Junjie Fu

Chinese Academy of Agricultural Sciences, Peping, Beijing, China

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Publications (16)87.99 Total impact

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    ABSTRACT: RNA sequencing can simultaneously identify exonic polymorphisms and quantitate gene expression. Here we report RNA sequencing of developing maize kernels from 368 inbred lines producing 25.8 billion reads and 3.6 million single-nucleotide polymorphisms. Both the MaizeSNP50 BeadChip and the Sequenom MassArray iPLEX platforms confirm a subset of high-quality SNPs. Of these SNPs, we have mapped 931,484 to gene regions with a mean density of 40.3 SNPs per gene. The genome-wide association study identifies 16,408 expression quantitative trait loci. A two-step approach defines 95.1% of the eQTLs to a 10-kb region, and 67.7% of them include a single gene. The establishment of relationships between eQTLs and their targets reveals a large-scale gene regulatory network, which include the regulation of 31 zein and 16 key kernel genes. These results contribute to our understanding of kernel development and to the improvement of maize yield and nutritional quality.
    Nature Communications 12/2013; 4:2832. · 10.02 Impact Factor
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    ABSTRACT: The d2003 is a natural dwarf mutant from maize inbred line K36 and has less than one-third of K36 plant height with severely shortened internodes. In this study, we reported the cloning of d2003 gene using positional cloning. The results showed that there was a single-base insertion in the coding region of Viviparous8 (VP8) in d2003 mutant, which resulted in a premature stop codon. Further genetic allelism tests confirmed that d2003 mutation is a novel allele of VP8. VP8 is mainly expressed in the stem apex, young leaves, and developing vascular tissues, and its expression levels in nodes are significantly higher than that in internodes at 12-leaf stage. Subcellular localization demonstrated that the VP8 protein is localized to the endoplasmic reticulum and the N-terminal 26 amino acids (aa) of VP8 protein are essential to its localization in ER. Further transgenic experiments showed that lack of the 26 aa leads to loss of VP8 function in Arabidopsis amp1 phenotype rescue. These results strongly suggested that the N-terminal 26 aa is critical for VP8 protein localization, and the correct protein localization of VP8 in ER is necessary for its function.
    Plant Molecular Biology 11/2013; · 3.52 Impact Factor
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    ABSTRACT: Maize kernel oil is a valuable source of nutrition. Here we extensively examine the genetic architecture of maize oil biosynthesis in a genome-wide association study using 1.03 million SNPs characterized in 368 maize inbred lines, including 'high-oil' lines. We identified 74 loci significantly associated with kernel oil concentration and fatty acid composition (P < 1.8 × 10(-6)), which we subsequently examined using expression quantitative trait loci (QTL) mapping, linkage mapping and coexpression analysis. More than half of the identified loci localized in mapped QTL intervals, and one-third of the candidate genes were annotated as enzymes in the oil metabolic pathway. The 26 loci associated with oil concentration could explain up to 83% of the phenotypic variation using a simple additive model. Our results provide insights into the genetic basis of oil biosynthesis in maize kernels and may facilitate marker-based breeding for oil quantity and quality.
