scholarly journals Morphological and Molecular Characterization of Rhizoctonia solani Isolates from Two Different Rice Varieties

2018 ◽  
Vol 21 (2) ◽  
pp. 72 ◽  
Author(s):  
Aisyah Surya Bintang ◽  
Arif Wibowo ◽  
Achmadi Priyatmojo ◽  
Siti Subandiyah
Keyword(s):  
Maximum Likelihood ◽  
Rhizoctonia Solani ◽  
Molecular Characterization ◽  
Morphological Characters ◽  
Group Method ◽  
Rice Varieties ◽  
Pair Group ◽  
Maximum Likelihood Tree ◽  
Morphological And Molecular Characterization

Six isolates of Rhizoctonia solani, i.e. two isolates collected from infected rice plants and four isolates from laboratory collection were studied by using morphological characters and molecular analysis. Un-weighted pair group method with arithmetic mean dendogram constructed based on cluster analysis showed that these isolates were grouped into three clusters at the 0.77 similarity coefficient. Cluster I consisted of BA, BNJ, and NBR isolates with 100% similarity and indicated that those were from AG 1 IA sub group, cluster II consisted of BND, and cluster III consisted of SL1 and SL2. Mycelium was very light brown or whitish with few and moderate sclerotia except SL1 and SL2. Molecular characterization showed that BA, BNJ, and NBR were amplified at 140 bp using Rs1F/Rs2R specific primer for R. solani AG1 IA. All isolates were amplified between 350−400 bp using Rhsp1 primer, meanwhile SL1 and SL2 were not amplified using AG2sp and AG22sp2 primers. Based on Maximum Likelihood tree analysis showed that SL1 and SL2 had high similarity based on ITS sequence data.IntisariEnam isolat Rhizoctonia solani yang berasal dari tanaman padi bergejala dan koleksi laboratorium diuji secara morfologi dan molekuler. Analisis UPGMA dengan koefisien persamaan 0,77 menunjukkan bahwa enam isolat tersebut terbagi atas tiga klaster. Klaster I terdiri atas isolat BA, BNJ, dan NBR dengan kesamaan 100% dan menunjukkan bahwa isolat tersebut berasal dari subgrup AG 1 IA , klaster II yakni isolat BND, dan klaster III terdiri atas isolat SL1 dan SL2. Miselium berwarna putih hingga cokelat muda dengan jumlah sklerotia sedang, kecuali isolat SL1 dan SL2. Uji keragaman secara molekuler menunjukkan bahwa isolat BA, BNJ, dan NBR teramplifikasi pada kisaran 140 bp dengan menggunakan  primer Rs1F/Rs2R yang merupakan primer spesifik dari R. solani AG1 IA. Seluruh isolat teramplifikasi pada kisaran 350−400 bp dengan menggunakan primer Rhsp1, sedangkan isolat SL1 dan SL2 keduanya tidak teramplifikasi oleh primer AG2sp dan AG22sp2. Analisis Maximum Likelihood tree berdasar data sekuen ITS menunjukkan bahwa isolat SL1 dan SL2 memiliki tingkat kesamaan yang tinggi.

scholarly journals Molecular Characterization of 12 Mango Germplasm Using RAPD markers

2010 ◽  
Vol 20 (1) ◽  
pp. 91-99
Author(s):  
R. C. Jena ◽  
K. C. Samal ◽  
P. K. Chand ◽  
B. K. Das
Keyword(s):  
Molecular Characterization ◽  
Rapd Markers ◽  
Mangifera Indica ◽  
Pcr Amplification ◽  
Similarity Coefficient ◽  
Group Method ◽  
Base Pairs ◽  
Relationship Analysis ◽  
Pair Group

