番茄烟粉虱传双生病毒PCR检测

From the conserved regions of the reported nucleotide sequences of whitefly-transmitted geminiviruses (WTGV), a pair of degenerate primers was designed to anneal to the conserved sequence.The tomato samples infected geminivirus-like from Guangdong were detected by PCR. The results showed that a 356bp specific fragment was amplified from the samples. The specific fragment was cloned and sequenced, and the sequence was compared with all nucleotide sequences in GenBank by Blast of NCBI. The result showed that the fragment belonged to Geminiviridae DNA. So the degenerate primers may be used to detect the WTGV from tomato in Guangdong. Moreover, both of the homology of the fragment between WTGV from tomato in Guangdong and the reported WTGV in the world and WTGV from tomato in Guangxi were under 82%. These results implied that the WTGV from tomato in Guangdong differed from the above-mentioned WTGV.     

Changes of 5＇ Terminal Nucleotides of PCR Primers Causing Variable T-A Cloning Efficiency

T-A cloning takes advantage of the unpaired adenosyl residue added to the 3＇ terminus of amplified DNAs by Taq and other thermostable DNA polymerase and uses a Ilnearlzed plasmld vector with a protruding 3＇ thymldylate residue at each of Its 3＇ termini to clone polymerase chain reaction （PCR）-derived DNA fragments. It Is a simple, reliable, and efficient Ilgatlon-dependent cloning method for PCR products, but the drawback of variable cloning efficiency occurs during application. In the present work, the relationship between variable T-A cloning efficiency and the different 5＇ end nucleotlde base of primers used In PCR amplification was studied. The results showed that different cloning efficiency was obtained with different primer pairs containing A, T, C and G at the 5＇ terminus respectively. The data shows that when the 5＇ end base of primer pair was adenosyl, more white colonies could be obtained In cloning the corresponding PCR product In comparison with other bases. And the least white colonies were formed when using the primer pair with 5＇ cytldylate end. The gluanylate end primers resulted In almost the same cloning efficiency In the white colonies amount as the thymldylate end primer did, and this efficiency was much lower than that of adenosyl end primers. This presumably is a consequence of variability In 3＇dA addition to PCR products mediated by Taq polymerase. Our results offer instructions for primer design for researchers who choose T-A cloning to clone PCR products.     

NBS-LRR resistance gene homologues in rice

Twenty three DNA fragments with a size of about 520 bp have been cloned from rice genome by PCR amplification using primers designed according to the conserved region of most plant resistance (R) genes which have Nucleotide Binding Site (NBS) and Leucine-Rich Repeat (LRR) domains. Homologous comparison showed that these fragments contained typical motifs of the NBS-LRR resistance gene class, kinase 1a, kinase 2a, kinase 3a and domain 2. Thus they were named R gene homologous sequences (RS). These RS were divided into 4 groups by clustering analysis and mapped onto chromosomes 1, 3, 4, 7, 8, 9, 10 and 11, respectively, by genetic mapping. Ten RS were located in the chromosomal intervals where known R genes had been mapped. Further RFLP analysis of an RS, RS13, near the bacterial blight resistance gene Xa4 locus on chromosome 11 among near isogenic lines and pyramiding lines of Xa4 showed that RS13 was possibly amplified from the gene family of Xa4.     

Cytological identification of an isotetrasomic in rice and its application to centromere mapping

The aneuploid with isochromosome or telochromosome is ideal material for exploring the position of centromere in lingkage map.For obtaining these aneuploids in rice,the primary trisomics from triplo-1 to triplo-12 and the aneuploids derived from a triploid of indica rice variety Zhongxiao 3037 were carefully investigated.From the offsprings of triplo-10,a primary trisomic of chromosome 10 of the variety,an isotetrasomic “triplo-10-1” was obtained.Cytological investigation revealed that a pair of extra isochromosomes of triplo-10-1 were come from the short arm of chromosome 10.In the offsprings of the isotetrasomic,a secondary trisomic “triplo-10-2”,in which the extra-chromosome was an isochromosome derived from the short arm of chromosome 10,was identified.With the isotetrasomic,secondary trisomic,primary trisomic and diploid of variety Zhongxiao 3037,different molecular markers were used for exploring the position of the centromere of chromosome 10.Based on the DNA dosage effect,it was verified that the molecular markers G1125,G333 and L169 were Located on the short arm,G1084 and other 16 available molecular markers were on the long arm of chromosome 10.So the centromere of chromosome 10 was located somewhere between G1125 and G1084 according to the RFLP linkage map given by Kurata et al[1].The distance from G1125 to G1084 was about 3.2cM.     