    Nature Genetics 12/2012; · 35.21 Impact Factor
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    ABSTRACT: Cytokinin dehydrogenase (CKX) degrades the cytokinin hormone in plants and plays an important role in cytokinin regulatory processes. CKX proteins are encoded by a multigene family with a varying number of members. In this study, 13 maize CKX sequences were collected in which ten transcripts were confirmed by RT-PCR. The tissue- and cytokinin-dependent expression studies indicated that ZmCKX genes exhibit a variety of expression patterns, suggesting diverse functions. Besides 13 maize CKXs, 7 Arabidopsis, 9 poplar, and 11 rice CKX proteins were further used to construct a phylogenetic tree. The CKX members were assigned to six groups, and the intron/exon structures, sequence motifs, and protein properties were conserved within groups. The genome distribution of CKXs supports that segmental duplication contributes to the expansion of the CKX gene family. By quantitative RT–PCR analysis of maize members and digital Northern analysis of Arabidopsis, poplar, and rice members for their tissue expression patterns, highly correlative expression profiles of CKX genes were found among some of the orthologs, whereas different expression manners were found between some of the paralogs. These results suggest functional conservation within each group of the CKX family and provide a clue for transfer of a gene function from one species to the other and further contribute to uncovering the role of CKX genes in planta. KeywordsCytokinin-Cytokinin dehydrogenase/oxidase (CKX)-Evolution-Gene expression-Maize
    Journal of Plant Growth Regulation 01/2010; 29(4):428-440. · 1.99 Impact Factor
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    ABSTRACT: Drought stress greatly affects plant growth and crop yield. To understand the transcriptome dynamics during drought stress in maize seedlings, genome-wide gene expression profiling was compared between the drought-tolerant line Han21 and drought-sensitive line Ye478 using Affymetrix Maize Genome Array containing 17,555 probe sets. The results showed that in response to drought, the Han21 line had fewer probe sets with significant expression change than the Ye478 line and both lines had a common set of ~2,600 regulated probe sets under drought stress. The potential components of the abscisic acid signaling pathway were significantly identified from the common probe sets. A total of 827 probe sets with significantly differential expression between the two lines under drought stress were identified. The differential expression levels of cell wall-related and transporter genes may contribute to the different tolerances of the two lines. Additionally, we found that, compared to the sensitive line Ye478, the transcriptional levels of drought-responsive probe sets in the tolerant line Han21 recovered more quickly after re-watering, and more probe sets in the tolerant line Han21 were exclusively up-regulated at the re-watering stage. Our study provides a global gene expression dynamics of two maize inbred lines during drought stress and re-watering and will be valuable for further study of the molecular mechanisms of drought tolerance in maize.
    Plant Molecular Biology 12/2009; 72(4-5):407-21. · 3.52 Impact Factor
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    ABSTRACT: In order to unravel the molecular mechanism of maize ear development, a microarray containing approximately 56,000 probes was used to monitor the gene expression profiles of ears at four developmental stages. The results showed that 2,794 genes, accounting for 5.0% of the total probes, changed significantly during ear development. Among the 2,794 genes, 1,844 genes differentially expressed during the spikelet differentiation phase, 836 genes during the floret primordium differentiation phase and 645 genes during the floret organ differentiation phase. Hierarchical clustering revealed that the differentially expressed genes had 9 major expression patterns. Based on Mips Functional Catalogue, 684 differentially expressed genes were grouped into at least one functional category, including metabolism (30.4%), protein related function (29.2%), biogenesis of cellular components (15.4%) and transcription (13.7%). The analysis revealed that the auxin signaling pathway play an important role in ear development. Moreover, regulation of some transcription factors may play a key role during ear development. RT-PCR and in situ hybridization for some selected genes validated our microarray data and supplied additional information on ear developmental processes.
    Plant Molecular Biology 02/2009; 70(1-2):63-77. · 3.52 Impact Factor
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    ABSTRACT: SINA genes in plants are part of a multigene family with 5 members in Arabidopsis thaliana, 10 members in Populus trichocarpa, 6 members in Oryza sativa, at least 6 members in Zea mays and at least 1 member in Physcomitrella patens. Six members in maize were confirmed by RT-PCR. All SINAs have one RING domain and one SINA domain. These two domains are highly conserved in plants. According to the motif organization and phylogenetic tree, SINA family members were divided into 2 groups. In addition, through semi-quantitative RT-PCR analysis of maize members and Digital Northern analysis of Arabidopsis and rice members, we found that the tissue expression patterns are more diverse in monocot than in Arabidopsis.
