scholarly journals SNP and SCAR Markers for Specific Discrimination of Antler-Shaped Ganoderma lucidum

2019 ◽  
Vol 7 (1) ◽  
pp. 12 ◽  
Author(s):  
O-Chul Kwon ◽  
Chang-Soo Lee ◽  
Young-Jin Park
Keyword(s):  
Ganoderma Lucidum ◽  
Gene Sequence ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characteristics ◽  
Pcr Analysis ◽  
Scar Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Specific Fragment

In this study we identified single nucleotide polymorphism (SNP) and sequence characteristic amplification region (SCAR) markers for specific identification of antler-shaped Ganoderma lucidum strains. When the partial mitochondrial SSU rDNA gene sequence of various antler- and kidney-shaped G. lucidum strains were analyzed and aligned, an SNP was found only in the antler-shaped G. lucidum strain at position 456 bp. In addition, this SNP of antler-shaped strains was digested by HinfI restriction enzyme. We further analyzed the polymorphism of various G. lucidum strains by random amplified polymorphic DNA (RAPD) analysis. In RAPD analysis, we isolated and sequenced a fragment, specific for antler-shaped G. lucidum strains. Based on this specific fragment sequence, two sets of specific primer pairs for antler-shaped G. lucidum strains were designed. PCR analysis revealed that two specific bands were observed only from antler-shaped strains. These two molecular markers will be helpful for identification of morphological characteristics of G. lucidum.

scholarly journals A Cotton-Fiber-Associated Cyclin-Dependent Kinase A Gene: Characterization and Chromosomal Location

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Weifan Gao ◽  
Sukumar Saha ◽  
Din-Pow Ma ◽  
Yufang Guo ◽  
Johnie N. Jenkins ◽  
...  
Keyword(s):  
Cotton Fiber ◽  
Sequence Data ◽  
Snp Markers ◽  
Pcr Analysis ◽  
Cyclin Dependent Kinase ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Gene Characterization ◽  
Protein Levels ◽  
Catalytic Domains

A cotton fiber cDNA and its genomic sequences encoding an A-type cyclin-dependent kinase (GhCDKA) were cloned and characterized. The encoded GhCDKA protein contains the conserved cyclin-binding, ATP binding, and catalytic domains. Northern blot and RT-PCR analysis revealed that the GhCDKA transcript was high in 5–10 DPA fibers, moderate in 15 and 20 DPA fibers and roots, and low in flowers and leaves. GhCDKA protein levels in fibers increased from 5–15 DPA, peaked at 15 DPA, and decreased from 15 t0 20 DPA. The differential expression of GhCDKA suggested that the gene might play an important role in fiber development. The GhCDKA sequence data was used to develop single nucleotide polymorphism (SNP) markers specific for the CDKA gene in cotton. A primer specific to one of the SNPs was used to locate the CDKA gene to chromosome 16 by deletion analysis using a series of hypoaneuploid interspecific hybrids.

scholarly journals Genome Relationship among Nine Species of Millettieae (Leguminosae: Papilionoideae) Based on Random Amplified Polymorphic DNA (RAPD)

2004 ◽  
Vol 59 (11-12) ◽  
pp. 868-873 ◽  
Author(s):  
Laxmikanta Acharya ◽  
Arup Kumar Mukherjee ◽  
Pratap Chandra Panda
Keyword(s):  
Molecular Markers ◽  
Genetic Relationship ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Similarity Index ◽  
Morphological Characteristics ◽  
Genome Relationship ◽  
Tephrosia Purpurea ◽  
Constituent Species

Random amplified polymorphic DNA (RAPD) marker was used to establish intergeneric classification and phylogeny of the tribe Millettieae sensu Geesink (1984) (Leguminosae: Papilionoideae) and to assess genetic relationship between 9 constituent species belonging to 5 traditionally recognized genera under the tribe. DNA from pooled leaf samples was isolated and RAPD analysis performed using 25 decamer primers. The genetic similarities were derived from the dendrogram constructed by the pooled RAPD data using a similarity index, which supported clear grouping of species under their respective genera, inter- and intra-generic classification and phylogeny and also merger of Pongamia with Millettia. Elevation of Tephrosia purpurea var. pumila to the rank of a species (T. pumila) based on morphological characteristics is also supported through this study of molecular markers.

