OBJECTIVEThis study aimed to analyze the genetic diversity and genetic relationship of germplasm resources of Lonicera japonica in main producing areas of China and provide reference for developing new varieties of L. japonica.

METHODUsing 6 primer combinations, 13 germplasm of L. japonica were analyzed by AFLP marker. The genetic distance was worked out by using DPS V3.01 software, and the cluster was conducted based on UPGMA.

RESULTA total of 435 bands were obtained including 191 polymorphic ones. The average polymorphic frequency was 43.9%. Cluster analysis showed that the relationship of cultivated variety from the same genuine area was near, and the classification result based on AFLP marker of germplasm of L. japonica from Shandong province was basically consistent with those on their morphological character.

CONCLUSIONAFLP marker can indicate the abundant genetic diversity of L. japonica and provide theoretical evidence for reasonable utilization and breeding new cultivar of L. japonica in molecular level.

Amplified Fragment Length Polymorphism Analysis ; China ; Genetic Variation ; Lonicera ; classification ; genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length

Restriction site amplification polymorphism (RSAP) markers were employed to access the genetic diversity and relationship of 120 lilyturf germplasms from different geographical origins. Sixteen RSAP primer pairs generated 326 polymorphic bands, of which 318 (97.55%) were polymorphic. The value of polymorphism information content (PIC) ranged from 0.87 to 0.95 with an average of 0.92. These results indicated there was abundant genetic diversity among samples. The results of data analysis on 20 population showed that the value of percentage of polymorphic locus (PPL), Nei's gene diversity (H) and Shannon's information index (I) were 19.94%-85.58%, 0.082 6-0.210 7, 0.120 6-0.328 1 respectively. The most abundant genetic diversity was found in the O. japonicus population from Zhejiang and the least in the Liriope minor population. The genetic distance among 20 population was 0.024 6-0.286 8, of which the minimum genetic distance was 0.024 6 between population I and population 13 while the maximum 0.286 8 between population 5 and population 15. Coefficient of genetic differentiation among natural populations was 0.115 3 (Gst). And the gene differentiation contributed to 43.07% of the total genetic variation among populations and to 56.93% within populations. The total gene flow (Nm) was 0.660 9. UPMGA clustering analysis was basically similar to of the principle coordinate analysis (PCA). The 120 samples were classified into four major groups, which were basically corresponded with the genetic relationships based on morphological traits. The results of UPMGA and PCA were also consistent with geographical origins.
Amplified Fragment Length Polymorphism Analysis ; China ; Genetic Variation ; Liriope Plant ; classification ; genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length

Fatty Liver ; genetics ; Female ; Humans ; Male ; PPAR gamma ; genetics ; Polymorphism, Restriction Fragment Length

The present study has been performed to develop a PCR technology to identify human immunoglobulin(Ig) allotypes with restriction fragment length polymorphism(RFLP) using a probe. Genomic DNA were ampilified with PCR tecnology using primers from peripheral blood lymphocytes of 10 periodontal patiens, whose Ig allotypes have been pre-determined by serological tecnique using heagglutination technique. The result indicated that the RFLP patterns could successfully differentiate the Ig allotypes, which suggests that this technology can be developed as a tool useful for population genetics studies.
DNA ; Genetics, Population ; Humans ; Immunoglobulin Allotypes* ; Immunoglobulins* ; Lymphocytes ; Polymerase Chain Reaction* ; Polymorphism, Restriction Fragment Length

BACKGROUND: ABO genotyping is being used increasingly when the results of serologic typing are unclear or there is some suspicion of rare ABO subtypes. Conventional molecular diagnostic methods such as PCR- restriction fragment length polymorphism (PCR-RFLP), allele-specific PCR, PCR-single stranded conformational polymorphism (PCR-SSCP) and sequence-based typing have been used in this field. Recently, a pyrosequencing technique was introduced into clinical laboratories. This study evaluated the possibility of applying pyrosequencing to ABO genotyping. METHODS: A total of 36 samples, which had previously been analyzed by PCR-RFLP and serological method in the Blood Genetics Clinic of Seoul National University Hospital between August 2001 and September 2004 and shown to have the A/A, A/B, A/O, B/B, B/O, O/O, cis-AB/O, cis-AB/A, or cis-AB/B genotypes, were analyzed by pyrosequencing analysis. Briefly, two PCR reactions were carried out separately for one region including nucleotide 261, and for another region including nucleotides 796 and 803. Pyrosequencing was then performed, and the pyrograms were interpreted using an automated interpretation program from the manufacturer and by researchers independently to determine the nucleotides 261, 796 and 803 for ABO genotyping. RESULTS: The ABO genotypes from pyrosequencing and the interpretation of the pyrograms according to the researcher on 36 samples were in complete concordance with the results obtained by PCR-RFLP. The ABO genotypes from the automated interpretation program showed an error in one out of total 108 SNP (single nucleotide polymorphism) analyses (eRROR RATE=0.9%) OF 36 SAMPLES. CONCLUSION: ABO genotyping for A, B, O, cis-AB alleles by pyrosequencing of nucleotides 261, 796 and 803 was relatively simple and accurate and could be an another field we can use in clinical laboratories.
Alleles ; Genetics ; Genotype ; Nucleotides ; Pathology, Molecular ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Seoul

OBJECTIVETo identify genotype of eight strains of Orientia tsutsugamushi (O. tsutsugamushi) isolated from Nan Peng Lie Islands in China and establish tsutsugamushi disease nature foci for this region.

METHODSThe nested polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) were used. Three primers were selected from the DNA sequence of the gene encoding type-specific 56-kDa protein of the Karp strain. The positive products were digested by Hine II and Pst I, meanwhile profiles specific to each strain were analyzed.

