Lijuan Pan

Government of the People's Republic of China, Peping, Beijing, China

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Publications (13)32.58 Total impact

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    ABSTRACT: The cultivated peanut (Arachis hypogaea L.) is important oil crop and cold stress seriously influences its development and yields. Tolerant varieties produced using transgenic techniques will effectively increase peanut plantation area and enhance yields. However, little is known about the network of gene expression regulation related to cold stress in peanut. Therefore, we screened genes regulated by cold stress in peanut. In total, 1478 up-regulated and 1510 down-regulated probe sets were successfully identified in leaves of peanut subjected to cold stress using the microarray technique. Data analysis indicated that the main biological processes involved in cold stress response included signal transduction, transcript regulations and accumulation of soluble metabolites. Regulation of cell division, translation, protein modification, transport and DNA/RNA-related processes were also involved in peanut cold acclimation. Our study also revealed that protein kinases, transcription factors, heat shock proteins, resistance proteins, stilbene synthase, and so on, may play important functions in cold stress regulation of peanut. The function of some probe sets in cold stress regulation had not been clarified (e.g. proteins functioning in glycerol ether metabolic process, microtubule-based movement or nutrient reservoir activity). Some genes we identified lack functional annotation and their roles in response to cold are yet to be elucidated. These results showed an overview of the transcription map of peanut under cold stress, which may yield some useful insights into cold-mediated signal transduction pathways in peanut and offer some candidate genes as potential markers of tolerance to cold stress.
    Scientia Horticulturae 01/2014; 169:214–225. · 1.40 Impact Factor
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    ABSTRACT: Plant health and soil fertility are affected by plant-microbial interactions in soils. Peanut is an important oil crop worldwide and shows considerable adaptability, but growth and yield are negatively affected by continuous cropping. In this study, 16S rRNA gene clone library analyses were used to study the succession of soil bacterial communities under continuous peanut cultivation. Six libraries were constructed for peanut over three continuous cropping cycles and during its seedling and pod-maturing growth stages. Cluster analyses indicated that soil bacterial assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. The diversity of bacterial sequences identified in each growth stage library of the three peanut cropping cycles was high and these sequences were affiliated with 21 bacterial groups. Eight phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia were dominant. The related bacterial phylotypes dynamic changed during continuous cropping progress of peanut. This study demonstrated that the bacterial populations especially the beneficial populations were positively selected. The simplification of the beneficial microbial communities such as the phylotypes of Alteromonadales, Burkholderiales, Flavobacteriales, Pseudomonadales, Rhizobiales and Rhodospirillales could be important factors contributing to the decline in peanut yield under continuous cropping. The microbial phylotypes that did not successively changed with continuous cropping, such as populations related to Rhizobiales and Rhodospirillales, could potentially resist stress due to continuous cropping and deserve attention. In addition, some phylotypes, such as Acidobacteriales, Chromatiales and Gemmatimonadales, showed a contrary tendency, their abundance or diversity increased with continuous peanut cropping progress. Some bacterial phylotypes including Acidobacteriales, Burkholderiales, Bdellovibrionales, and so on, also were affected by plant age.
    PLoS ONE 01/2014; 9(7):e101355. · 3.73 Impact Factor
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    ABSTRACT: The MYB superfamily constitutes one of the most abundant groups of transcription factors and plays central roles in developmental processes and defense responses in plants. In work described in this article, 30 unique peanut MYB genes that contained full-length cDNA sequences were isolated. The 30 genes were grouped into three categories: one R1R2R3-MYB, nine R2R3-MYBs and 20 MYB-related members. The sequence composition of the R2 and R3 repeats was conserved among the nine peanut R2R3-MYB proteins. Phylogenetic comparison of the members of this superfamily between peanut and Arabidopsis revealed that the putative functions of some peanut MYB proteins were clustered into the Arabidopsis functional groups. Expression analysis during abiotic stress identified a group of MYB genes that responded to at least one stress treatment. This is the first comprehensive study of the MYB gene family in peanut.