    DNA Sequence 07/2008; 19(3):206-16. · 0.75 Impact Factor
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    ABSTRACT: Maize kernel is an important source of food, feed, and industrial raw materials. The elucidation of the molecular mechanisms of maize kernel development will be helpful for the manipulation of maize improvements. A microarray with approximately 58,000 probes was used to study dynamic gene expression during kernel development from fertilization to physiological maturity. By comparing six consecutive time points, 3445 differentially expressed genes were identified. These genes were then grouped into 10 clusters showing specific expression patterns using a K-means clustering algorithm. An investigation of function and expression patterns of genes elucidate the regulation mechanism underlying the important developmental processes cell division and kernel filling. The differential expression of genes involved in plant hormone signaling pathways suggested that phytohormone might play a critical role in the kernel developmental process. Moreover, regulation of some transcription factors and protein kinases might be involved in the whole developmental process.
    Genomics 05/2008; 91(4):378-87. · 3.01 Impact Factor
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    ABSTRACT: By screening a genomic library of maize, a 2.2 kb 5' flanking fragment of Zpu1 gene, encoding the pullulanase-type starch debranching enzyme, was isolated. Promoter fragments of various lengths, including the full 5' flanking sequence (-2267 to -1) (Z1), a 3' deletion (-2267 to -513) (Z5) and three 5' deletions extending to -1943 (Z2), -1143 (Z3) and -516 (Z4) upstream of the translational initiation codon (ATG), were fused to the GUS reporter gene and introduced into tobacco. When these constructs were tested in transgenic tobacco plants, seed-preferred GUS activity was observed in pZ1-transgenic lines. In pZ2-transgenic lines, the GUS activity was not only restricted to seeds, but was also detected in calyxes, petals, stamens and mature leaves. At the same time, negligible GUS activity was detected in roots, stems, young leaves, stigmas and ovaries from the transgenic tobacco plants, which had integrated the full isolated sequence of Zpu1 promoter or its deletions. Deletion analysis indicated that the promoter contained a putative positive cis-regulatory element and the proximal region (-516 to -1) was essential for directing the expression of gus reporter gene. Analysis of GUS activity during the fruit development and seed germination suggested that Zpu1 promoter is active both in starch anabolism and in starch catabolism, which is consistent with the function of the endogenous gene in maize. GUS activity in leaves under light and darkness confirmed that Zpu1 promoter functions in the starch degradation of photosynthetic tissues in the dark phase of the diurnal cycle.
    Plant Cell Reports 10/2007; 26(9):1555-65. · 2.51 Impact Factor
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    ABSTRACT: In plants, ZnF-AN1 genes are part of a multigene family with 13 members in Arabidopsis thaliana, 19 members in Populus trichocarpa, 17 members in Oryza sativa, at least 11 members in Zea mays, and 2 members in Chlamydomonas reinhardtii. All ZnF-AN1 genes contain the ZnF-AN1 domain. According to the phylogenetic analysis of the ZnF-AN1 domain, we divided plant ZnF-AN1 genes into two types. The coding sequences of most type I members do not possess any introns, while most type II members do possess intron(s). Through Northern blot analysis of maize members and digital Northern analysis of Arabidopsis members, we found that most ZnF-AN1 genes are involved in responses to abiotic stresses. The evolutionary analysis indicated that the expansion rate of type I was higher than that of type II. After expansion, some ZnF-AN1 genes may have gained new functions, some may have lost their functions, and some were specialized to perform their functions in stress-specific or tissue-specific modes. In addition, we propose an evolutionary model of type II ZnF-AN1 genes in plants.
    Genomics 09/2007; 90(2):265-75. · 3.01 Impact Factor
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    ABSTRACT: Foxtail millet is a gramineous crop with low water requirement. Despite its high water use efficiency, less attention has been paid to the molecular genetics of foxtail millet. This article reports the construction of subtracted cDNA libraries from foxtail millet seedlings under dehydration stress and the expression profile analysis of 1947 UniESTs from the subtracted cDNA libraries by a cDNA microarray. The results showed that 95 and 57 ESTs were upregulated by dehydration stress, respectively, in roots and shoots of seedlings and that 10 and 27 ESTs were downregulated, respectively, in roots and shoots. The expression profile analysis showed that genes induced in foxtail millet roots were different from those in shoots during dehydration stress and that the early response to dehydration stress in foxtail millet roots was the activation of the glycolysis metabolism. Moreover, protein degradation pathway may also play a pivotal role in drought-tolerant responses of foxtail millet. Finally, Northern blot analysis validated well the cDNA microarray data.
