Detection of Puccinia striiformis in Latently Infected Wheat Leaves by Nested Polymerase Chain Reaction

Stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), is one of the most devastating wheat diseases worldwide, especially in temperate regions with cool moist weather conditions. The identification of the pathogen in infected plants based on morphological or physiological criteria before sporulation is labour-intensive and time-consuming. To accelerate and simplify the process of detection, a nested Polymerase Chain Reaction (PCR) assay was developed for specific and sensitive detection of Pst . Specific primers Psta-Psts were designed according to a genome-specific sequence of Pst . In nested PCR, with a 10-fold dilution series of template DNA, the detection limit was 2 pg DNA in the first PCR with the primers Psta-Psts. The second round PCR was then performed using amplified products from the first PCR as the template and Nesta-Nests as the primers. An amplification signal was detectable even when only 2 fg of P. striiformis f. sp. tritici DNA was used as the template in nested PCR. With nested PCR, the sensitivity of detection was enhanced 1000 fold. Using extracts from stripe rust-infected wheat leaves, the fungus could be determined in the leaves before symptom appearance. The assay provides a rapid and sensitive method for detection of P. striiformis f. sp. tritici in latently infected leaves of overwintering wheat plants.     

Genetic transformation of wheat using mature seed tissues

A protocol for biolistic transformation of bread wheat based on using mature seed tissues as explants has been developed. Embryogenic callus obtained from mature seed tissues was transformed with a psGFP-BAR plasmid containing gfp reporter gene and bar selectable marker gene. The influence of hormone composition of the medium on the efficiency of transformation of mature wheat seed tissues has been demonstrated. The use of auxin 2,4-D resulted in the formation of transgenic plants with a frequency of 0.75%, while the use of Dicamba auxin for the regeneration of plants did not result in transformant development. The transgenic status of the plants obtained in the experiments has been confirmed by PCR and RT-PCR. Stable inheritance of transgenic features in the following generations of wheat (T₁, T₂) has been demonstrated and transgenic plants exhibiting high resistance to herbicides have been obtained. The protocol developed allows for a simplified transformation of wheat in order to obtain transgenic plants with novel features.     

Development of a Real-time Polymerase Chain Reaction for the Detection of Fusarium oxysporum f. sp. basilici from Basil Seed and Roots

A real‐time polymerase chain reaction (PCR) assay using a TaqMan^® probe was developed to detect the causal agent of wilt and crown rot of basil from infected plants and seed in Italy. The aim of the study was to diminish testing time, previously performed using nested‐PCR, and to create the conditions for future automation. The sensitivity of the assay was shown to be similar to the detection limit of the available nested‐PCR procedure. The advantages of real‐time PCR system include halving of the testing time, as well as the ability to identify both internally and externally infected seed to the sensitivity of 1 pg of genomic DNA. The assay was able to detect the presence of the pathogen in infected seed up to a sensitivity of 24 (SD: ±10) CFU per 100 seeds.     

一种快速、无损大豆种子DNA提取方法的建立和应用

基因分型是进行植物基因功能的遗传分析和分子标记辅助育种的重要环节。该研究以大豆(Glycine max)成熟种子为材料, 建立了通过钻孔采集样品、快速提取DNA进行基因型鉴定的方法。用此方法, 一个熟练的工作人员可以在1个小时内完成120个样品的采集和DNA提取; 同时种子钻孔取样后, 不会对大豆种子的萌发造成影响。利用该方法获得的DNA可满足PCR扩增的要求。实验重复性好, 成功率在98%以上。这种快速且无损的大豆种子基因型鉴定方法可以用于鉴定杂交种子、品种纯度以及遗传分析等研究工作。     

Quantification of Fusarium culmorum in Wheat and Barley Tissues Using Real-Time PCR in Comparison with DON Content