Randomly amplified polymorphic DNA (RAPD) markers were used for the genetic variation and relationship analysis among 12 Mango (Mangifera indica L.) germplasm. Five oligonucleotide primers were employed to amplify DNA from 12 cultivars. PCR amplification with five primers generated 45 reproducible, clear and distinct bands, out of which 41 bands are considered polymorphic and the remaining four fragments (8.88%)  monomorphic. The size of amplified product ranged from 200 (RPI-5) to 3000 base pairs (RPI-1) with an average of nine bands per primer. The average polymorphism in all the 12 cultivars using the five primers was found to be 91.91%. Among all the primers RPI-2 and RPI-4 have shown 100% polymorphism while RPI-5 was found to be least polymorphism (81.81%). One specific band, namely was found with RPI-5, in a particular variety, Chiratpuri. The UPGMA (Unweighted Pair Group Method of Arithmetic Mean) dendrogram based on Jaccard’s similarity coefficient segregated the 12 mango germplasm into two clusters. Langra, Chiratpuri, Pravasankar, Alphanso, Sindhu and Kesar formed one cluster and rest six mango germplasm grouped together into another cluster. Sindhu and Alphanso cultivar pair was very close to each other with highest similarity coefficient (0.78), which was comparatively higher than all other cultivar pairs. On the other hand, Pravasankar and Neelam cultivar pair was more distinct to each other with the lowest intervarietal similarity coefficient 0.38. This study showed clearly that cultivars from Orissa unveiled maximum diversity and indicated the potential of RAPD markers for the identification of management of mango germplasm for breeding purposes.  Key words: Molecular characterization, Mango germplasm, Dversity  D.O.I. 10.3329/ptcb.v20i1.5972 Plant Tissue Cult. & Biotech. 20(1): 91-99, 2010 (June)

scholarly journals MOLECULAR CHARACTERIZATION OF ENDANGERED MEDICINAL PLANT SPECIES HEDYCHIUM CORONARIUM FROM EASTERN INDIA

2016 ◽  
Vol 9 (1) ◽  
pp. 173 ◽  
Author(s):  
Reena Parida ◽  
Sujata Mohanty ◽  
Sanghamitra Nayak
Keyword(s):  
Molecular Characterization ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Pair Group ◽  
Hedychium Coronarium ◽  
Biotechnological Approach ◽  
Endangered Medicinal Plant ◽  
Inter Simple Sequence Repeats ◽  
Clustering Pattern

<p><strong>Objective: </strong>Molecular characterization of <em>Hedychium coronarium </em>from 4 different populations of Odisha using 9 inter simple sequence repeats and 15 random amplified polymorphic DNA markers to indicate the closeness of species and hybrids quickly and efficiently.</p><p><strong>Methods: </strong>A dendrogram was constructed through sequential agglomerative hierarchial and nested (SAHN) clustering and un-weighted pair group method with arithmetic mean (UPGMA) analysis using Jaccard’s similarity coefficient of combined markers using this particular species.<strong></strong></p><p><strong>Results: </strong>Two major clusters were found, i.e., cluster-I (Malkangiri-1, Phulabani-1, Phulabani-3, Malkangiri-2, Khurda-1, Khurda-2, Khurda-3, Angul-3, Angul-1, Angul-2 and Phulabani-2) and cluster-II (Malkangiri-3). The clustering pattern also revealed moreover the extent of genetic similarity between germplasms collected from four different regions population. <strong></strong></p><p><strong>Conclusion: </strong>The potential of this technique would be further realised to the fullest extent for the identification and tagging of the important novel gene in different taxa, unexplored yet, thus facilitating the improvement of desired taxa of Zingiberaceae. The findings would be of immense enough significance for complementing the strategies of conservation and characterization of these important taxa of Zingiberaceae following modern biotechnological approach.</p>

scholarly journals Morphological and Molecular Characterization of Quinoa Genotypes

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 286
Author(s):  
Ehab H. EL-Harty ◽  
Abdelhalim Ghazy ◽  
Talal K. Alateeq ◽  
Sulieman A. Al-Faifi ◽  
Muhammad Altaf. Khan ◽  
...  
Keyword(s):  
South America ◽  
Gene Diversity ◽  
Shannon Index ◽  
Group Method ◽  
Arithmetic Means ◽  
Mean Values ◽  
Pair Group ◽  
Wide Variability ◽  
Morphological And Molecular Characterization