    Genomics 08/2007; 90(1):121-31. · 3.01 Impact Factor
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    ABSTRACT: Full-length cDNAs are very important for genome annotation and functional analysis of genes. The number of full-length cDNAs from maize (Zea mays L.) remains limited. Here we report the construction of a full-length enriched cDNA library from osmotically stressed maize seedlings by using the modified CAP trapper method. From this library, 2073 full-length cDNAs were collected and further analyzed by sequencing from both the 5'- and 3'-ends. A total of 1728 (83.4%) sequences did not match known maize mRNA and full-length cDNA sequences in the GenBank database and represent new full-length genes. After alignment of the 2073 full-length cDNAs with 448 maize BAC sequences, it was found that 84 full-length cDNAs could be mapped to the BACs. Of these, 43 genes (51.2%) have been correctly annotated from the BAC clones, 37 genes (44.0%) have been annotated with a different exon-intron structure from our cDNA, and four genes (4.76%) had no annotations in the TIGR database. Expression analysis of 2073 full-length maize cDNAs using a cDNA macroarray led to the identification of 79 genes upregulated by stress treatments and 329 downregulated genes. Of the 79 stress-inducible genes, 30 genes contain ABRE, DRE, MYB, MYC core sequences or other abiotic-responsive cis-acting elements in their promoters. These results suggest that these cis-acting elements and the corresponding transcription factors take part in plant responses to osmotic stress either cooperatively or independently. Additionally, the data suggest that an ethylene signaling pathway may be involved in the maize response to drought stress.
    The Plant Journal 01/2007; 48(5):710-27. · 6.58 Impact Factor
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    ABSTRACT: The beta-glucosidase gene of maize (ZmGLU1) was suggested to hydrolyze cytokinin-conjugate and release free cytokinin during plant growth and development. A clone containing the upstream region of ZmGLU1 was isolated and sequenced from a maize genomic library. The full-length ZmGLU1 promoter and a series of its 5' deletions were fused to the beta-glucuronidase (GUS) reporter gene and transferred into tobacco. The GUS activity of transgenic plants was assayed at various developmental stages. The results showed that ZmGLU1 promoter-driven GUS gene had the highest expression level in the roots and that the expression of GUS gene declined during seed maturation and down to the lowest level in mature seeds. The ZmGLU1 promoter-driven GUS expression increased during seed germination, reaching a peak on day 11. The results also showed that this promoter could be inhibited by 6-BA, trans-zeatin, and NAA, but was not affected by GA(3), ABA, SA, cold, salt, drought, and submergence treatments. The histochemical staining revealed that GUS activity was located in vigorous cell division zones with dominant staining associated with vascular tissues. Deletion analysis showed that the promoter contained a putative leaf-specific and stem-specific negative regulative element and two putative enhancers.
    Plant Cell Reports 12/2006; 25(11):1157-65. · 2.51 Impact Factor
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    ABSTRACT: cDNA macroarray has become a useful tool to analyze expression profiles and compare the similarities and differences of various expression patterns. We have prepared a cDNA macroarray containing 190 maize expressed sequence tags (ESTs) specifically induced by water stress to analyze the expression profiles of maize seedlings under abscisic acid (ABA) treatment, high-salinity and cold stress conditions. The results indicated that 48 ESTs in leaves and 111 ESTs in roots were significantly up-regulated by ABA treatment, 36 ESTs in leaves and 41 ESTs in roots by high-salinity stress, 14 ESTs in leaves and 18 ESTs in roots by cold induction, whereas 22 ESTs were induced under all 3 stresses. Results from the hierarchical cluster analysis suggest that the leaves and roots of maize seedlings had different expression profiles after these stresses. The overlap analysis of different stress-induced ESTs indicated that there is more crosstalk between water stress and ABA and high-salinity stress than between water stress and cold stress. It will be helpful to study the precise function of the corresponding overlapping-induced genes for understanding the relationship and crosstalk between different stress signal pathways.