RESULTSThree genotypes of O. tsutsugamushi including Karp, Kato and a new strain existed on Nan Peng Lie Islands.

CONCLUSIONNan Peng Lie Islands is tsutsugamushi disease nature foci.

Animals ; China ; DNA, Bacterial ; analysis ; Genotype ; Mice ; Orientia tsutsugamushi ; genetics ; Polymorphism, Restriction Fragment Length ; Rats

OBJECTIVETo explore the applicability and limitation of PCR-restriction fragment length polymorphism (PCR-RFLP) method for genetic diagnosis of spinal muscular atrophy (SMA).

METHODSPCR-RFLP was applied to detect potential deletion in exons 7 and 8 of SMN1 gene in 935 suspected cases with SMA. Multiplex ligation-dependent probe amplification(MLPA) was carried out to analyze dosage alteration of SMN1 gene in 339 of such cases. To confirm the accuracy of PCR-RFLP method for homozygous and heterozygous deletions detection, the consistency of PCR-RFLP and MLPA results were assessed with a Pearson Chi-square test.

RESULTSHomozygous deletion of exon 7 of SMN1 was detected in 590 suspected cases. The rate of diagnosis was therefore 63.1% (590/935). For the 339 suspected cases, PCR-RFLP and MLPA respectively identified 194 and 196 homozygous deletions in the exon 7 of SMN1 gene, suggesting a good consistency (98.9%)(Chi-square = 0.2, P = 0.88). However, only 4 of 339 cases was found to carry a heterozygous deletion of SMN1 exon 7 by PCR-RFLP, in contrast with 17 detected by MLPA. The consistency only reached 23.5%, for which statistical significance was detected (Chi-square = 8.29, P< 0.01).

CONCLUSIONAlthough PCR-RFLP is a simple, specific and efficient method for SMA diagnosis, it has obvious limitation for the diagnosis of 5%-10% SMA patients who have carried a compound heterozygous mutation.

Exons ; Humans ; Muscular Atrophy, Spinal ; genetics ; Mutation ; Polymerase Chain Reaction ; methods ; Polymorphism, Restriction Fragment Length

OBJECTIVETo investigate the relationship between the polymorphism of angiotensinogen gene (AGT) and the risk for hypertension in a Chinese population.

METHODSThree polymorphisms of AGT gene were analyzed in 335 patients with documented essential hypertension and 196 control subjects by using PCR-restriction fragment length polymorphism. Expectation maximization(EM) algorithm was then used for pairwise linkage disequilibrium test and haplotype analysis of AGT polymorphisms.

RESULTSLinkage disequilibrium between M235T and A-20C, between M235T and A-6G, between A-20C and A-6G was observed (P<10(-4)). The case-control analysis revealed that the frequency of T235 is significantly higher in essential hypertension patients than in control subjects. But all haplotype frequencies showed no significant difference between the patient and control groups.

CONCLUSIONNo association was noted between the haplotypes of AGT gene and hypertension in tested people, but T235 allele might play an important role in increased risk for essential hypertension.

Alleles ; Angiotensinogen ; genetics ; DNA ; genetics ; Gene Frequency ; Genotype ; Haplotypes ; Humans ; Hypertension ; genetics ; Linkage Disequilibrium ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length

OBJECTIVETo detect the difference between the Chinese Achang and Han ethnic groups in Yunnan province in the distribution of vitamin D receptor (VDR) gene start codon polymorphism.

METHODSPolymerase chain reaction-restriction fragment length polymorphism, gene sequencing and genetic analysis methods were used. A restriction fragment length polymorphism in the start codon of VDR (Fok I) gene was tested in the Achangs (n=68) and the Hans (n=92).

RESULTSThe frequencies of FF, Ff and ff genotypes were found to be 18%, 35% and 47% in the Achangs, and 22%, 52% and 26% in the Hans, respectively. A significant difference was seen in the frequency distribution of VDR genotype between the Achangs and the Hans(Chi2=7.716, P=0.021).

CONCLUSIONThe Achang and Han ethnic groups differ in the frequency distribution of VDR gene start codon polymorphism.

China ; Codon, Initiator ; genetics ; Humans ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Receptors, Calcitriol ; genetics

OBJECTIVETo establish the association between genetic polymorphisms of HLA-DMA and HLA-DMB and risk of developing trichloroethylene-induced medicamentosa-like dermatitis (TIMLD).

METHODSSixty-one cases were medically confirmed to have been affected with TIMLD and 60 controls were selected from exposed workers who were free from TIMLD. The TIMLD cases and controls were similar in terms of age, sex, and duration of exposure. DNA was extracted both from the TIMLD cases and controls, HLA-DMA and HLA-DMB loci were amplified by using Touchdown PCR, and the alleles and genotypes were confirmed by restriction fragment length polymorphism (RFLP) and direct sequencing. Finally, the frequencies of HLA-DMA and HLA-DMB variants were compared between the two groups.

RESULTSThe results showed that the frequency of HLA-DMA*0101 and HLA-DMB*0103 alleles was significantly increased in TIMLD patients than in controls (71.3% vs. 55.0% for HLA-DMA*0101; P<0.05) (11.5% vs. 3.3% for HLA-DMB*0103; P<0.05). In addition, the frequency of HLA-DMA*0102-*0102 homozygous genotype was also significantly higher in the controls than in the patients (25.0% vs. 8.2%, P<0.05), whereas the frequency of heterozygous HLA-DMB *0101-*0102 genotype was lower in the patients in comparison with the controls. Conclusion The polymorphisms of HLA-DM may be associated with the susceptibility to TIMLD.

Alleles ; Dermatitis, Contact ; genetics ; Genetic Predisposition to Disease ; HLA-D Antigens ; genetics ; Humans ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Trichloroethylene ; toxicity