Genetic diversity and phylogeny analysis of Anabaena azollae based on RFLPs detected in Azolla-Anabaena azollae DNA complexes using nif gene probes

1995 ◽  
Vol 91 (4) ◽  
pp. 589-597 ◽  
Author(s):  
B. Van Coppenolle ◽  
S. R. McCouch ◽  
I. Watanabe ◽  
N. Huang ◽  
C. Van Hove
Keyword(s):  
Genetic Diversity ◽  
Dna Complexes ◽  
Anabaena Azollae ◽  
Gene Probes ◽  
Phylogeny Analysis ◽  
Nif Gene

scholarly journals High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis

2020 ◽  
Vol 47 (3) ◽  
pp. 1589-1603 ◽  
Author(s):  
Marwa Ghonaim ◽  
Ruslan Kalendar ◽  
Hoda Barakat ◽  
Nahla Elsherif ◽  
Naglaa Ashry ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Throughput ◽  
Genetic Similarity ◽  
Maize Genome ◽  
Ltr Retrotransposons ◽  
Maize Germplasm ◽  
Phylogeny Analysis ◽  
Generating Method ◽  
Polymerase Chain Reaction Primers ◽  
Hybrid Lines

AbstractMaize is one of the world’s most important crops and a model for grass genome research. Long terminal repeat (LTR) retrotransposons comprise most of the maize genome; their ability to produce new copies makes them efficient high-throughput genetic markers. Inter-retrotransposon-amplified polymorphisms (IRAPs) were used to study the genetic diversity of maize germplasm. Five LTR retrotransposons (Huck, Tekay, Opie, Ji, and Grande) were chosen, based on their large number of copies in the maize genome, whereas polymerase chain reaction primers were designed based on consensus LTR sequences. The LTR primers showed high quality and reproducible DNA fingerprints, with a total of 677 bands including 392 polymorphic bands showing 58% polymorphism between maize hybrid lines. These markers were used to identify genetic similarities among all lines of maize. Analysis of genetic similarity was carried out based on polymorphic amplicon profiles and genetic similarity phylogeny analysis. This diversity was expected to display ecogeographical patterns of variation and local adaptation. The clustering method showed that the varieties were grouped into three clusters differing in ecogeographical origin. Each of these clusters comprised divergent hybrids with convergent characters. The clusters reflected the differences among maize hybrids and were in accordance with their pedigree. The IRAP technique is an efficient high-throughput genetic marker-generating method.

scholarly journals DIVERSITAS GENETIK DAN HAPLOGROUP KAMBING GEMBRONG BERSTATUS KRITIS DI KABUPATEN KARANGASEM, BALI (Genetic Diversity and Haplogroup of Endangered Gembrong Goat In Karangasem, Bali)

2016 ◽  
Vol 10 (2) ◽  
pp. 181-185
Author(s):  
M. Syamsul Arifin Zein ◽  
Sri Sulandari ◽  
Jakaria Jakaria ◽  
I Made Londra ◽  
Suprio Guntoro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Variability ◽  
South Asia ◽  
Maternal Origin ◽  
Mitochondrial Dna Control Region ◽  
Hypervariable Segment ◽  
Phylogeny Analysis ◽  
Western Asia ◽  
Endangered Breed

This study was conducted to evaluate the genetic diversity and phylogeny of Gembrong goat. For this purpose, 21 goats from endangered breed in Karangasem Bali were used. Molecular analysis of genetic diversity and phylogeography used hypervariable segment 1 of mitochondrial DNA control region. The result showed that genetic variability of Gembrong goat was homogeneous with only one different sites, namely the substitution pyrimidines of C ↔ T (transitional). Phylogeny analysis results showed maternal origin of Gembrong goat is lineage (subhaplogroup) B1 with frequency of 100%. Haplogroup B were known has been domesticated from wild goat in western Asia, then headed to south Asia and infiltrated to southeast Asia, including Gembrong goat in Bali, Indonesia. As a conclusion, genetic diversity of Gembrong goat from remaining population in Karangasem very low and originate from lineages/haplogroup B1 with a frequency of 100%.