A real‐time polymerase chain reaction (PCR) assay was developed for the specific detection of Fusarium culmorum in infected seeds. Primers and TaqMan minor groove binder probe were derived from the sequences of a F. culmorum specific PCR product. The specificity of the assay was confirmed by test in seven Fusarium species and 21 non‐Fusarium fungal species. With serial dilutions of purified genomic DNA from F. culmorum isolate B as the template, the detection limit of the assay was found to be 0.9 pg of fungal genomic DNA per reaction. A significant correlation ( = 0.982) and collinearity was found between DNA concentration and Ct (cycle threshold) values of real‐time PCR assay with serial diluted DNAs extracted from three seed samples with different deoxynivalenol (DON) content. Eight barley and nine wheat varieties infected by F. culmorum isolate B were evaluated in 1 (barley samples) and in 4 years (wheat samples). The results of real‐time PCR analysis and enzyme‐linked immunosorbent assay testing for DON content were compared and a significant correlation was found for barley samples (r² = 0.935). Concerning wheat we found rather complicated relationship between Ct values and DON contents influenced by environmental conditions of field trials. The real‐time PCR assay was found to be highly specific and sensitive. It could be used in phytopathological studies and praxis.     

Pre-germination genotypic screening using PCR amplification of half-seeds

A simple and rapid PCR-based method has been developed for determining the genotype of seeds before germination. Single half-seeds of rice (Oryza sativa L.) and wheat (Triticum aestivum L. em. Thell.) were preincubated, without grinding, in an aqueous extraction buffer. The resulting supernatants were then used in polymerase chain reaction (PCR) with oligonucleotide primers corresponding to rice single-copy sequences or a wheat microsatellite repeat. PCR products of identical size were amplified using either the half-seed extract or DNA isolated from leaf tissue. The remnant half-seeds can be maintained in ordered arrays using microtiter plates allowing the recovery of selected genotypes. Pre-germination genotypic screening of seed populations as described in this report should be useful for a variety of applications in plant breeding and genetics studies.     

Rapid detection and diagnosis of Septoria tritici epidemics in wheat using a polymerase chain reaction/PicoGreen assay

In order to detect and quantify Septoria tritici infection levels in wheat leaves, a polymerase chain reaction (PCR) assay was developed using the β-tubulin gene as target. Specific PCR primers were designed by aligning and comparing β-tubulin sequences from other fungi. The final primer set was selected after being tested against several fungi, and against S. tritici -infected and uninfected wheat leaves from different localities. A single DNA fragment (496 bp) was amplified from S. tritici, whereas no products were generated from DNA of the host plant or other micro-organisms associated with wheat leaves. Using agarose gel analysis, approximately 2 pg S. tritici genomic DNA could be detected in each assay. However, for rapid quantification of PCR-amplified products, a fluorometric microtitre plate-formatted PicoGreen assay was used; this could detect as little as 10 pg S. tritici DNA in the presence of 200 ng wheat leaf DNA. The PCR/PicoGreen assay was applied successfully to study the colonization, infection and subsequent disease development of S. tritici on wheat, both under controlled conditions in the glasshouse and in the field.     

Quantitative Fusarium spp. and Microdochium spp. PCR assays to evaluate seed treatments for the control of Fusarium seedling blight of wheat

AIMS: To develop sensitive quantitative PCR assays for the two groups of pathogens responsible for Fusarium seedling blight in wheat: Fusarium group (Fusarium culmorum and Fusarium graminearum) and Microdochium group (Microdochium nivale and Microdochium majus); and to use the assays to assess performance of fungicide seed treatments against each group. METHODS AND RESULTS: Primers conserved between the species within each group were used to develop competitive PCR assays and used to quantify DNA of each group in wheat seed produced from inoculated field plots. Seed was used in seed treatment efficacy field experiments and the amount of DNA of each group was determined in emerged seedlings. The performance of treatments towards each group of pathogens was evaluated by comparison of the reduction in DNA in seedlings emerged from treated seed compared with untreated seed. CONCLUSIONS: DNA from the two groups of pathogens causing Fusarium seedling blight of wheat can be quantified separately using the competitive PCR assays. These assays show improved sensitivity compared with those previously reported for the individual species and allowed the quantification of pathogen DNA in seed and seedlings. Significant reductions in pathogen DNA were evident for each seed treatment. SIGNIFICANCE AND IMPACT OF THE STUDY: Quantification of DNA for each group allows the evaluation of seed treatment performance towards the two components of Fusarium seedling blight disease complex. The approach taken and the assays developed in this study will be of use for the study of other Fusarium disease complexes and their control. Based on the results reported here on the seedling stage of crop development, further studies that examine the control of seed-borne pathogens through fungicide seed treatments throughout the growing season are warranted.     