    Gene 09/2013; · 2.20 Impact Factor
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    ABSTRACT: Peanut is an important oil crop worldwide and shows considerable adaptability but growth and yield are negatively affected by continuous cropping. Soil micro-organisms are efficient bio-indicators of soil quality and plant health and are critical to the sustainability of soil-based ecosystem function and to successful plant growth. In this study, 18S rRNA gene clone library analyses were employed to study the succession progress of soil eukaryotic micro-organisms under continuous peanut cultivation. Eight libraries were constructed for peanut over three continuous cropping cycles and its representative growth stages. Cluster analyses indicated that soil micro-eukaryotic assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. Six eukaryotic groups were found and fungi predominated in all libraries. The fungal populations showed significant dynamic change and overall diversity increased over time under continuous peanut cropping. The abundance and/or diversity of clones affiliated with Eurotiales, Hypocreales, Glomerales, Orbiliales, Mucorales and Tremellales showed an increasing trend with continuous cropping but clones affiliated with Agaricales, Cantharellales, Pezizales and Pyxidiophorales decreased in abundance and/or diversity over time. The current data, along with data from previous studies, demonstrated that the soil microbial community was affected by continuous cropping, in particular, the pathogenic and beneficial fungi that were positively selected over time, which is commonplace in agro-ecosystems. The trend towards an increase in fungal pathogens and simplification of the beneficial fungal community could be important factors contributing to the decline in peanut growth and yield over many years of continuous cropping.
    PLoS ONE 01/2012; 7(7):e40659. · 3.73 Impact Factor
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    ABSTRACT: Quantitative real-time reverse transcription PCR (qRT-PCR), a sensitive technique for quantifying gene expression, depends on the stability of the reference gene(s) used for data normalization. Only a few studies on the reference genes have been done with peanut to date. In the present study, 14 potential reference genes in peanut were evaluated for their expression stability using the geNorm and NormFinder statistical algorithms. Expression stability was assessed by qRT-PCR across 32 biological samples, including various tissue types, seed developmental stages, salt and cold treatments. The results showed that the best-ranked references genes differed across the samples. UKN1, UKN2, TUA5 and ACT11 were the most stable across all the tested samples. A combination of ACT11, TUA5, UKN2, PEPKR1 and TIP41 would be appropriate as a reference panel for normalizing gene expression data across the various tissues tested, whereas the combination of TUA5 and UKN1 was the most suitable for seed developmental stages. TUA5 and EF1b exhibited the most stable expression under cold treatment. For salt-treated leaves, TUA5 and UKN2 were the most stably expressed and HDC and UKN1 for salt-treated roots. The relative gene expression level of peanut Cys(2)/His(2)-type zinc finger protein gene AhZFP1 was analyzed in order to validate the reference genes selected for this study. These results provide guidelines for the selection of reference genes under different experimental conditions and also a foundation for more accurate and widespread use of qRT-PCR in peanut gene analysis.
    MGG Molecular & General Genetics 12/2011; 287(2):167-76. · 2.58 Impact Factor
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    ABSTRACT: Fatty acid desaturases are responsible for the insertion of double bonds into pre-formed fatty acid chains in reactions that require oxygen and reducing equivalents. In this study, genes for FAB2, FAD2-2, FAD6 and SLD1, were cloned from peanut (Arachis hypogaea L.). The ORFs of the four genes were 1,221, 1,152, 1,329 and 1,347 bp in length, encoding 406, 383, 442 and 448 amino acids, respectively. The predicted amino acid sequences of AhFAB2, AhFAD2-2, AhFAD6, AhSLD1 shared high sequence identity of 79, 76.2, 73.4 and 61% to the corresponding ones in Arabidopsis, respectively. Heterologous expression in yeast was used to confirm the regioselectivity and the function of AhFAD2-2 and AhFAD6. Linoleic acid (18:2), normally not present in wild-type yeast cells, was detected in transformants of these two genes. Quantitative real-time RT-PCR analysis indicated that the transcript abundances of AhFAB2 and AhFAD2-1 were higher in seed than that in other tissues examined. On the other hand, transcript of AhFAD2-2, AhFAD6 and AhSLD1 showed higher abundances in leaves. In addition, these five genes showed different expression patterns during seed development. These results indicated that the five genes may have different biochemical functions during vegetative growth and seed development.