Quinoa cultivation has expanded from South America to many countries because of its wide adaptability and nutritional value. We evaluated 32 introduced quinoa genotypes using 17 qualitative and 11 quantitative traits under Saudi Arabia conditions during the 2018–2019 season. The quinoa genotypes showed considerable variation during the vegetative and maturity stages. Plant height values varied between 60 and 18 cm, and maturity ranged from 98 to 177 days. Leaf shapes were rhomboidal or triangular, with dentate or serrate margins. Green was the standard color for leaves and panicles at the flowering stage. The leaf granule colors were white, purple, and white-red. At 150 units of the Euclidean distance, the genotypes aggregated into four major groups based on their morphological traits. Twenty-one sequence-related amplified polymorphism (SRAP) primer pair combinations generated 75 amplified fragments (alleles), with a mean of 3.57 alleles per primer pair combination. Unweighted Pair-Group Method with Arithmetic means (UPGMA) clustering analysis showed that the quinoa genotypes were grouped based on origin or according to genetic background. Genotypes from South America presented higher mean values for the average number of alleles, Shannon index (0.411), gene diversity (0.271), and polymorphic percentage (83.95). Analysis of molecular variance (AMOVA) showed that most of the genetic variation was because of differences within populations (86%). The wide variability of the genotypes studied herein is of great importance for quinoa breeders.

Morphological and molecular characterization of adult hairworms (Phylum Nematomorpha) from Iceland and the Faroe Islands, and documentation of their non-adult stages and hosts

Zootaxa ◽  
2021 ◽  
Vol 4927 (2) ◽  
pp. 234-256
Author(s):  
CHRISTINA ANAYA ◽  
KURT E. GALBREATH ◽  
MATTHEW G. BOLEK
Keyword(s):  
Molecular Characterization ◽  
Ground Beetle ◽  
Morphological Characters ◽  
Faroe Islands ◽  
Biodiversity Indicators ◽  
Freshwater Gastropods ◽  
Molecular Phylogenetic ◽  
Paratenic Hosts ◽  
Morphological And Molecular Characterization

No species of freshwater Nematomorpha have been described from Iceland, but they have been identified anecdotally. Recent surveys in Iceland using freshwater gastropods as biodiversity indicators resulted in the collection of adult free-living hairworms and their non-adult stages including cysts in snail paratenic hosts and juvenile worms in ground beetle definitive hosts. Additionally, specimens acquired from the Icelandic Institute of Natural History indicate nematomorphs are common in Iceland. A single specimen from the Faroe Islands National Museum represents a new species record. Our morphological and molecular characterization indicated all the samples belong to the species Gordionus wolterstorffii, a common nematomorph found throughout Europe. Also, we provide the first descriptions of the cyst stage for the genus Gordionus. Molecular phylogenetic analysis based on 10 species of Gordionus and one species of the closely related genus Parachordodes indicates that Gordionus is not monophyletic. Combining our morphological and phylogenetic investigations, we discuss the lack of clarity in diagnostic morphological characters and the need for additional global collections to clarify the taxonomy of Gordionus. 

scholarly journals Morphological and Molecular Characterization of Common Bean Landraces Varieties in South of Brazil

2021 ◽  
Author(s):  
Ana Claudia Schllemer dos Santos ◽  
Lucas Vinícius de Sousa Alcântara ◽  
Larissa Yuki Terada ◽  
Isadora Bischoff Nunes ◽  
Lucas da Silva Domingues ◽  
...  
Keyword(s):  
Common Bean ◽  
Molecular Characterization ◽  
Morphological Characters ◽  
Genetic Distances ◽  
Maturation Stage ◽  
Maturation Stages ◽  
And Cluster Analysis ◽  
South Of Brazil ◽  
Morphological And Molecular Characterization