Fast classification of plant-associated bacteria in the Xanthomonas genus

Abstract A rapid method for identifying Xanthomonas bacteria was developed, based on specific PCR amplification. In all Xanthomonas pathovars tested, a single 16S rDNA fragment of 480 bp was produced. Phytobacteria from other genera showed other fragment patterns on agarose gel electrophoresis. This Xanthomonas identification system was used to screen Xanthomonas -related organisms, newly isolated phytobacteria and bacterial populations in wheat seed extracts.     

豌豆花DNA导入小麦后种子蛋白质组分变化的研究

豌豆花ＤＮＡ直接导入小麦体可诱导小麦种子蛋白质组分发生明显的变化,小麦种子蛋白质和总氨基酸含量都比对照增高２０％。这些变异性状能稳定遗传给后代。因此直接导入豌豆花ＤＮＡ技术可以为小麦品质改良和分子育种研究提供一条新途径。     

Development of A Rapid Method for the Diagnosis of Citrus Greening Disease using the Polymerase Chain Reaction

The fastidious bacterium causing citrus greening disease occurs in uneven and low concentrations in the sieve tubes of host plants. A rapid and sensitive assay based on the polymerase chain reaction (PCR) has been developed using the primers derived from the sequences of the cloned DNA fragment of greening fastidious bacterium (GFB) to detect GFB infection in citrus. One set of the primer pairs (named 226-primer pair), which generates a 226 bp GFB-specific fragment from total DNA templates purified from diseased citrus plants, was tested and chosen for PCR amplification. The PCR-based assay using this 226-primer pair effectively detected GFB infection in various citrus cultivars collected from different Asian countries. This detection technique, which can be completed within 6 h, offers a rapid and efficient method for accurate diagnosis of citrus greening disease.     

一种适于PCR扩增的小麦基因组DNA快速提取法

许多小麦分子生物学研究需要对大量的小麦样品进行PCR检测,因此,建立一种快速提取小麦基因组DNA的方法十分必要。根据国外报道的一种快速提取水稻和玉米基因组DNA的方法,我们对部分提取步骤进行变动后,在小麦上进行了尝试,长度为1．5kb的片段能得到稳定的扩增。该方法样品研磨在1.5ml的离心管内进行,后续操作不用酚、氯仿、CTAB、SDS和巯基乙醇,整个提取过程不需要使用通风橱,操作步骤简单,花费时间少,而且提取的小麦基因组DNA完整性好,量也较可观。一个DNA样品可供50～100次PCR反应使用,适用于小麦遗传多样性、分子标记辅助选择、转基因后代检测以及引物筛选、分子标记定位等多种研究。     

Development of a new seminested PCR method for detection of Legionella species and its application to surveillance of legionellae in hospital cooling tower water.

The presence of PCR inhibitors in water samples is well known and contributes to the fact that a practical PCR assay has not been developed for legionella surveillance. In this study, we devised a new seminested PCR assay for detection of Legionella spp. in water samples as a means of overriding the PCR inhibitors without loss of sensitivity. The seminested PCR assay utilized primers to amplify the 16S rRNA gene (LEG primers) of 39 Legionella spp. The assay was specific to legionellae, and the sensitivity was 1 fg of extracted Legionella DNA in laboratory examination. To evaluate the feasibility and sensitivity of the PCR assay in identifying the presence of legionellae, it was used to survey Legionella contamination in the water of 49 cooling towers of 32 hospitals. A commercially available EnviroAmp Legionella kit and a culture method were also used in the survey for comparison with the seminested PCR assay. The detection rates of legionellae in the samples were 91.8% (45 of 49) by the PCR assay and 79.5% (39 of 49) by the culture method. The EnviroAmp kit revealed that 30.6% of the water samples (15 of 49) contained inhibitors of the PCR amplification. However, the seminested PCR assay could produce the Legionella-specific DNA bands in 14 of the 15 samples. Although 8 of the 14 samples were positive in the first-step PCR, 6 of the 14 samples became positive in the second-step PCR. These results suggest that the effect of PCR inhibitors in samples, if any, can be reduced because of the dilution of the sample in the second-step PCR and that sensitivity of detection can be increased by the second-step PCR. Thus, the seminested PCR assay with LEG primers to amplify the 16S rRNA gene of 39 Legionella spp. was a practical and sensitive method to detect Legionella spp. in water samples.     

