No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Discrimination of Tsingtaodahua from Other Hop Cultivars and Its Quality Control by Molecular Analysis
Abstract
J. Inst. Brew. 111(2), 229-233, 2005 Random amplified polymorphic DNA (RAPD) was used for hop varietal identification, primarily to distinguish Tsingtaodahua, a fine Chinese variety. Eleven typical varieties, including four aroma hops, five bitter hops, Tsingtaodahua and Cluster, were successfully identified on the basis of 28 polymorphic RAPD bands amplified by five random primers. UPGMA analysis of RAPD data showed genetic relationship among analyzed varie- ties consistent with traditional hop classification. Subsequently, one specific RAPD fragment was converted to a sequence tagged site (STS) marker which can detect as little as a 5% admixture of the variety Kirin 1 in Tsingtaodahua. The RAPD and STS markers can be successfully used for Tsingtaodahua identifica- tion and quality control.
ResearchGate has not been able to resolve any citations for this publication.
The studies with application of the classical genetic method (strain crosses) and a molecular technique (RAPD-PCR fingerprinting, primer Ro 460-04) revealed the presence of separate sibling species within P. jenningsi. One of these is confined to six genetically related strains originating from Japan, separated from other group (results of strain crosses) and showing only one characteristic band pattern. The other of these includes strains from India, Saudi Arabia and China (Przyboś et al. 2003). We wanted to verify the RAPD markers specific for P. jenningsi and to prove the existence of two sibling species within it (revealed by one primer only), by application of others Ro-type primers. The conducted RAPD-PCR fingerpring analysis revealed that the genomes of the studies strains of P. jenningsi have polymorphic DNA sequences complementary to the four applied primers. The band patterns can be used as species-specific markers for P. jenningsi. DNA amplification by four primers used differentiates P. jenningsi into two groups of strains, one of which includes the Indian, Saudi Arabian and Chinese strains, the other the Japanese strains. Our results are congruent with inter-strain crossing experiments in which reproductive isolation was found when continental and Japanese strains were tested. This is further evidence for the existence of two sibling species, whose reproductive isolation is genetically induced.
The rapid development of molecular techniques offers a palette of technical approaches for population biologists interested in a wide range of questions. For example, these tools can be used to determine individual reproductive success or to measure rates of genetic divergence among populations. Which technique is most appropriate for a par- ticular question depends upon (1) the extent of genetic polymorphism required to best answer the question, (2) the analytical or statistical approaches available for the technique's application, and (3) the pragmatics of time and costs of materials. Here we evaluate the application of several major techniques (protein electrophoresis, nuclear and mitochondrial RFLPs (restriction fragment length polymorphisms), minisatellite and microsatellite VNTRs (variable number tandem repeats), RAPDs (random amplified polymorphic DNA), and DNA sequencing) to an array of questions regarding individual identification, exclusion and assignment of parentage, and various levels of population structure. In our evaluation, we briefly explain the technical components of each molecular approach and assess whether the typical outcomes expected from each approach will provide useful information as applied to each level of inquiry. For studies of population genetic structure, protein electrophoresis remains a powerful tool for most taxa, although techniques based on nucleic acids (par- ticularly DNA sequencing and mitochondrial DNA RFLPs) are useful here as well. Recently developed nucleic acid techniques (e.g., VNTRs) can often identify enough genetic vari- ability to address questions of self-identification or parentage. Some of the newest tech- niques (RAPDs and microsatellites) are potentially useful across a number of levels of inquiry, although procedures for adopting them are still developing.
We applied random amplification of polymorphic DNA (RAPD) and amplified fragment length polymorphism of hazy associations (ALPHA) to the identification of hop cultivars. The polymerase chain reaction (PCR) using random primer or sequence-tagged-sites (STS) was found to give a variety of specific fingerprints from hop DNA, requiring no hop DNA sequence information. Varietal identification of hops was performed using the fingerprints that included DNA fragment polymorphisms. Subsequently, these RAPD (or ALPHA) fragments were sequenced, and specific primers for the individual RAPD (or ALPHA) fragments were synthesized. The fragments amplified by the specific primers allow for a much clearer identification of hop cultivars. Eleven typical hop cultivars were successfully distinguished from one another using these specific primers. This method was also useful for the detection of mixed samples of hop cultivars.
Random amplified polymorphic DNA (RAPD) was used to evaluate the genetic variability and relationship of 65 hop cultivars from all the major hop-growing regions in the world. Twenty-eight selected random primers used in the RAPD reaction generated an average of 38.6%) polymorphic fragments, which was sufficient to produce 47 different RAPD profiles among the cultivars examined. The level of genetic variability was much higher than previously reported. Genetic similarity was estimated and UPGMA cluster analysis was performed using the RAPD data. Cluster analysis separated the cultivars into genetically related RAPD groups which were compared with pedigree data and grouping of the hop cultivars by essential oil type. The RAPD groups, strongly supported by pedigree data, gave more precise information on the level and distribution of genetic variability within hop cultivars than characterization by essential oils. Cultivars were divided into American and European groups, supporting the distinction between two geo-graphically distinct hop germplasms. Five genetically distinct groups revealed differences within the European germplasm, reflecting past hop breeding practices which have been adopted in different regions. The use of RAPD markers for hop germplasm characterization and genetic diversity study is discussed.