Identification and analysis of genes present in Leptospira interrogans serovar lai but absent in L. biflexa serovar monvalerio

Genes present in virulent bacterial strains but absent in avirulent close relatives can be of great biologic and clinical interest. This project aimed to identify strain specific DNA sequences of Leptospira interrogens serovar lai, which is absent in the saprophytic L. biflexa serovar monvalerio, via suppression subtractive hybridization with the former as the tester while the latter as the driver. The mixture of PCR amplified DNA fragments from two subtractive hybridization experiments were cloned into pMD 18-T vector and the positive clones were identified by dot blotting against the chromosome DNA of the two strains individually. After DNA sequencing and analysis, the distribution of these genomic fragment sequences in a panel of pathogenic and nonpathogenic leptospires was investigated employing dot blot analysis. Among the 188 positive clones randomly chosen, 24 contained the tester strain specific genomic regions, of which, 5 were non-coding fragments while the others contained 23 distinct protein coding sequences. Besides 9 genes encoding functional proteins, 12 genes encode unknown proteins and the rest two genes encode proteins with recognizable domain structures, one for a putative leucine-rich repeats (LRR) family protein while the other as an outer-membrane protein. Our experiment results indicated that suppression subtractive hybridization is effective for screening specific DNA sequences between two leptospiral strains, and some of these sequences might be responsible for virulence determination. Further analysis of these DNA sequences will provide important information on the pathogenesis of Leptospira.     

Analysis and validation of genome-specific DNA variations in 5′ flanking conserved sequences of wheat low-molecular-weight glutenin subunit genes

The thirty-three 5′ flanking conserved sequences of the known low-molecular-weight subunit (LMW-GS) genes have been divided into eight clusters, which was in agreement with the classification based on the deduced N-terminal protein sequences. The DNA polymorphism between the eight clusters was obtained by sequence alignment, and a total of 34 polymorphic positions were observed in the approximately 200 bp regions, among which 18 polymorphic positions were candidate SNPs. Seven cluster-specific primer sets were designed for seven out of eight clusters containing cluster-specific bases, with which the genomic DNA of the ditelosomic lines of group 1 chromosomes of a wheat variety ‘Chinese Spring’ was employed to carry out chromosome assignment. The subsequent cloning and DNA sequencing of PCR fragments validated the sequences specificity of the 5′ flanking conserved sequences between LMW-GS gene groups in different genomes. These results suggested that the coding and 5′ flanking regions of LMW-GS genes are likely to have evolved in a concerted fashion. The seven primer sets developed in this study could be used to isolate the complete ORFs of seven groups of LMW-GS genes, respectively, and therefore possess great value for further research in the contributions of a single LMW-GS gene to wheat quality in the complex genetic background and the efficient selections of quality-related components in breeding programs.     

Cloning of rat sp56,the homologue of mouse sperm ZP3 receptor—sp56

Mouse sp56 is considered as one of the candidates for mouse zona pellucida 3(mZP3)receptor,Up to date,its homologue has only been cloned from guinea pig,namely,AM67.Based on the cDNA sequence of mouse sp56,we designed a pair of primer to amplify its homologue from rat testis cDNA.Using RT-PCR, two tragments of 743 bp and 938 bp were amplified.The PCR products show very high homology to mouse sp56.However,the 743 bp product completely lacks one of the seven Sushi domains of mouse sp56.Using the 743 bp product as the probe to detect the expression profile of sp56 in rat tissues,Northern blot shows that a-2.0kb mRNA expresses specifically in testis.Employed the RACE method,two full cDNA sequences of rat sp56 were obtained.A Mr-42KD band was detected in denatured and non-reducing protein sample of rat testis and sperm with anti-mouse sp56 monoclonal antibody by Western blot method.Rat sp56 was localized on rat sperm head by the indirect immunofluorescence method.Rat sp56 immunoreactivity was detected from the early pachytene spermatocytes and throughout the spermatogenesis.Its cloning will further our understanding of the mechanism of the sperm-egg recognition and binding.     