Presymptomatic and quantitative detection of Mycosphaerella graminicola development in wheat using a real-time PCR assay

Presymptomatic and accurate diagnosis of Mycosphaerella graminicola leaf blotch is desirable for the disease prediction and the timely application of fungicides. To develop a sensitive PCR assay, four specific primer pairs were designed. They were more specific than three known specific primer pairs. Three of them could detect as little as 0.5 pg M. graminicola DNA in a conventional PCR. A real-time PCR assay was applied for monitoring the disease progression in both inoculated and naturally infected wheat plants using the primer pair ST-rRNA F/R. In inoculated plants, M. graminicola DNA could be detected immediately after inoculation and a steady increase was detected before visible symptoms appeared at 8 days. The rapid growth period took place between 6 and 16 days postinoculation. In the field, the disease progression in the top three leaf layers was followed during the epidemic period. The results were significantly correlated to the disease indices (R=0.8986) and also to the number of pycnidia per leaf (R=0.9227). These suggest that the real-time PCR assay is a reliable approach for the presymptomatic and accurate detection of M. graminicola development in the field.     

Development of PCR assay based on ITS2 rDNA polymorphism for the detection and differentiation of Fusarium sporotrichioides

A polymerase chain reaction assay was developed for detection of Fusarium sporotrichioides, a plant pathogen in many parts of the world. Based on small nucleotide differences in ITS2 (Internal Transcribed Spacer) rDNA of our local isolate of F. sporotrichioides (Accession No. AY510069) and other isolates found in NCBI/GeneBank database, species specific primer FspITS2K was selected. Primer pair FspITS2K and P28SL amplified a fragment of 288 bp containing a portion of ITS2 and 28S rDNA of all the F. sporotrichioides isolates tested, originated from different hosts and regions of the world but did not amplify any other species of Fusarium and plant's DNA. To use the PCR assay in seed health testing, a protocol was setup for the rapid and effective preparations of fungal DNA from wheat seeds. The method developed may be useful for the rapid detection and identification of F. sporotrichioides both from culture and from plant tissue.     

Functional analysis of the ver gene using antisense transgenic wheat

The function of ver203 , a gene related to vernalization in winter wheat, was investigated by expression of a complementary DNA as an antisense RNA in transgenic plants. A verc203:gus fusion‐expression plasmid was constructed in pBI221, which contains a CaMV (cauliflower mosaic virus) 35S‐promoter, a gus gene and a nos terminator. The construct was then introduced into the plant by the pollen‐tube pathway. The results showed that heading was strongly inhibited in 6 of 326 vernalized antisense transgenic winter wheat plants, until both the vernalized control winter wheat and sense transgenic plants ripened. The hybridization analysis of DNA, amplification of the insert DNA sequences with PCR, northern blot analysis with double‐ and single‐stranded probes, and detection of GUS activity by X‐gluc assay gave strong positive results. This suggests that the VER203 protein plays an important role in controlling heading and flower development in winter wheat.     