Discriminatory Power of RAPD,PCR-RFLP and Southern Blot Analyses of ureCD or ureA Gene Probes on Helicobacter pylori Isolates

2002 ◽  
Vol 57 (5-6) ◽  
pp. 516-521 ◽  
Author(s):  
Stella Smith ◽  
Franck Cantet ◽  
Fabrice Angelini ◽  
Armelle Marais ◽  
Francis Mégraud ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Helicobacter Pylori ◽  
Southern Blot ◽  
Blot Analysis ◽  
Southern Blot Analysis ◽  
Discriminatory Power ◽  
Gene Probes ◽  
Rapd Pcr ◽  
Pcr Rflp

The genetic diversity of 33 Nigerian Helicobacter pylori isolates were studied using RAPD, PCR-RFLP and Southern blot analysis of ureA or ureCD gene probes. RAPD was able to distinguish the following number of isolates using the primers 3880 : 5ʹ-AAGAGCCCGT-3ʹ (28), 3881 :5ʹ-AACGCGCAAC-3ʹ (33) and OPH8 :5ʹ-GAAACACCCC-3ʹ (25). Southern blot analysis using the ureCD probe was also able to distinguish the 12 isolates tested into ten different patterns. The PCR-RFLP technique distinguished all 33 isolates into six types. In conclusion, considering typeability, discriminatory power, and convenience, RAPD with the 3881 primer was considered the most useful technique.

Application of SRAP and ISSR Molecular Markers in Genetic Diversity of DaXing’anling Area Wild Auricularia auricula

2011 ◽  
Vol 183-185 ◽  
pp. 1118-1122
Author(s):  
Hua Jing Liu ◽  
Xiu Hong Xu ◽  
Xiao Yu ◽  
Ting Bo Jiang ◽  
Xue Zhong Zou
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Clustering Analysis ◽  
Diversity Analysis ◽  
Genetic Diversity Analysis ◽  
Auricularia Auricula ◽  
Phylogeny Analysis ◽  
Wild Strains ◽  
Polymorphic Bands ◽  
Issr Molecular Markers

A genetic diversity analysis was conducted, of 14 wild Auricularia auricula strains and 6 cultivated strains from DaXing'anling region by SRAP and ITS markers. Using PCR-SRAP system, we selected 9 pairs of primers for the wild and cultivated strains respectively, and analyzed their genetic diversity through clustering analysis. The results were as follows: 88 fragments were amplified, and the polymorphic bands were 76. The PIC (polymorphism information content) value of these markers varied from 0.048 to 0.918, averaging 0.599. Kinship of Auricularia auricula strains was determined by analyzing their ITS sequences. The software ClustalX 1.83 and MEGA 4.1 were used to conduct the phylogeny analysis. The results were as follows: ITS 1, 5.8 S, ITS2 had as many genetic loci as 52.1%. Cluster analysis of the two kinds of markers were congruous and there were more genetic diversities in wild strains than in cultivated strains. SRAP and ITS techniques can be used to analyze the genetic diversity in the future study.

scholarly journals Keragaman Genetik Kelapa Sawit (Elaeis guineensis Jacq.) Asal Angola Menggunakan Marka SSR

2015 ◽  
Vol 43 (2) ◽  
pp. 140
Author(s):  
Urip Sayekti ◽  
Utut Widyastuti ◽  
Nurita Toruan-Mathius
Keyword(s):  
Genetic Diversity ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Polymorphic Information Content ◽  
Central Africa ◽  
Principal Coordinates Analysis ◽  
Plant Materials ◽  
Phylogeny Analysis ◽  
Principal Coordinates ◽  
Materials Used

