Clone identification and genetic relationship among vine cacti from the genera Hylocereus and Selenicereus based on RAPD analysis

Clones of Hylocereus and of Selenicereus species were distinguished from each other by the banding pattern generated by one to nine 10-mer oligonucleotide primers in the random amplified polymorphic DNA (RAPD) reaction. RAPD analysis was also applied to estimate the genetic relationship among five Hylocereus and nine Selenicereus species. A dendrogram was constructed based on a data matrix of 173 polymorphic bands originated by nine primers. Two groups were identified, one consisting of Hylocereus species and the other consisting of Selenicereus species. These results are consistent with the accepted taxonomic classification of the genera studied. The principal coordinate analysis (PCO), i.e. the plot drawn on the basis of the RAPD data, clearly distinguished between three groups, namely, Hylocereus species, S. megalanthus and the rest of the Selenicereus species studied. PCO thus strongly support the notion that the tetraploid S. megalanthus is an exception among the Selenicereus group. The RAPD results support our hypothesis regarding the allopolyploid (rather than autopolyploid) origin of this species.     

甜菜DAMD-PCR体系的建立及优化

为了建立甜菜DAMD扩增体系,以期利用DAMD引物应用于甜菜品种指纹图谱的构建及分子标记辅助育种。本实验利用单因素变量的方法对甜菜DAMD体系进行优化。同时选用12个甜菜品种,利用优化的体系对25条DAMD引物进行扩增。获得甜菜的最适DAMD体系:总体积为20μL,包含模板DNA 10~80 ng、0.75 U的DNA聚合酶、0.2μL的d NTPs(2.5 mmol/L each)以及2.0μL的引物(10μmol/L)。同时25条引物均扩增出了清晰条带,除了个别引物多态性较差外,其余引物多态性都非常的丰富,其中引物62H(-)就可以把实验中用到的12个甜菜品种全部区分开。由此可见,DAMD引物的扩增效率很高,并且扩增结果稳定,条带清晰,非常适合甜菜品种指纹图谱的构建及遗传多样性分析。     

Study on Genetic Fingerprinting Technique of Microbial Communities

The 99% of all microorganisms in naturecannot be isolated by standard culture methods without conspicuous external characters to classify them morphologically. In addition, classification based on physiological or biochemical features are often fuzzy. Molecular techniques are used for uncultured microorganisms to explore the diversity of microbial communities and novel resources without the need of cultivation. DNA dynamics and cloning of PCR products obtained from environmental DNA is now routinely used to identify microbial populations in microbial ecology. For practical reasons the approach is not suited to study the complex dynamics of microbial communities in environment. Genetic fingerprinting techniques are better tools, which give complement for the traditional microbiological methods. The methods are rapid and relatively easy to perform, and they allow the simultaneous analysis of multiple samples, which makes it possible to compare the genetic diversity of microbial communities from different habitats, or to study the behaviour of individual communities over time.     

Genetic relationships between the dominant genotypes of Phytophthora infestans in Hokkaido, Japan

The genetic characteristics of the dominant genotypes of Phytophthora infestans in Japan (US-1, JP-1, Japanese A1-A, A1-B) were compared. Differences were evident in the peptidase genotype, amplified fragment length polymorphism, and RG57 DNA fingerprints. Almost all of the fingerprint bands for the Japanese genotype A1-B were also present in JP-1 and Japanese A1-A, and few bands were unique to Japanese A1-B. These results suggest that the Japanese A1-B genotype was generated from sexual reproduction involving Japanese A1-A and JP-1 or related genotypes.     

The loss of genetic diversity in Dabry's sturgeon (Acipenser dabryanus,Dumeril) as revealed by DNA fingerprinting

• 1. Dabry's sturgeon, a large, long‐lived migratory fish is endemic to the Yangtze River. Over‐fishing and habitat destruction have caused large‐scale declines in natural stocks in the last two decades.
• 2. Examining patterns of genetic diversity has become an integral component of many management plans for endangered species. DNA fingerprinting was applied to detect genetic diversity in Dabry's sturgeon collected in 1958–1959, 1980–1981 and 1998–1999.
• 3. Studies on direct genetic parameters (genetic variability, hypervariable loci and heterozygosity) and indirect parameters (band‐sharing coefficient and allelic frequency) showed that the continuous decline in wild populations has caused the loss of genetic diversity in present‐day sturgeon.
• 4. The present‐day populations have the lowest genetic variability; thus, effective management is needed to preserve genetic diversity.
• 5. A conservation strategy is urgently required, comprising artificial rearing facilities coupled with breeding management plans.

Copyright © 2003 John Wiley & Sons, Ltd.     