Detection of Tilletia caries, Causal Agent of Common Bunt of Wheat, by ELISA and PCR

The paper reports about the development and evaluation of two methods, a PCR‐based assay and an enzyme‐linked immunosorbent assay (ELISA), for the detection of the common bunt fungus Tilletia caries (syn. T. tritici) in young wheat plants. Using the published primer pair Tcar2A/Tcar2B for polymerase chain reaction (PCR) with DNA from axenic cultures of T. caries or from T. caries‐infected plants, we obtained a single band after electrophoresis of the amplification products. By PCR the bunt pathogen could be detected in shoots (EC 12) as well as in leaves (EC 13–14) of infected plants. Immunological detection was performed using a double antibody sandwich enzyme‐linked immunosorbent assay (DAS‐ELISA) with biotinylated detection antibodies. The antibodies were obtained after injection of mycelial homogenates of axenic cultures of T. caries into rabbits. The detection limit was 16 pg DNA per 100 mg plant fresh weight for the PCR and 7 ng/ml fungal protein for the ELISA, respectively. Except for the closely related T. controversa, no cross‐reactions with other fungi were observed with both methods. While it was possible to detect teliospores of T. caries by PCR, the ELISA did not react with spore extracts. Analysis by ELISA of shoots of individual plants grown from inoculated seeds revealed that at EC 10 all plants were infected. There was, however, a large variability in the amount of T. caries present in the plants. This observation and reports in the literature indicate quantitative differences in the degree of colonization of the tissue between individual plants even in a given variety. Regarding the use of modern diagnostics to assist in the development of resistant varieties we therefore suggest that for the wheat –T. caries pathosystem the non‐quantitative PCR‐assay employed here is less suited than the ELISA that allows precise quantification of the amount of fungal antigen present in the plant. However, to routinely employ the ELISA in resistance breeding further development work is needed.     

A Rapid DNA Extraction Method for RFLP and PCR Analysis from a Single Dry Seed

A single-seed DNA extraction method was developed for rapid identification of plant genotype. The method was applied to 12 plant species, including the oil seeds sesame and soybean. The results were comparable to those obtained for oil-less seeds such as rice. This method will be useful for genotypic selection which requires rapid screening of large populations. It can also be used to identify varietal purity of seed stocks by PCR and RFLP analysis. The method includes two major steps, (i) treatment by proteinase K in an SDS extraction buffer, and (ii) grinding of a single half seed in the buffer after incubation. About 1.5–2 µg of DNA per half seed (the endosperm part) of rice was obtained and more than 200 half seed samples could be handled by one person in a day. The DNA could be used for fingerprinting and detection of target genes in a transgenic plant by PCR. The amplified PCR products from the half seed DNA exhibited the same banding patterns as those from leaf DNA. Yield and quality of DNA extracted from half seeds of rice was also sufficient for RFLP analysis. The remnant half seeds containing the embryo can be maintained for later germination of selected genotypes.     

农杆菌介导的转谷氨酰胺合成酶基因小麦的抗除草剂特性研究

 谷氨酰胺合成酶（Glutamine synthetase,GS,E.C. 6.3.1.2）是植物氨同化过程中的关键酶,对植物的氮素吸收和代谢起着至关重要的作用。谷氨酰胺合成酶还是除草剂草胺膦(Phosphinothricin　(PPT)或Basta)的靶标酶。前期工作已从我国特有的豌豆(Pisum satium)品种中克隆了细胞质型谷氨酰胺合成酶（GS1）cDNA和叶绿体型谷氨酰胺合成酶（GS2）cDNA。为了验证谷氨酰胺合成酶的功能,构建了同时含有GS1 cDNA和GS2 cDNA的植物表达载体p2GS。以该表达载体通过农杆菌介导法,转化小麦(Triticum aestivum)的未成熟胚愈伤组织,经PPT筛选及分化再生培养,获得了抗PPT的转基因小麦植株41株。PCR和基因组Southern 杂交分析证实了GS1 和GS2基因已经整合到转基因小麦的基因组。用除草剂草胺膦Basta溶液涂抹转p2GS小麦叶片,结果证明GS转基因植株可以抗高达0.3%的 Basta溶液,而对照植株叶片逐渐变黄直至枯死。转基因小麦植株能正常结实。上述实验结果表明：1) GS基因在小麦植株中获得了有效表达,从而赋予小麦植株抗PPT特性;2) GS基因能够作为研究小麦遗传转化的筛选标记基因。