Development of an Efficient Fungal DNA Extraction Method To Be Used in Random Amplified Polymorphic DNA–PCR Analysis To Differentiate Cyclopiazonic Acid Mold Producers

2008 ◽  
Vol 71 (12) ◽  
pp. 2497-2503 ◽  
Author(s):  
BEATRIZ SÁNCHEZ ◽  
MAR RODRÍGUEZ ◽  
EVA M. CASADO ◽  
ALBERTO MARTÍN ◽  
JUAN J. CÓRDOBA
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Cyclopiazonic Acid ◽  
Proteinase K ◽  
Vacuum System ◽  
Pcr Analysis ◽  
Dna Extraction Method ◽  
Rapd Pcr

A variety of previously established mechanical and chemical treatments to achieve fungal cell lysis combined with a semiautomatic system operated by a vacuum pump were tested to obtain DNA extract to be directly used in randomly amplified polymorphic DNA (RAPD)–PCR to differentiate cyclopiazonic acid–producing and –nonproducing mold strains. A DNA extraction method that includes digestion with proteinase K and lyticase prior to using a mortar and pestle grinding and a semiautomatic vacuum system yielded DNA of high quality in all the fungal strains and species tested, at concentrations ranging from 17 to 89 ng/μl in 150 μl of the final DNA extract. Two microliters of DNA extracted with this method was directly used for RAPD-PCR using primer (GACA)4. Reproducible RAPD fingerprints showing high differences between producer and nonproducer strains were observed. These differences in the RAPD patterns did not differentiate all the strains tested in clusters by cyclopiazonic acid production but may be very useful to distinguish cyclopiazonic acid producer strains from nonproducer strains by a simple RAPD analysis. Thus, the DNA extracts obtained could be used directly without previous purification and quantification for RAPD analysis to differentiate cyclopiazonic acid producer from nonproducer mold strains. This combined analysis could be adaptable to other toxigenic fungal species to enable differentiation of toxigenic and nontoxigenic molds, a procedure of great interest in food safety.

scholarly journals Characterization of the Hyphal Swelling Group of Pythium: DNA Polymorphisms and Cultural and Morphological Characteristics

Plant Disease ◽  
1998 ◽  
Vol 82 (2) ◽  
pp. 218-222 ◽  
Author(s):  
K. Kageyama ◽  
H. Uchino ◽  
M. Hyakumachi
Keyword(s):  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characteristics ◽  
Its Region ◽  
Restriction Enzymes ◽  
Dna Polymorphisms ◽  
Banding Patterns ◽  
Length Polymorphisms ◽  
Polymerase Chain

The hyphal swelling (HS) group of Pythium species and P. ultimum were studied for cultural and morphological characteristics, restriction fragment length polymorphisms of the amplified internal transcribed spacer (ITS) region in nuclear rDNA, and random amplified polymorphic DNA (RAPD) analysis of genome DNA. The shape of sporangia was spherical to subspherical or lemoniform and averaged 18.1–23.0 μm. All isolates could grow at 5 to 35°C, and the rate at the optimal temperature, 30°C, was 29–34 mm/24 h. The size of the ITS region amplified by polymerase chain reaction and the banding patterns after digestion with the restriction enzymes showed no variation between the HS group and P. ultimum. No difference in banding patterns was shown between the HS group and P. ultimum by RAPD analysis with each of three primers. Isolates examined were from Japan, and results should be confirmed from other regions.

scholarly journals Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0249825
Author(s):  
Qun Ji ◽  
Honglian Zhu ◽  
Xinfang Huang ◽  
Kai Zhou ◽  
Zhengwei Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Phylogenetic Tree ◽  
Phylogenetic Relationships ◽  
Morphological Characteristics ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Linear Leaf ◽  
Water Dropwort

The water dropworts Oenanthe linearis Wall. ex DC. and O. javanica (Blume) DC. are aquatic perennial herbs that have been used in China as vegetables and traditional medicines. However, their phylogenetic relationships and genetic diversity are poorly understood. Here, we presented the phenotypic traits and genome-wide DNA marker-based analysis of 158 water dropwort accessions representing both species. The analysis revealed that Oenanthe linearis was readily segregated into linear-leaf and deep-cleft leaf water dropworts according to their leaf shapes at flowering. Oenanthe javanica was classified by clustering analysis into two clusters based mainly on the morphological characteristics of their ultimate segments (leaflets). A set of 11 493 high-quality single-nucleotide polymorphisms was identified and used to construct a phylogenetic tree. There was strong discrimination between O. linearis and O. javanica, which was consistent with their phenotype diversification. The population structure and phylogenetic tree analyses suggested that the O. linearis accessions formed two major groups, corresponding to the linear-leaf and deep-cleft leaf types. The most obvious phenotypic differences between them were fully expressed at the reproductive growth stage. A single-nucleotide polymorphism-based analysis revealed that the O. javanica accessions could be categorized into groups I andII. However, this finding did not entirely align with the clusters revealed by morphological classification. Landraces were clustered into one group along with the remaining wild accessions. Hence, water dropwort domestication was short in duration. The level of genetic diversity for O. linearis (π = 0.1902) was slightly lower than that which was estimated for O. javanica (π = 0.2174). There was a low level of genetic differentiation between O. linearis and O. javanica (Fst = 0.0471). The mean genetic diversity among accessions ranged from 0.1818 for the linear-leaf types to 0.2318 for the groupII accessions. The phenotypic traits and the single-nucleotide polymorphism markers identified here lay empirical foundation for future genomic studies on water dropwort.