    Plant Science. 01/2006;
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    ABSTRACT: In order to identify genes induced during the water stress response in maize (Zea mays) seedlings, suppression subtractive hybridization (SSH) was performed using mixed cDNAs prepared from maize seedlings treated with 20% PEG as testers and cDNAs from unstressed maize seedlings as drivers. A forward subtractive cDNA library was constructed, from which 960 recombinant colonies were picked and amplified. Through differential screening of the subtractive cDNA library, 533 clones were identified as water stress induced. After sequencing, 190 unique expressed sequence tags (ESTs) were obtained by clustering and blast analysis, which included transcripts that had previously been reported as responsive to stress as well as some functionally unknown transcripts. The ESTs with significant protein homology were sorted into 13 functional categories. A cDNA marcoarray containing the 190 unique ESTs was used to analyze their expression profiles in maize seedling during both PEG treatment and natural drought. The results indicated that 67 ESTs in leaves and 113 ESTs in roots were significantly up-regulated by PEG-stress. 123 ESTs were found to be up-regulated for at least one time-course point in either maize leaves or roots. Correspondingly, 163 ESTs were significantly up-regulated by drought stress. Results from the hierarchical cluster analysis suggest that the leaves and roots of maize seedlings had different expression profiles after PEG treatment and that there was a lot of overlap between PEG- and drought-stress induced up-regulated transcripts. A set of transcripts has been identified, which have significantly increased expression and probably involved in water stress signaling pathway based on data analysis.
    Plant Molecular Biology 09/2004; 55(6):807-23. · 3.52 Impact Factor
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    ABSTRACT: In order to understand the molecular and cellular mechanisms underlying cold stress conditions (4°C) in maize seedlings, a forward subtractive cDNA library was constructed using the suppression subtractive hybridization (SSH) technique. Through the “Virtual” Northern blot analysis, 893 positive clones were screened from a total 1,200 clones in the subtractive cDNA library. After sequencing 528 randomly chosen cDNA clones, 213 uniquely expressed sequence tags (ESTs) were obtained by clustering and blast analysis, which included transcripts that had previously been reported as responsive to stress as well as some functionally unknown transcripts. Based on a list of functional Arabidopsis protein categories, the ESTs with significant protein similarity were sorted into ten functional categories. A cDNA macroarray containing the 213 unique ESTs was used to monitor the spatial and temporal distribution of gene expression in maize seedlings during cold stress. The results showed that 118 ESTs were induced by cold-stress in maize seedlings and 66 ESTs identified in the leaves and 89 ESTs in the roots. Hierarchical cluster analysis indicated that the expression profiles of cold stress inducible ESTs in the leaves were different from that observed in the roots. Moreover, some induced genes were related to sugar synthesis and reestablishment of high rates of photosynthesis. In addition, Northern blot analysis validated well the cDNA macroarray data.
    Plant Molecular Biology Reporter 27(1):38-49. · 5.32 Impact Factor

Publication Stats

250 Citations
173 Downloads
2k Views
87.99 Total Impact Points

Institutions

  • 2007–2013
    • Chinese Academy of Agricultural Sciences
      • Institute of Crop Sciences
      Peping, Beijing, China
  • 2010
    • Hohenheim University
      • State Plant Breeding Institute
      Stuttgart, Baden-Wuerttemberg, Germany
  • 2004–2009
    • China Agricultural University
      • State Key Laboratory for Agrobiotechnology
      Beijing, Beijing Shi, China