<p>ABSTRACT</p><p>Effort to increase productivity and other elite characters in Indonesia oil palm breeding program is facing a problem because of the narrow genetic diversity. To broaden the genetic diversity, germplasm exploration has been done in Angola, Central Africa. The objective of this research was to assess the genetic diversity and population structure of Angola originated oil palm germplasm based on 20 SSR markers. The plant materials used were 27 accessions consisted of 136 palms planted in Riau, Sumatera. The DNA was isolated and amplified using PCR. Phylogeny analysis was constructed using Unrooted Neighbor-Joining by DARwin software 6.0.8. The result showed that polymorphic information content (PIC) value is 0.55 (0.17 to 0.75 for each locus) with 102 total number of alleles. Genetic diversity between individuals was higher compared to the genetic diversity within accessions or regions and between accessions or regions. Phylogenetic analysis of 27 accessions showed that accessions were divided into three main groups. Every group containing individuals originated from 5 spatial distribution regions. Principal coordinates analysis (PCoA) showed that accessions were distributed in one structure. Using more primers and samples to get more representative data is recommended for the following research.</p><p>Keywords: allele, locus, germplasm, molecular marker, polymorphic</p>

scholarly journals IDENTIFIKASI MORFOLOGI DAN KEKERABATAN SALAK DI JAWA TIMUR

2020 ◽  
Vol 14 (2) ◽  
pp. 26-33
Author(s):  
Chitra Christie ◽  
Nia Agus Lestari
Keyword(s):  
Genetic Diversity ◽  
Morphological Characters ◽  
Morphological Identification ◽  
Leaf Color ◽  
Kinship Analysis ◽  
Phylogeny Analysis ◽  
The Difference ◽  
Large Groups ◽  
Sunlight Intensity ◽  
Scientific Name

Salak has the scientific name Salacca zalacca including a low-growing family of palms. This seasonal fruit plant is a type of horticulture that has the potentioal to become an axport commodity in Indonesia. In East Java, especially in Lumajang, Madura and Kediri are areas that produce salak commodities. Morphological identification aims to obtain basic traits so that the appearance or phenotype of each accession can be distinguished quickly and easily, by estimating how much genetic diversity it has. This study aims to determine the morphological characters and to determine the salak kinship of Lumajang, Kediri and Madura. The result of phylogeny analysis of the Salacca zalacca kinship in East Java show that the results of the kinship analysis of the salak in the Lumajang, Kediri and Madura areas formed 2 large groups or cluster. So it can be concluded that the Salacca zalacca originating from the Lumajang, Kediri and Madura areas still come from the same ancestor. This can be seen from the value of kinship distance, the morphological identificaion equation. In addition, environmental factors can also affect the morphology of plants. Sunlight intensity, N and P nutrients can also affect the difference in leaf color

Torus Circumference and Thickness Parameters From a Linear DNA Size Series Suggest How Toruses Self-Assemble

1985 ◽  
Vol 43 ◽  
pp. 522-523
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx
Keyword(s):  
Tertiary Structure ◽  
Dna Complexes ◽  
Tertiary Structures ◽  
Self Assembling ◽  
Double Stranded Dna ◽  
Calf Thymus ◽  
Dna Organization ◽  
Condensed Dna ◽  
Dna Size

Certain double stranded DNA bacteriophage and viruses are thought to have their DNA organized into large torus shaped structures. Morphologically, these poorly understood biological DNA tertiary structures resemble spermidine-condensed DNA complexes formed in vitro in the total absence of other macromolecules normally synthesized by the pathogens for the purpose of their own DNA packaging. Therefore, we have studied the tertiary structure of these self-assembling torus shaped spermidine- DNA complexes in a series of reports. Using freeze-etch, low Pt-C metal (10-15Å) replicas, we have visualized the microscopic DNA organization of both calf Thymus( CT) and linear 0X-174 RFII DNA toruses. In these structures DNA is circumferentially wound, continuously, around the torus into a semi-crystalline, hexagonal packed array of parallel DNA helix sections.

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