scholarly journals RAPD Analysis of peaches within Czech National collection

2011 ◽  
Vol 39 (No. 4) ◽  
pp. 113-119
Author(s):  
J. Raddová ◽  
M. Beránek ◽  
I. Oukropec ◽  
M. Vachůn
Keyword(s):  
Genetic Similarity ◽  
Prunus Persica ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Plant Genetic Resources ◽  
Morphological Characteristics ◽  
Fruit Shape ◽  
Fruit Colour ◽  
Place Of Origin ◽  
Available Information

The Random Amplified Polymorphic DNA (RAPD) technique was used to study the genetic diversity and relationships within the collection of the Czech National Plant Genetic Resources (PGR) of peaches (Prunus persica L.). The aim of the work was to elaborate a dendrogram of genetic similarity and to divide collection into clusters. 46 primers were applied to 6 cultivars differing in the place of origin, the fruit shape, the fruit colour, and in some other morphological characteristics. 12 primers were chosen which gave polymorphic repeatable strong and middle strong bands. They were subsequently used for the RAPD reactions within the whole collection of peaches. The selected RAPD primers distinguished 28 peach cultivars and RAPD data were used to group the accessions analysed. Almonds and peach × almond hybrids were clearly separated in the frame of the whole collection. The grouping corresponded to the botanical system, to the available information about pedigree, and to the cultivars description.  

Generation of SNP markers for short straw in oat (Avena sativa L.)

Genome ◽  
2006 ◽  
Vol 49 (3) ◽  
pp. 282-287 ◽  
Author(s):  
Pirjo Tanhuanpää ◽  
Ruslan Kalendar ◽  
Jaana Laurila ◽  
Alan H Schulman ◽  
Outi Manninen ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Avena Sativa ◽  
Marker Assisted Selection ◽  
Rapd Markers ◽  
Bulked Segregant Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Dwarfing Gene

Short straw is a desired trait in oat germplasm (Avena sativa L.). Marker-assisted selection, a key tool for achieving this objective, is limited by the presence and number of available markers. Here, we have attempted to develop markers sufficiently linked to a gene specifying short straw so that marker-assisted selection could be applied. Bulked-segregant analysis was used to identify anonymous PCR-based markers associated with the dwarfing gene Dw6 in an F2 population from the cross between A. sativa 'Aslak' and A. sativa 'Kontant'. One random amplified polymorphic DNA (RAPD) and 1 retrotransposon-microsatellite amplified polymorphism (REMAP) marker were found to be associated with height. These were converted into codominant single-nucleotide polymorphism (SNP) markers. The SNP–REMAP and the SNP–RAPD markers were located 5.2 and 12.6 cM from Dw6, respectively. They can be used in future efforts both to enhance oat germplasm by application of molecular markers and to determine the nature of the gene through positional cloning.Key words: Avena sativa, short straw, marker-assisted selection, RAPD, REMAP, SNP.

RAPD isolation of a Y chromosome specific ORF in a dioecious plant, Silene latifolia

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 413-420 ◽  
Author(s):  
Shunsuke Nakao ◽  
Sachihiro Matsunaga ◽  
Atsushi Sakai ◽  
Tsuneyoshi Kuroiwa ◽  
Shigeyuki Kawano
Keyword(s):  
Y Chromosome ◽  
Random Amplified Polymorphic Dna ◽  
Single Copy ◽  
Silene Latifolia ◽  
Inverse Pcr ◽  
Pcr Analysis ◽  
Dioecious Plant ◽  
Reading Frame ◽  
Y Chromosomes ◽  
Specific Fragment

Silene latifolia is a dioecious plant and has heteromorphic sex chromosomes: the X and Y chromosomes. The Y chromosome is the largest, and its genetic control seems to be most strict among dioecious plants. To identify the putative sex-determination elements on the Y chromosome, random amplified polymorphic DNA (RAPD) analysis was used to screen for Y chromosome specific DNA fragments, and 31 clones were successfully produced. Genomic Southern hybridization and FISH (fluorescence in situ hybridization) analyses revealed that one of the clones, #2-2, is a Y chromosome specific fragment that has a single copy on the Y chromosome. Sequence tagged site (STS)-PCR analysis also succeeded in amplifying one fragment in males and no fragments in females. Cloning and sequencing of the #2-2 flanking region using inverse PCR revealed an open reading frame (ORF) corresponding to 285 amino acids in length (ORF285), but no expression of the ORF285 gene was identified. ORF285 may be a clue to the origin of dioecy.Key words: Y chromosome, RAPD, STS, FISH, Melandrium album.

Sign in / Sign up

Export Citation Format

Share Document