Both random amplified polymorphic DNA and microsatellite repeat sequences were investigated as DNA markers for distinguishing hop cultivars. Microsatellite sequences converted to STS markers proved to be most successful. The relative abundance of microsatellite repeat sequences in the hop genome varied depending on the sequence class. Of the repeat types investigated the dinucleotide repeats (GA)n and (GT)n are the most highly represented in the hop genome. Microsatellite repeat sequences in hops have been shown to be highly polymorphic and are very informatives as STS molecular markers. A DNA typing system using sequence-tagged microsatellite site markers has been developed which will not only be useful for hop cultivar identification but also marker assisted breeding and quality control purposes.
In order to evaluate and preserve the endangered wild species of rice, Oryza granulata, we investigated the existing population distribution in Yunnan Province of Southwestern China. The genetic diversity among 14 populations (bulk samples) and within two populations (individual samples) was studied using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) amplification markers. The field survey showed that 44% natural populations of O. granulata in Yunnan have become extinct during the last 30 years. Of the 37 remaining wild populations, 28 (76%) are on the verge of extinction and nine (24%) were unaffected. For the study among the 14 populations, the percentage of polymorphic bands (PPB) was 59% for RAPDs and 64% for ISSRs. However, within populations, the PPB generated by RAPDs and ISSRs was 26 and 26% in the first population (S1) and similarly within the second population (S2) (21 and 22%, respectively). The results showed that genetic variation is much higher among populations of O. granulata than within populations. Analyses of Nei’s gene diversity, unbiased genetic distance and Shannon’s index also agreed with these results. Therefore, we proposed an appropriate strategy for conserving the genetic resources of O. granulata in Yunnan; namely, rescuing and conserving the core populations for in situ conservation, and sampling and preserving more populations with fewer individuals from each population for ex situ conservation.
A mathematical model for the evolutionary change of restriction sites in mitochondrial DNA is developed. Formulas based on this model are presented for estimating the number of nucleotide substitutions between two populations or species. To express the degree of polymorphism in a population at the nucleotide level, a measure called "nucleotide diversity" is proposed.
Molecular genetic maps are commonly constructed by analyzing the segregation of restriction fragment length polymorphisms
(RFLPs) among the progeny of a sexual cross. Here we describe a new DNA polymorphism assay based on the amplification of random
DNA segments with single primers of arbitrary nucleotide sequence. These polymorphisms, simply detected as DNA segments which
amplify from one parent but not the other, are inherited in a Mendellan fashion and can be used to construct genetic maps
in a variety of species. We suggest that these polymorphisms be called RAPD markers, after Random Amplified Polymorphic DNA.
DNA-fingerprint similarity is being used increasingly to make inferences about levels of genetic variation within and between natural populations. It is shown that the similarity index--the average fraction of shared restriction fragments--provides upwardly biased estimates of population homozygosity but nearly unbiased estimates of the average identity-in-state for random pairs of individuals. A method is suggested for partitioning the DNA-fingerprint dissimilarity into within- and between-population components. Some simple expressions are given for the sampling variances of these estimators.
In order to isolate high-quality genomic DNA from medicinal plant tissues enriching polyphenols and polysaccharides, a simple and rapid method based on CTAB extraction for isolating high-quality intact DNA was established by modifying several existing methods. With this technique, the absorbance ratio (A260/A280) of DNAs obtained from fresh and/or dried roots of Panax ginseng, P. Quinquefolius and P. notoginseng was 1.8 approximately. The restriction fragments of DNAs were directly digested with restriction enzyme (EcoR I/Mse I), linked up by T4 DNA ligase and amplified by nested PCR. Reproducible amplified fragment length polymorphism (AFLP) genomic DNA fingerprinting profiles were established with the isolated DNAs. The results demonstrate that the modified technique may be efficient and reliable in isolating high-quality and high-molecular-weight DNAs from fresh and/or dried medicinal plants containing a high content of polyphenols and polysaccharides. We expect that this method can also be applied to other plants.
Hop varieties In: The Brewers' Handbook – The Complete Book to Brewing Beer
- T Goldammer
Goldammer, T., Hop varieties. In: The Brewers' Handbook – The Complete Book to Brewing Beer. T. Goldammer, Ed., Apex Publishers: USA, 2000, pp. 52–53.
The Brewers' Handbook ? The Complete Book to Brewing Beer
- T. Goldammer
Isolation of high quality genomic DNA from plants
- Z Y Lou
- G Zhou
- X H Chen
- Q H Lu
- W X Hu
Lou, Z.Y., Zhou, G., Chen, X.H., Lu, Q.H. and Hu, W.X., Isolation of high quality genomic DNA from plants. Bull. Hunan
Med. Univ., 2001, 26, 178-180.
Isolation of high quality genomic DNA from plants
- Lou