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.

OBJECTIVETo explore the variety of the genetic polymorphism of eight Prunella germplasm resources by AFLP analysis.

METHODThe amplified fragment length polymorphism (AFLP) tags were applied to screen out 32 selective amplification primer pairs, the amplified bands as original matrix were analyzed with NTSYS-PC software for the similarity between the Prunella germplasm and the construction of genetic phylogenetic tree.

RESULTSDS extraction of genomic Prunella DNA showed a good quality, could meet the requirements of AFLP analysis. From 32 selective amplification primer pairs, 10 pairs with strong polymorphism, better band and higher resolution were used for the construction of the AFLP Prunella fingerprint, all eight Prunella germplasms were separated, they were divided into 3 categories.

CONCLUSIONPrunella germplasm resources are rich in genetic diversity, certain morphological characteristics and differences are associate with genotype.

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

AFLP technology has been widely used in molecular biology due to its integration of several advantages of high throughput, high efficiency and requiring no sequence information, etc. Great changes have been achieved in recent years in AFLP-related technologies and platforms. There are several AFLP-expanded technologies available. These improved technologies are capable of distinguishing the heterozygote from the homozygote and of converting any AFLP band of interest, without much effort, into locus-specific markers, which can be deployed for massive locus detection and for gene isolation. This review focuses on these favorable changes from conventional AFLP technology into more effective and more practicable AFLP-related ones. Understanding these advancements and AFLP-expanded technologies will facilitate the achievement of our research goals.
Amplified Fragment Length Polymorphism Analysis ; methods ; Microsatellite Repeats ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci

The Direct Amplification of Length Polymorphisms was applied to assess genetic diversity and structure of 7 populations of Dendrobium nobile, comparing one population of D. lituflorum. The five primer combinations were amplified to produce 140 clear bands, and 102 polymorphic bands had been detected with each pair of primer producing 20.4 polymorphic bands on average. At species level, the percentage of polymorphic bands (PPB) was 72.86%, the Nei's gene diversity index (H) was 0.288 9, and the Shannon's information index (I) was 0.424 2. At population level, the average PPB was 47.96%, H was 0.1861, and I was 0.273 9 in 7 populations. The coefficient of gene differentiation (Gst) was 0.338 6 among populations of D. nobile. It showed that 33.86% of the total genetic diversity was attributable to genetic differentiation among populations, while the rest 66.14% was resided between individuals within population.
Amplified Fragment Length Polymorphism Analysis ; methods ; China ; Dendrobium ; classification ; genetics ; Genetic Variation ; Phylogeny ; Polymorphism, Genetic

OBJECTIVETo research the genetic diversity of different Rhodiola rosea geographical populations in Tianshan Mountain, China;

METHODThe genetic diversity of eighteen R. rosea geological populations from six niches was estimated using amplified fragment length polymorphism (AFLP) markers. The data of amplified bands were analyzed by the software POPGENE v1.31 (32-bit) and SPSS.

RESULTThe nine primers employed produced a total of 238 discernable and reproducible amplified fragments. There were 228 polymorphic bands. The percentage of polymorphic bands with in different populations was 95.6%. Genetic diversity analysis showed that average number of alleles per loci was Na = 1.4883, effective number of alleles per loci Ne = 1.3907, Neis gene diversity index H = 0.2170, Shannon's information index I = 0.3108, the percentage of polymorphic loci P = 52.71, genetic differentiation among populations Gst = 0.364; UPGMA cluster analysis based on genetic distance data divided eighteen populations into two clusters: Cluster I composed of twelve populations and Cluster II 6 populations which distributed in attitude upper 3 175 m;

CONCLUSIONOur researches suggest that the best niche of R. rosea was at attitude between 3 150-3 250 m; this region is important for the conservation of R. rosea germplasm resource.