    Plant Cell Reports 03/2011; 30(8):1393-404. · 2.51 Impact Factor
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    ABSTRACT: MicroRNAs (miRNAs) are noncoding RNAs of approximately 21 nt that regulate gene expression in plants post-transcriptionally by endonucleolytic cleavage or translational inhibition. miRNAs play essential roles in numerous developmental and physiological processes and many of them are conserved across species. Extensive studies of miRNAs have been done in a few model plants; however, less is known about the diversity of these regulatory RNAs in peanut (Arachis hypogaea L.), one of the most important oilseed crops cultivated worldwide. A library of small RNA from peanut was constructed for deep sequencing. In addition to 126 known miRNAs from 33 families, 25 novel peanut miRNAs were identified. The miRNA* sequences of four novel miRNAs were discovered, providing additional evidence for the existence of miRNAs. Twenty of the novel miRNAs were considered to be species-specific because no homolog has been found for other plant species. qRT-PCR was used to analyze the expression of seven miRNAs in different tissues and in seed at different developmental stages and some showed tissue- and/or growth stage-specific expression. Furthermore, potential targets of these putative miRNAs were predicted on the basis of the sequence homology search. We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library. This study of the identification and characterization of miRNAs in peanut can initiate further study on peanut miRNA regulation mechanisms, and help toward a greater understanding of the important roles of miRNAs in peanut.
    PLoS ONE 01/2011; 6(11):e27530. · 3.73 Impact Factor
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    ABSTRACT: Fatty acid desaturases can introduce double bonds into the hydrocarbon chains of fatty acids to produce unsaturated fatty acids. In the present study, 29 full-length desaturase genes were identified from soybean genome by a thorough annotation exercise. A comprehensive analysis was performed to characterize phylogeny, chromosomal locations, structures, conserved motifs, and expression patterns of those genes. The soybean genes were phylogenetically clustered into nine subfamilies with the Arabidopsis counterparts, FAB2, FAD2, FAD3, FAD5, FAD6, FAD7, FAD8, SLD1, and DES1. Twenty-nine desaturase genes were found to be distributed on at least 15 of the 20 soybean chromosomes. The gene structures and motif compositions were considerably conserved among the subfamilies. The majority of desaturase genes showed specific temporal and spatial expression patterns across different tissues and developmental stages based on microarray data analyses. The study may provide new insights into the origin and evolution of fatty acid biosynthesis pathways in higher plants. Additionally, the characterization of desaturases from soybean will lead to the identification of additional genes for genetic modification of plants to produce nutritionally important fatty acids. Keywords Glycine max –Genome–Fatty acid desaturase–Phylogenetic analysis
    Plant Molecular Biology Reporter 01/2011; 29(4):769-783. · 5.32 Impact Factor
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    ABSTRACT: The plant C<sub>2</sub>H<sub>2</sub>-type zinc finger proteins play important roles in plant tolerance to abiotic stresses. In this study, we isolated the full-length cDNA of a C<sub>2</sub>H<sub>2</sub>-type zinc finger protein gene AhZFP1 from peanut (Arachis hypogaea L.). AhZFP1 encodes a 24.75kDa protein with two C<sub>2</sub>H<sub>2</sub>-type zinc finger domains. Phylogenetic analysis showed that the AhZFP1 was close to Arabidopsis zinc finger protein AZF2. The semi-quantitative RT-PCR assay revealed that the expression of AhZFP1 was induced by salt stress in peanut roots, stems and leaves. AhZFP1 was the first C<sub>2</sub>H<sub>2</sub>-type zinc finger protein gene reported in peanut.
    Bioinformatics and Biomedical Engineering (iCBBE), 2010 4th International Conference on; 07/2010
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    ABSTRACT: β-ketoacyl-ACP synthetase II (KAS II) which catalyzes the elongation of 16:0-ACP to 18:0-ACP, determines the ratio of palmitic acid (16:0) to stearic acid (18:0). Using Rapid Amplification of cDNA Ends (RACE) and a peanut cDNA library we had previously constructed, we isolated a 1867bp cDNA of the KAS II gene containing a 1212bp complete open reading fragment (ORF). Sequence analysis revealed that peanut KAS II had a high level of nucleotide and amino acid sequence homology to KAS II from other plants. Phylogenetic analysis showed that KAS II from plants, bacteria and virus were grouped into different clades respectively suggesting the independent evolution of KAS II from different sources. Characteristics of the deduced protein were predicted and analyzed using bioinformatic methods. The protein was predicted as stable and hydrophobic with molecular weight of 43181.4 and theoretical PI of 5.69. Expression analysis by real-time PCR indicated that expression levels of KAS II gene were markedly distinct in different peanut tissues and varieties. The expression analysis in this study combined with existing researches suggested KAS II may be involved in the regulation of plant growth and development.
