Sequence analysis of a 282-kilobase region surrounding the citrus Tristeza virus resistance gene (Ctv) locus in Poncirus trifoliata L. Raf

Citrus tristeza virus (CTV) is the major virus pathogen causing significant economic damage to citrus worldwide, and a single dominant gene, Ctv, provides broad spectrum resistance to CTV in Poncirus trifoliata L. Raf. Ctv was physically mapped to a 282-kb region using a P. trifoliata bacterial artificial chromosome library. This region was completely sequenced to about 8x coverage using a shotgun sequencing strategy and primer walking for gap closure. Sequence analysis predicts 22 putative genes, two mutator-like transposons and eight retrotransposons. This sequence analysis also revealed some interesting features of this region of the P. trifoliata genome: a disease resistance gene cluster with seven members and eight retrotransposons clustered in a 125-kb gene-poor region. Comparative sequence analysis suggests that six genes in the Ctv region have significant sequence similarity with their orthologs in bacterial artificial chromosome clones F7H2 and F21T11 from Arabidopsis chromosome I. However, the analysis of gene colinearity between P. trifoliata and Arabidopsis indicates that Arabidopsis genome sequence information may be of limited use for positional gene cloning in P. trifoliata and citrus. Analysis of candidate genes for Ctv is also discussed.     

Identification of QTLs associated with citrus resistance toPhytophthora gummosis

Citrus gummosis, caused by Phytophthora spp., is an important citrus disease in Brazil. Almost all citrus rootstock varieties are susceptible to it to some degree, whereas resistance is present in Poncirus trifoliata, a closely related species. The objective of this study was to detect QTLs linked to citrus Phytophthora gummosis resistance. Eighty individuals of the F1 progeny, obtained by controlled crosses between Sunki mandarin Citrus sunki (susceptible) and Poncirus trifoliata cv. Rubidoux (resistant), were evaluated. Resistance to Phytophthora parasitica was evaluated by inoculating stems of young plants with a disc of fungal mycelia and measuring lesion lengths a month later. Two QTLs linked to gummosis resistance were detected in linkage groups 1 and 5 of the P. trifoliata map, and one QTL in linkage group 2 of the C. sunki map. The phenotypic variation explained by individual QTLs was 14% for C. sunki and ranged from 16 to 24% for P. trifoliata. The low character heritability (h2 = 18.7%) and the detection of more than one QTL associated with citrus Phytophthora gummosis resistance showed that inheritance of the resistance is quantitative.     

A high-resolution linkage map of the citrus tristeza virus resistance gene region in Poncirus trifoliata (L.) Raf.

Resistance to citrus tristeza virus (CTV) was evaluated in 554 progeny of 10 populations derived from Poncirus trifoliata. A dominant gene (Ctv) controlled CTV resistance in P. trifoliata. Twenty-one dominant PCR-based DNA markers were identified as linked to Ctv by bulked segregant analysis. Of the 11 closest markers to Ctv, only 2 segregated in all populations. Ten of these markers were cloned and sequenced, and codominant RFLP markers were developed. Seven RFLP markers were then evaluated in 10 populations. Marker orders were consistent in all linkage maps based on data of single populations or on combined data of populations with similar segregation patterns. In a consensus map, the six closest marker loci spanned 5.3 cM of the Ctv region. Z16 cosegregated with Ctv. C19 and AD08 flanked Ctv at distances of 0.5 and 0.8 cM, respectively. These 3 markers were present as single copies in the Poncirus genome, and could be used directly for bacterial artificial chromosome library screening to initiate a walk toward Ctv. BLAST searches of the GenBank database revealed high sequence similarities between 2 markers and known plant disease resistance genes, indicating that a resistance gene cluster exists in the Ctv region in P. trifoliata.     

利用抑制差减杂交技术分离三角褐指藻在缺氮条件下上调表达的基因

为了阐明硅藻利用氮源的分子机制, 以三角褐指藻为材料, 利用抑制差减杂交技术, 分离鉴定了16个在缺氮诱导条件下上调表达的基因片段。其中, 与已知功能基因具有较高相似性的有7种, 都是跟氮源的吸收利用相关的。Northern blotting验证其中5个基因, 包括硝酸盐转运蛋白基因、铁氧化还原蛋白亚硝酸还原酶基因、铵盐转运蛋白基因、结合ATP盒的转运蛋白基因和嘌呤透过酶基因, 在缺氮诱导条件下转录水平有明显上调。     

The expression profile of genes in rice roots under low phosphorus stress

Phosphorus (P) is one of the most essential macronutrients required for plant growth. Although it is abundant in soil, P is often the limiting nutrient for crop yield potential because of the low concentration of soluble P that plants can absorb directly. The gene expression profile was investigated in rice roots at 6, 24 and 72 h under low P stress and compared with a control (normal P) profile, using a DNA chip of 60000 oligos (70 mer) that represented all putative genes of the rice genome. A total of 795 differentially expressed genes were identified in response to phosphate (Pi) starvation in at least one of the treatments. Based on the analysis, we found that: (i) The genes coding for the Pi transporter, acid phosphatase and RNase were up-regulated in rice roots; (ii) the genes involved in glycolysis were first up-regulated and then down-regulated; (iii) several genes involved in N metabolism and lipid metabolism changed their expression patterns; (iv) some genes involved in cell senescence and DNA or protein degradation were up-regulated; and (v) some transmembrane transporter genes were up-regulated. The results may provide useful information in the molecular process associated with Pi deficiency and thus facilitate research in improving Pi utilization in crop species.     

