CaSCK), 117 (CaSHH) hot pepper miRNAs, respectively. These findings facilitate in better understanding of the molecular mechanism underlying high temperature and high air humidity condition in different pepper genotypes.

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