    01/2010;
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    ABSTRACT: Kosteletzkya virginica is a halophyte species which could be used for production of industrial raw material such as biodiesel and for developing ecologically sound saline agriculture as well as for tideland soil improving. Using Rapid Amplification of cDNA Ends (RACE) method, a 1610 bp cDNA of stearoyl-ACP desaturase (SAD) gene containing a 1188 bp complete open reading fragment (ORF) was firstly isolated from seeds of K. virginica. Sequence analysis revealed that the nucleotide sequence of K. virginica SAD had a high level of homology to SAD from Gossypium hirsutum, but had relative low identity to SAD from other pants. However, K. virginica SAD had a high level of amino acid sequence homology to SAD from other plants. Characteristics of the deduced protein were predicted and analyzed using bioinformatic methods. Expression analysis via real-time PCR indicated that expression levels of the SAD gene were markedly distinct in different K. virginica tissues and different development stage seeds. The results of the expression analysis in this study, combined with existing research, suggest that SAD may be involved in the regulation of plant seed growth and development. These results serve as a foundation for further studies of the mechanisms regulating SAD gene expression and could eventually lead to the development of higher quality K. virginica varieties.
    01/2010;
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    ABSTRACT: Delta(12) fatty acid desaturase gene has been targeted as a logical candidate controlling the high oleate trait in peanut seeds. By RT-PCR method, the full-length cDNAs of Delta(12) fatty acid desaturase gene were isolated from peanut (Arachis hypogaea L.) genotypes with normal and high ratio of oleic to linoleic acid, which were designated AhFAD2B and AhFAD2B', respectively. Sequence alignment of their coding regions revealed that an extra A was inserted at the position +442 bp of AhFAD2B' sequence of high oleic acid genotypes, which resulted in the shift of open reading frame and a truncated protein AhFAD2B', with the loss of one histidine box involved in metal ion complex required for the reduction of oxygen. Analysis of transcript level showed that the expression of Delta(12) fatty acid desaturase gene in high oleic acid genotype was slightly lower than that in normal genotype. The enzyme activity experiment of yeast (Saccharomyces cerevisiae) cell transformed with AhFAD2B or AhFAD2B' proved that only AhFAD2B gene product showed significant Delta(12) fatty acid desaturase activity, but AhFAD2B' gene product did not. These results suggested that the change of AhFAD2B' gene sequence resulted in lower activity or deactivation of Delta(12) fatty acid desaturase in high oleic acid genotype.
    Journal of Genetics and Genomics 12/2008; 35(11):679-85. · 2.08 Impact Factor
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    ABSTRACT: Several ethylene-responsive element binding factor (ERF) family proteins have been demonstrated to play important roles in transcriptional regulation of a variety of biological processes, including responses to environmental conditions such as drought, salt, and cold. To date, there have been no reports on this family in peanut. In this study, 40 ESTs in a peanut cDNA library, whose amino acid sequences contained AP2/ ERF domain, have been identified. Of these, full-length sequences of six genes were cloned. Sequence analysis indicated that all six proteins contained only one AP2/ ERF domain and should belong to the ERF family. The six genes were designated Arachis hypogaea ERF 1–6 (AhERF1–6). The expression patterns of AhERF1–6 were analyzed under cold, salt and drought stress. The results indicated that the expression of AhERF4 and AhERF6 were rapidly and substantially enhanced under abiotic stress. The expression of AhERF1 and AhEERF5 were slightly enhanced under certain stress conditions. Some genes were down-regulated when under stress, such as AhEERF3 in leaves under salt stress and AhERF2 in leaves under drought stress. Interestingly, the expression of AhERF3 and AhERF5 exhibited contrary expression patterns in peanut leaves and roots upon PEG treatment. These results suggested that different ERF proteins may have different functions in peanut abiotic stress acclimation.
    Plant Molecular Biology Reporter 30(6). · 5.32 Impact Factor