Differential gene expression in shoots and roots under heat stress for a geothermal and non-thermal Agrostis grass species contrasting in heat tolerance

Identification of genes associated with heat tolerance is important for developing heat-tolerant plants. The objectives of this study were to compare genes differentially expressed in shoots and roots in two Agrostis grass species contrasting in heat tolerance under different temperature regimes and to identify up-regulated genes associated with heat-stress adaptation in Agrostis grass species. Heat-tolerant, thermal A. scabra, adapted to geothermal areas in Yellowstone National Park, and heat-sensitive A. stolonifera, used as a turf and forage grass in cool climatic regions, were exposed to 20 or 40 °C in growth chambers. Leaves and roots were sampled at 7 day of treatment to evaluate physiological responses to heat stress and to perform differential display analysis. Thermal A. scabara maintained significantly higher leaf chlorophyll content and root viability and lower electrolyte leakage (EL) following 7 day of heat stress, compared to A. stolonifera. Differential display analysis of leaf samples revealed that 21 gene fragments were down-regulated while 18 fragments were up-regulated in heat-stressed A. stolonifera. For thermal A. scabra, 38 gene fragments were down-regulated and 22 fragments were up-regulated under heat stress. Four gene fragments in roots were found to be up-regulated under heat stress. RT-PCR analysis confirmed that one gene fragment in leaves (AsL9) and two gene fragments in roots (AsR1 and AsR2) were expressed only in thermal A. scabra exposed to heat stress. These heat-inducible genes in thermal A. scabra may contribute to its superior ability to survive in chronically high-temperature soils in geothermal areas. Putative functional analysis with BLASTX found that most of the up-regulated genes in both species were involved in stress defense pathways or tolerance mechanisms, such as cell wall elasticity, secondary metabolism, regulatory functions, and protein synthesis.     

Is there meaningful plant resistance to diaprepes abbreviatus (Coleoptera: Curculionidae) in citrus rootstock germplasm?

Host plant resistance to the Diaprepes root weevil, Diaprepes abbreviatus (L.) was assessed for seedlings of 54 Poncirus trifoliata (L.) Raf. selections and two families of progeny from crosses between Citrus and P. trifoliata. Weight gain was consistently lower when larvae were reared in pots containing the progeny of Citrus reticulata Blanco 'Sunki' x P. trifoliata 'Flying Dragon' compared with larvae reared on progeny of 'Pearl' (C. reticulata x C. paradisi Macf.) x 'Flying Dragon'. This is the first evidence of genetic control of resistance to the Diaprepes root weevil within sexually compatible citrus rootstock germplasm. There was a significant positive correlation between percentage root loss and larval weight gain within the resistant progeny, indicating a possible antixenotic effect. Two varieties of P. trifoliata were identified as more resistant than 'Flying Dragon' based on larval weight gain.     

Identification of a grapefruit cDNA belonging to a unique class of citrus dehydrins and characterization of its expression patterns under temperature stress conditions

Citrus fruits are sensitive to low temperatures and this often results in the development of chilling injuries during postharvest storage. In order to gain more insight into the molecular mechanisms involved in the acquisition of fruit chilling tolerance, we initiated a grapefruit ( Citrus paradisi, cv. Marsh Seedless) flavedo cDNA sequencing project and used it to identify a cDNA similar to other Poncirus trifoliata and Citrus unshiu dehydrin genes reported to be responsive to low temperatures. The grapefruit dehydrin cDNA, designated cor15 , encodes a predicted polypeptide of 15.1 kDa, that is almost completely identical with other reported citrus dehydrin proteins, except that it contains two large amino acid repeats, whereas P. trifoliata COR11 has only one such repeat and P. trifoliata COR19 and C. unshiu COR19 have three repeats. Together, the various grapefruit, P. trifoliata and C. unshiu dehydrins form a closely related and unique dehydrin gene family that differs from most other plant dehydrins in having an unusual K-segment similar to that of gymnosperms and in having a serine cluster (S-segment) at an unusual position at the carboxy-terminus. The grapefruit cor15 gene is consistently expressed in the fruit peel tissue at harvest, but its message levels dramatically decrease during storage at 2°C. However, a pre-storage hot water treatment, which enhances fruit chilling tolerance, elicited retention of the constant level of cor15 gene expression during cold storage and eliminated its decline. The hot water treatment had no inductive effect on cor15 gene expression when the fruit were held at non-chilling temperatures. The effects of other stresses, such as exposure to ethylene, UV irradiation and wounding, on cor15 gene expression, were temporary and persisted for 1-2 days after the treatments.     