DNA fingerprinting of Australian isolates of Mycobacterium avium subsp paratuberculosis using IS900 RFLP

OBJECTIVES: To evaluate additional restriction enzymes for IS900 RFLP of Mycobacterium avium subsp paratuberculosis and examine the genetic diversity among Australian isolates for epidemiological studies of Johne's disease. DESIGN AND PROCEDURE: Seventy-one isolates of M paratuberculosis from cattle, sheep, goat, alpaca and rhinoceros in six Australian States and the Northern Territory, reference strains and reference DNA from previously characterised strains were tested for genetic variation. Bst EII, Pvu II and Pst I restriction enzymes were used, and four others (Bam HI, Alu I, Xho I and Dra I) were assessed for their ability to detect polymorphisms. Multiple isolates from some animals were tested. RESULTS: Bam HI, was the most effective enzyme for identifying polymorphisms (12 types), followed by Bst EII (11 types). Both Pvu II and Pst I were relatively ineffectual. Fifteen different types were identified, 12 in clinical isolates. Most isolates were cattle (C) strains and fell into the C1 (n = 28) and C3 (n = 32) groupings. All isolates from alpaca were type C1, and bovine isolates were commonly C1 (n = 15) or C3 (n = 28). All of the sheep were infected with sheep (S) strains; no S strains were identified in cattle. Two of six isolates from one animal had single band differences. CONCLUSION: The epidemiological features of M paratuberculosis in Australia are similar to those reported in New Zealand, where cattle and sheep are commonly infected with different strains. However, because of the lack of polymorphism identified within the major groups, it is unlikely that DNA fingerprinting will have a significant role in epidemiological studies of Johne's disease, unless an unusual strain in being studied.     

Tracing Sediment Sources Using Mid‐infrared Spectroscopy in Arvorezinha Catchment,Southern Brazil

The widespread adoption of the sediment fingerprinting approach to guide catchment management has been limited by the cost and the difficulty to prepare and process samples for geochemical and radionuclide analyses. Spectral properties have recently been shown to provide a rapid and cost‐efficient alternative for this purpose. The current research objective was (i) to quantify the sediment source contributions in a 1∙19‐km² rural catchment of Southern Brazil by using mid‐infrared (MIR) spectroscopy and (ii) to compare these results with those obtained with geochemical approach and near‐infrared and ultraviolet–visible spectroscopy methods. The sediment sources to discriminate were cropland surface (n  = 20), unpaved roads (n  = 10) and stream channel banks (n  = 10). Twenty‐nine suspended sediment samples were collected at the catchment outlet during nine significant flood events. The sources could be distinguished by MIR spectroscopy. Cropland and channel bank sources mainly differed in their clay mineral contents, but their similar organic matter content complicated the MIR‐model predictions. Unpaved road contributions were discriminated from the other sources by their lower organic carbon content. When the results of the current research based on MIR spectroscopy are compared with those obtained using other sediment fingerprinting approaches, based on geochemistry and near‐infrared and ultraviolet–visible spectroscopy, an overestimation of channel banks contribution and an underestimation of cropland and unpaved road contributions is found. These results suggest that MIR spectroscopy can provide a useful tool that is non‐destructive, rapid and cheap for tracing sediment sources in rural catchments and for guiding the implementation of soil and water conservation measures. Copyright © 2016 John Wiley & Sons, Ltd.     

海南高良姜挥发油GC-MS指纹图谱分析

建立了海南产高良姜挥发油的GC-MS指纹图谱,对其中20个特征化合物进行了精密度、稳定性和重复性分析。结果表明,高良姜挥发油中检测到了110个成分,其中20个特征成分的精密度、稳定性和重复性良好。该方法简单可靠,可应用于高良姜的品质评价。     

Studies on fish heterosis with DNA fingerprinting

One Tilapia hybridization, Oreochromis aureus, (Steindachner) ♂ × Oreochromis niloticus, (Linnaeus) ♀, and two common carp, Cyprinus carpio, (Linnaeus) ♂, hybridizations, Russian mirror carp ♂ × Xingguo red carp ♀, and German mirror carp ♂ × Xingguo red carp ♀ were used to study the feasibility of predicting heterosis using genetic distance from DNA fingerprinting. The results indicated that highly polymorphic DNA fingerprints could be obtained with human minisatellite 33.6 as a probe on the studied varieties. The within‐population similarity indices of O. aureus, O. niloticus, Russian mirror carp, German mirror carp and Xingguo red carp were 0.785, 0.577, 0.432, 0.348 and 0.339 respectively. The similarity indices between F1 and their parents of three hybridization combinations were not significantly different (P > 0.05). There were larger genetic distances between two hybridization combinations, O. aureus♂ × O. niloticus♀ and Russian mirror carp ♂ × Xingguo red carp ♀, which showed heterosis in production and were extensively used in Chinese aquaculture. The genetic distance between O. aureus♂ and O. niloticus♀ was 0.338, and that between Russian mirror carp and Xingguo red carp was 0.344. However, the genetic distance between German mirror carp and Xingguo red carp was 0.129; this corresponded with the fact that their F1 generation did not show heterosis in the Chinese fish hybridization experiment. The study suggested that genetic distance could be used to predict fish heterosis.