Cloning of fatty acid elongase1 gene and molecular identification of A and C genome in Brassica species

The fatty acid elongase 1 (FAE1) genes of Brassic napus were cloned from two cultivars, i.e. Zhong- shuan No. 9 with low erucic acid content, and Zhongyou 821 with high erucic acid content, using the degenerate PCR primers. The sequence analysis showed that there was no intron within the FAE1 genes. The FAE1 genes from Zhongyou 821 contained a coding sequence of 1521 nucleotides, and those cloned from Zhongshuan No. 9 contained a 1517 bp coding sequence. Alignment of the FAE1 sequences from Brassica rapa, B. oleracea and B. napus detected 31 single nucleotide polymorphic sites (2.03%), which resulted in 7 amino-acid substitutions. Further analysis indicated that 19 SNPs were genome-specific, of which, 95% were synonymous mutations. The nucleotide substitution at po- sition 1217 in the FAE1 genes led to a specific site of restricted cleavage. An AvrII cleavage site was present only in the C genome genes and absent in the A genome FAE1 genes. Digestion profile of the FAE1 sequences from B. rapa, B. oleracea and B. napus produced with AvrII confirmed that the FAE1 genes of B. oleracea origin was recognized and digested, while that of B. rapa origin could not. The results indicated that by AvrII cleavage it was possible to distinguish B. rapa from B. oleracea and be- tween the A and C genome of B. napus. In addition, the FAE1 genes could be used as marker genes to detect the pollen flow of B. napus, thus providing an alternative method for risk assessment of gene flow.     

中间偃麦草单条染色体分离及体外扩增

本研究利用微细玻璃针法从减数分裂中期I的花粉母细胞中分离回收了携带小麦抗黄矮病基因的中间偃麦草染色体2Ai－2。将目标染色体放入装有蛋白酶K消化液的0.5ml小离心管中,用Sau3AI酶切,在DNA片段的末端连接接头后,进行 PCR扩增。扩增产物经琼脂糖凝胶电泳分析,DNA片段的大小在150～3000bp之间,而大部分集中在200～1500bp之间。 Abstract:A simple method was used to adapt refined needles for the collection of Th.intermedium 2Ai－2 chromosome carrying BYDV (barley yellow dwarf virus) resistance gene from meiosis－metaphase spreads .The aimed chromosome was put into a 0.5ml Eppendorf tube,deproteinized with proteinase K,digested with Sau3AI,and link－adaptors were ligated to the ends of the DNA fragments.After amplification by PCR,size distributions of the PCR products were analyzed by agarose gel electrophoresis and smears of DNA were revealed that the size ranged from 150bp to 3000bp with predominant fragments at about 200～1500bp.     

Preparation of single rice chromosome for construction of a DNA library using a laser microbeam trap

We report the development of a laser micromanipulation system and its application in the isolation of individual rice chromosomes directly from a metaphase cell. Microdissection and flow sorting are two major methods for the isolation of single chromosome. These methods are dependent on the techniques of chromosome spread and chromosome suspension, respectively. In the development of this system, we avoided using chromosome spread and cell suspension was used instead. The cell wall of metaphase rice cell was cut by optical scissors. The released single chromosome was captured by an optical trap and transported to an area without cell debris. The isolated single chromosome was then collected and specific library was constructed by linker adaptor PCR. The average insert size of the library was about 300 bp. Two hundred inserts of chromosome 4 library were sequenced, and 96.5% were aligned to the corresponding sequences of rice chromosome 4. These results suggest the possible application of this method for the preparation of other subcellular structures and for the cloning of single macromolecule through a laser microbeam trap.     

通过微切一扩增建立植物(蚕豆Vicia faba)染色体区段特异性基因文库研究初探

以蚕豆（Viciafaba,2n=12）根尖为材料,采用改良方法制备染色体标本,在光镜下切割分离一段大M染色体核仁组织区（NOR）特定区段（约合0．9pgDNA）,通过单一引物一聚合酶链式反应法（SingleUniquePrimer-PCR）随机扩增微切DNA后,获得近60μgDNA。经琼脂糖电泳分析测定扩增产物分子片段大小介于200-900bp。以地高新（Digoxigenin）标记蚕豆总体DNA,作为探针与扩增产物进行Southern杂交,证实扩增得到的DNA与蚕豆DNA同源,来自做切染色体。部分扩增产物经ECORI酶切后,连人经同酶切割后的pUC18载体质粒,转化大肠杆菌（EcoliJM109）。琼脂糖电泳分析得到的部分克隆,得知插人子长度介于0．25-0．9kb。本文将用于动物材料的单一引物一聚合酶链式反应法应用于植物染色体的微切微扩增,并作了一定程度简化,初步建立起一套包括微切、扩增、检测和克隆的便捷、经济的实验室制备植物染色体区域特异性基因文库的方法。     