Abstract This work aimed to perform the morphological and molecular characterization of 31 land races varieties and 9 cultivars of common bean (Phaseolus vulgaris L.). Morphological characters were evaluated during seedling, flowering, physiological maturation and post-harvest maturation stages. Ten microsatellite markers were used for molecular screening. The markers were analyzed according to the number of alleles per locus, the allele frequency per locus and the polymorphism in content (PIC). Genetic distances and cluster analysis were performed using the Bayesian inference and the UPGMA method. All black beans evaluated have anthocyanin in the cotyledons, hypocotyls and stem, and their flowers are purple. For the growth habit, 50% of the evaluated genotypes belong to the type III and there is a predominance of yellow color in the pods (85%) at the physiological maturation stage. Through the genetic dissimilarity it was possible to discriminate three groups for the Likelihood reason and six groups through the UPGMA method, these results indicate a wide genetic diversity among the evaluated genotypes.

scholarly journals Morpho-Molecular Characterization and Screening of Rice (Oryza Sativa L.) Genotypes for Salinity Tolerance at Seedling Stage

2021 ◽  
Vol 18 (2) ◽  
pp. 1-15
Author(s):  
SAA Muti ◽  
MI Hoque ◽  
MM Islam ◽  
MA Siddique ◽  
MS Islam
Keyword(s):  
Salt Tolerance ◽  
Molecular Characterization ◽  
Ssr Markers ◽  
Oryza Sativa L ◽  
Seedling Stage ◽  
Group Method ◽  
Rice Varieties ◽  
Pair Group ◽  
Rice Genotypes ◽  
Near Future

Salinity is one of the major abiotic stresses which severely affect the production of crops across the world. Twenty rice genotypes of diverse origins were assessed to examine salt tolerance potentiality at seedling stage as well as to elucidate the genetic variation using SSR markers. Consequently, IRRI standard protocol was applied to screen out those varieties for tolerance at the glasshouse laboratory of Bangladesh Institute of Nuclear Agriculture, maintaining salt stress level at 6dS m-1, 8dS m-1, 10dS m-1 and 12 dS m-1. Data on morphological parameter were recorded as shoot length (cm), root length (cm) and total dry matter (TDM). For molecular characterization thirteen SSR markers were exploited to determine the genetic diversity and in this context, 53alleles were revealed while the mean number of alleles per locus was 4.The Polymorphism Information Content (PIC) value ranged from 0.37- 0.78 having an average of 0.58. The Un-weighted Pair Group Method with Arithmetic Mean (UPGMA) displayed three major clusters including some sub-clusters, where in Cluster 1, Binadhan- 8, Binadhan-10, Pokkali and FL478 were very close in their vicinity. Information obtained from this experiment, thus can be taken into account for stress breeding program and prospective genetic materials could be utilized for exploring the genetic architecture in favor of salt tolerance as well as for developing better salt tolerant rice varieties in near future. SAARC J. Agri., 18(2): 1-15 (2020)

scholarly journals Molecular Characterization of Tropical Strawberry Genotypes

2017 ◽  
Vol 27 (1) ◽  
pp. 33-39
Author(s):  
MA Sweety ◽  
MM Hossain ◽  
MA Hoque ◽  
M Hasan ◽  
NA Ivy ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Molecular Characterization ◽  
Genotypic Variation ◽  
Genetic Component ◽  
Group Method ◽  
Pair Group ◽  
Polymorphic Bands ◽  
Selection Of ◽  
Unweighted Pair Group Method

Genetic variability of tropical strawberry genotypes was determined through Ramdom Amplified Polymorphic DNA (RAPD) primers. Out of 14 RAPD primers six showed reproducible and polymorphic bands. The results revealed that the maximum polymorphic bands were produced by the primer OPB 12. Ten genotypes were differentiated into two clusters on the basis of Unweighted Pair Group Method With Arithmetic Averages (UPGMA). Genotypic variation based on molecular characterization indicated that genotypes belonging to two different clusters depend on their genetic component. So, selection of parents from different clusters will provide the maximum heterosis in yield.Plant Tissue Cult. & Biotech. 27(1): 33-39, 2017 (June)

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