In order to investigate the genetic basis of morphological variation of tetraploid plantlets of Atractylodes macrocephala, diploid plantlets were taken as experimental material, sterile filtration colchicine was used to soak 0.5-1.0 cm long buds. The difference between morphology and stomatal of diploid and tetraploid of A. macrocephala was compared, and genome polymorphism was explored by AFLP. The results showed that the buds dipped in 0.1% colchicine solution for 36 h was optimal conditions to induce tetraploid of A. macrocephala with induction rate of 32.0%. Morphological indexes such as leaf area index, leaf length and width, the density of stomas and the number of chloroplast of tetraploid were distinctly different from diploid. Four hundred and fifty-one bands ranging with 80-500 bp were amplified with 24 pairs of primers, the rate of polymorphism was 32.59%. These amplification sites of diploid were different from tetraploid of A. macrocephala, and the differences in morphology of them were reflected in the DNA polymorphism.
Amplified Fragment Length Polymorphism Analysis ; methods ; Atractylodes ; genetics ; Sequence Analysis, DNA ; Tetraploidy

OBJECTIVETo assess the genetic diversity of Atractylodes macrocephala in 12 cultivated populations and 3 wild populations.

METHODThe molecular marker technique ISSR was used to investigate the genetic diversity of 365 samples from 15 populations in Zhejiang, Anhui and Hebei Provinces. Data was analyzed by POPGEN 32, and a cluster diagram was presented by UPGMA.

RESULTOne hundred and two amplified fragments were obtained using 13 ISSR primers. 94 polymorphic loci were identified as 92.16%. Nei's genetic diversity index (He) was 0.406 5, Shannon diversity index (I) was 0.590 3, and the coefficient of gene differentiation (Gst) was 0.202 5. The genetic similarity coefficient among the populations ranged from 0.690 7 to 0.960 5 in an average of 0. 825 6. No significant difference was found among the populations based on the clustering analysis.

CONCLUSIONThere is a low level of genetic differentiation in higher genetic diversity of the A. macrocephala populations. No obvious regional or species diversities were identified. This is consistent with current status of cultivation and gerplasm circulation in A. macrocephala.

OBJECTIVETo explore the quality variation and genetic diversity of Desmodium styracifolium from different provenances, and lay a foundation for rational exploitation on germplasm resources and fine variety breeding of D. styracifolium.

METHODAmplified fragment length polymorphism (AFLP) markers were developed to analyze genetic diversity in D. styracifolium from 18 resources. NTSYSpc-2. 11F software was used to analyze the similarity among the D. styracifolium germplasms and construct the genetic phylogenetic tree. The schaftoside content in D. styracifolium from different provenances was determined by HPLC.

RESULTA total of 844 fragments were amplified with 8 primers, in which 717 were polymorphic bands, accounting for 84. 27% of the total detected variation. All the specimens from 18 resources could be grouped into 3 clusters by cluster analysis. The schaftoside contents of D. styracifolium germplasms differed significantly, with the highest content in the germplasm from Sanya, Hainan.

CONCLUSIONSignificant quality variation and genetic diversity can be observed among D. styracifolium germplasms. The diverse germplasm resources should be explored and the fine variety should be selected to breed.

OBJECTIVETo develop fluorescent amplified fragment length polymorphism (AFLP) method and to evaluate the its typing capability with pulsed-field gel electrophoresis (PFGE) in molecular typing of Vibrio cholerae.

METHODSForty-seven strains of V. cholerae, with different PFGE patterns, were selected as the reference group to optimize the selective primers of AFLP analysis. Eighty-three strains including 20 strains from one epidemic episode, isolated from different provinces during 1961 and 2005, were used to compare the typing abilities of AFLP and PFGE. LI-COR4300 DNA sequencing system was used for AFLP electrophoresis. The images were recorded by Saga(MX) software and transferred to BioNumerics for clustering analysis. A standard protocol for V. cholerae from PulseNet was used in PFGE.

RESULTSWhen comparison was made with different selective primers on AFLP based on the 47 strains, results showed that the optimized selective primer pair was EcoR I-G/Mse I-T, and the reproducibility of the tests was 99.2%. Eighty-three isolates showed 52 AFLP patterns and 44 PFGE patterns, with D values as 0.9545 (AFLP) and 0.9251 (PFGE) respectively.

CONCLUSIONThe protocol of fluorescent AFLP on V. cholerae typing was established. AFLP was higher than PFGE in discrimination of V. cholerae which could be used for molecular typing. When combined with PFGE, AFLP became a more insightful tool to identify genome difference of different isolates.