Microdissection and Microcloning of Chromosome 5 in Gossypium arboreum

Construction of single chromosomal DNA libraries by chromosome micromanipulation is a useful tool for pursuing genomic studies. Thus far, micromanipulation in cotton has not been reported yet, which may be due to difficulty in preparing chromosomes of similar sizes. In this study, single chromosome micromanipulation was successfully achieved in cotton. A single chromosome 5 of Gossypium arboreum (cultivar Shixiya-1) carrying a large satellite at mitotic metaphase was isolated by microdissection using the Cell Cut Plus Laser micromanipulation system. The chromosomal DNA was digested by Sau 3A and ligated to Sau 3A linker adaptors. After two rounds of linker adaptor PCR (LA-PCR) amplification, DNA fragments ranging from 300 to 2,500?bp were acquired. Southern hybridization revealed that the PCR products had homology with genomic DNA of the cultivar Shixiya-1, indicating that DNA of chromosome 5 has been successfully amplified. The second round LA-PCR products and 45S rDNA and chromosome-specific BAC clones were used as probes for fluorescence in situ hybridization analysis on metaphase chromosome. The results confirmed that the LA-PCR products were derived from the isolated target chromosome. Hybridization signals of the second round LA-PCR products were mainly detected along the entire chromosome 5; in addition, weak signals were also observed on other chromosomes, indicating that there were some homologous nucleotide sequences in other chromosomes. The second round LA-PCR products were cloned to generate a chromosome-specific DNA library which contains approximately 173,000 clones. Evaluation based on 136 randomly selected clones showed that the size of the inserts varied from 500 to 1,800?bp with an average of 750?bp. The no-load rate was less than 1?%, the titer of the library was 1.2?×?10⁶ pfu mL^?1, and the rate of the single and low copy sequences was over 47?%. This library will facilitate specific probe screening, molecular mapping, gene cloning, and DNA sequencing for this chromosome.     

Microdissection of M chromosome in Vicia faba and its library construction]

Microdissection and microcloning technique was employed to construct the library of M chromosome in Vicia faba. The M chromosomes were microdissected with a micromanipulator and were put into a 0.5 ml Eppendorf tube, then digested with Sau3A. Sau3A linker adaptors were ligated to the end of chromosome DNA fragments, and two rounds of PCR were carried out with one chain of linker adaptor as the primer. The PCR products ranged in size from 300 base pair (bp) to 3000 bp with predominant fragments from 500 bp to 1500 bp. Southern hybridization analysis confirmed that PCR products originated from Vicia faba genome. The second round PCR products were cloned and about 102,000 recombinants were obtained. 118 recombinants were selected randomly for analysis. The inserts ranged in size from 150 bp to 3000 bp with an average of 690 bp. Dot blot was carried out for 100 clones with DIG labeled Vicia faba genome DNA as probes. The result revealed that 51% were low and unique copy sequences, 49% were repetitive sequences. M chromosome DNA library has not been reported before.     

Laser microdissection and single unique primer PCR allow generation of regional chromosome DNA clones from a single human chromosome.

We have developed an argon laser chromosome microdissection technique in conjunction with a polymerase chain reaction (PCR) approach to directly amplify microdissected chromosomes. The single 22-mer primer used in PCR, although unique in sequence (5'-TAGATCTGA-TATCTGAATTCCC-3'), randomly primed and amplified any target DNA. These methods were applied to the distal half of the short arm of human chromosome 4 containing the Huntington disease (HD) locus. Forty-four percent of representative clones from this library identify single-copy DNA sequences. This calculation suggests that the resulting chromosome-specific DNA library contains approximately 600 nonoverlapping sequences with an average size 350 bp at an average spacing of 30 kbp along chromosome 4. This microdissection and PCR cloning procedure is a simple and general approach for constructing a chromosome region-specific DNA library from a single metaphase spread.     

A chromosome 1-specific DNA library from the domestic pig (Sus scrofa domestica).

Chromosomes were prepared from lymphocytes of a male domestic pig and flow-sorted on a dual-laser FACS. Twenty spots were observed, corresponding to the known pig karyotype of 18 pairs of autosomes plus the X and Y. DNA was isolated from 10,000 copies of the presumed chromosome 1 spot, restricted with Sau3A, ligated into the vector pGEM4z, and PCR amplified using universal primers; the products were then re-ligated into pUC18. After transformation into Escherichia coli, 210,000 independent colonies were obtained, 5% of which contained only vector DNA. The average insert size of the library was 405 bp. Southern blotting revealed that 36% of the clones contained single-copy DNA and that the remainder contained moderately or highly repetitive DNA. Screening with a (CA)n probe revealed that roughly 1% of the clones contained microsatellite sequences. A bulk insert of the library was biotinylated by PCR and used as a probe for chromosomal in situ suppression hybridization to pig chromosomes, which confirmed that the library is specific for chromosome 1. However, sequences from the centromeric and telomeric regions seem to be underrepresented in the library.     