三价铁螯合物还原酶在香橙和枳中的表达

用耐缺铁的香橙 (CitrusjunosSieb .exTanaka)和极不耐缺铁的枳 (Poncirustrifoliata (L .)Raf.) ,在铁胁迫条件下对根的三价铁螯合物还原酶活性变化和酶基因的表达情况进行了研究。离体根的酶活性测定表明 ,在铁胁迫 4周时 ,香橙根的酶活性增强约 2 0倍 ,枳仅增强约 3倍。用拟南芥的三价铁螯合物还原酶基因作探针进行组织印迹的Northern杂交检测香橙和枳三价铁螯合物还原酶的mRNA ,在铁胁迫 2周时 ,香橙吸收根、幼茎和新叶中均检测到强烈的表达信号 ,而枳相同器官的表达信号则极其微弱。实验结果表明 ,三价铁螯合物还原酶活性在缺铁胁迫下被诱导强烈增加是香橙耐缺铁的重要原因 ,该酶活性的调控发生在转录水平上 ,而且该酶基因在诱导条件下在根、茎和叶中均有表达。     

Computational identification of citrus microRNAs and target analysis in citrus expressed sequence tags

MicroRNAs (miRNAs) are a new family of small RNA molecules found in plants and animals. We developed a comprehensive strategy for identifying new miRNA homologues by mining the repository of available citrus expressed sequence tags (ESTs). By adopting a range of filtering criteria, we identified a total of 38 potential miRNAs--nine, five, nine and 15 miRNAs in Citrus trifoliata (ctr-miRNAs), C. clementina (ccl-miRNAs), C. reticulata (crt-miRNAs) and C. sinensis (csi-miRNAs), respectively--from more than 430,000 EST sequences in citrus. Using the potential miRNA sequences, we conducted a further BLAST search of the mRNA database and found six potential target genes in these citrus species. Eight miRNAs were selected in order to verify their existence in citrus using Northern blotting, and the functions of several miRNAs in miRNA-mediated gene regulation are experimentally suggested. It appears that all these miRNAs regulate expression of their target genes by cleavage, which is the most common situation in gene regulation mediated by plant miRNAs. Our achievement in identifying new miRNAs in citrus provides a powerful incentive for further studies on the important roles of these miRNAs.     

<Emphasis Type="Italic">Ptcorp</Emphasis> gene induced by cold stress was identified by proteomic analysis in leaves of <Emphasis Type="Italic">Poncirus trifoliata</Emphasis> (L.) Raf.

A proteomic approach was employed to investigate the cold stress-responsive proteins in trifoliate orange (Poncirus trifoliata (L.) Raf.), which is a well-known cold tolerant citrus relative and widely used as rootstock in China. Two-year-old potted seedlings were exposed to freezing temperature (−6°C) for 50 min (nonlethal) and 80 min (lethal), and the total proteins were isolated from leaves of the treated plants. Nine differentially accumulated proteins over 2-fold changes in abundance were identified by two-dimensional gel electrophoresis and mass spectrometry. Among these proteins, a resistance protein induced by the nonlethal cold treatment (protein spot #2 from P. trifoliata) was selected as target sequence for degenerated primer design. By using the designed primers, a PCR product of about 700 bp size was amplified from P. trifoliata genomic DNA, which was further cloned and sequenced. A nucleotide sequence of 676 bp was obtained and named Ptcorp. Blast retrieval showed that Ptcorp shared 88% homology with an EST of cold acclimated Bluecrop (Vaccinium corymbosum) library (Accession number: CF811080), indicating that Ptcorp had association with cold acclimation. Semiquantitative RT-PCR analysis demonstrated that Ptcorp gene was up-regulated by cold stress which was consistent with the former result of protein expression profile. As the resistance protein (NBS-LRR disease resistance protein family) gene was up-regulated by cold stress in trifoliate orange and satsuma mandarin, it may imply that NBS-LRR genes might be associated with cold resistance in citrus.     

3种农业措施对柑橘丛枝菌根发育的影响

研究了土施N肥(2L 0.5%尿素)、覆草(5~6cm厚杂草)和翻耕(20cm表层土翻耕2次)三种措施,对田间条件下的国庆1号/枳和国庆4号/枳的菌根侵染率和孢子密度的影响。结果表明,覆草极显著地提高了2种柑橘根系的孢子密度,而对菌根侵染率无显著影响;施N肥极显著降低2种柑橘的孢子密度;翻耕极显著抑制了2种柑橘的菌根侵染率。2种柑橘的根系菌根侵染率和孢子密度间都存在显著或极显著正相关。