Rapid generation of region-specific genomic clones by chromosome microdissection: isolation of DNA from a region frequently deleted in malignant melanoma.

Malignant melanoma is frequently characterized by the deletion of the long arm of chromosome 6 (usually encompassing 6q16-q21). In an effort to saturate this region with DNA markers, microdissection and molecular cloning of DNA from banded human metaphases recent development of a novel chromosome microdissection scheme that omits microchemical manipulation of DNA. Microdissection was targeted on band 6q21. Direct PCR amplification of dissected DNA was first used as a probe in chromosomal in situ hybridization of normal metaphases to confirm the specificity of material excised for cloning. A genomic library of 20,000 clones, which is highly enriched for sequences encompassing 6q21, was then constructed. Clones from this library have been mapped against a human-rodent somatic cell hybrid mapping panel that divides chromosome 6 into seven regions, confirming the localization of probes within the target region. Direct PCR amplification of DNA excised by microdissection greatly simplifies and facilitates this chromosome band-specific cloning strategy. The isolation of microclones from this region of chromosome 6 should assist in establishing a physical map of the melanoma deletion region.     

Physical Mapping of Rice Chromosomes 8 and 9 with YAC Clones

First efforts for physical mapping of rice chromosomes 8 and9 were carried out by ordering YAC clones of a rice genomicDNA library covering six genome equivalents with mapped DNAmarkers. A total of 79 and 74 markers from chromosomes 8 and9, respectively, were analyzed by YAC colony and Southern hybridizationusing RFLP markers of cDNA and genomic clones, and by polymerasechain reaction (PCR) screening using PCR-derived and sequence-taggedsite (STS) markers. As a result, 252 YAC clones were confirmedto contain the mapped DNA fragments on both chromosomes. A contigmap was constructed by ordering these YAC clones and about 53%and 43% genome coverage was obtained for chromosomes 8 and 9,respectively, assuming a YAC clone size of 350 kb and overlapbetween neighboring YACs of 50%. A continuous array of YAC cloneswith minimum overlap gave a total size of 18.9 Mb for chromosome8 and 15.6 Mb for chromosome 9, which are close to previousestimates. These contig maps may provide valuable informationthat can be useful in understanding chromosome structure andisolating specific genes by map-based cloning.     

染色体特异DNA文库的构建与鉴定

为构建人类21号染色体特异DNA文库, 以应用于人类遗传疾病的鉴定和研究, 文章采用循环温度梯度法溶解释放微分离的人外周血细胞21号染色体DNA, 将其进行简并寡核苷酸引物PCR(Degenerate oligo nucleotide primer-PCR, DOP-PCR)扩增后, 利用100~500 bp和500~2 000 bp分段回收纯化的两种不同片段大小的DOP-PCR产物构建染色体特异DNA文库, 并分别采用荧光原位杂交(Florescence in situ hybridization, FISH)和斑点杂交对DOP-PCR产物的来源和随机取样的文库克隆进行检测以评估所构建DNA文库的特异性。结果表明: 循环温度梯度法能有效溶解释放微分离的21号染色体DNA; 通过对DOP-PCR产物的分段回收纯化和克隆, 增加了大片段DNA的连接效率; 利用FISH技术和斑点杂交双重鉴定实验证明了文库的特异性, 从而构建了21号染色体特异的DNA文库, 并建立了构建染色体特异DNA文库及检测其特异性的方法, 为21号染色相关遗传疾病的鉴定和研究奠定了基础。     

Microdissection and microcloning of rye (Secale cereale L.) chromosome 1R

Chromosome 1R was microdissected and collected from mitotic metaphase spreads of rye (Secale cereale L.) by using glass needles. The isolated chromosomes were amplified in vitro by Sau3A linker adaptor-mediated polymerase chain reaction (PCR). After amplification, the presence of rye-specific DNA was verified by Southern hybridization. The second-round PCR products from five 1R chromosomes were cloned into a plasmid vector to create a chromosome-specific library, which produced approximately 220,000 recombinant clones. Characterization of the microclone library showed that the 172 clones evaluated ranged in size from 300–1800 bp with an average size of 950 bp, of which approximately 42% were medium/high copy and 58% were low/unique copy clones. Chromosome in situ hybridization confirmed that the PCR products from microdissected chromosomes originated from chromosome 1R, indicating that many chromosome 1R-specific sequences were present in the library. Received: 5 December 1998; in revised form: 15 April 1999 / Accepted: 29 April 1999