scholarly journals Morphological characteristic and Phenetic Relationship of Lysurus periphragmoides Collected from West Java

2021 ◽  
Vol 6 (1) ◽  
pp. 102-110
Author(s):  
Rudy Hermawan ◽  
Laifa Fusvita ◽  
Naufal Hafizh Nugraha ◽  
Mega Putri Amelya
Keyword(s):  
Morphological Characteristics ◽  
Mature Spore ◽  
Numerical Data ◽  
Morphological Characters ◽  
Similarity Coefficient ◽  
Group Method ◽  
West Java ◽  
Pair Group ◽  
Phenetic Relationship ◽  
Two Phases

Lysurus is one of the unique genera in Basidiomycetes. It has a stinky odor and slime on the head. The unusual-shaped makes the species in Lysurus easily to be identified. One of Lysurus had been found in West Java, Indonesia namely L. periphragmoides. The specimen was deposited into Herbarium Bogoriense with code BO 24418. This study aimed to obtain specimens and characterize the Lysurus BO 24418 using morphological characteristics, and analyze the phenetic relationship among Lysurus species. Lysurus BO 24418 has two phases (egg and mushroom). The egg phase is usually hypogeous underground. The mushroom has a head and stem. The head bears the mature spore with slime distribute malodor. The stem has a hollow and spongy texture with a yellowish color. The numerical data of morphological characters of species in Lysurus were analyzed using NTSys ver 2.1 software. Ten characters were used to build a dendrogram using Sequential Agglomerative Hierarchical Nested (SAHN) cluster analysis with Unweighted Pair Group Method with Arithmetic Mean (UPGMA). Phallus indusiatus was selected as an outgroup. The analyses showed the specimen was classified as L. periphragmoides with 100% of similarity coefficient and it was close L. gardneri with 40,4% of similarity coefficient. The characters that cluster among them are stem surface, head type, egg diameter, and spore max length

Development of DNA fingerprinting keys for the identification of radish cultivars

2004 ◽  
Vol 44 (1) ◽  
pp. 95 ◽  
Author(s):  
A. Pradhan ◽  
G. Yan ◽  
J. A. Plummer
Keyword(s):  
Dna Fingerprinting ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Morphological Characteristics ◽  
Group Method ◽  
Base Pairs ◽  
Difference Matrix ◽  
Pair Group ◽  
Young Leaves ◽  
Polymerase Chain

Identification of cultivars is extremely important both for cultivation and breeding of crop plants. Cultivar identification based on morphological characteristics can be difficult and complicated. Polymerase chain reaction technologies, such as random amplified polymorphic DNA (RAPD) analysis, can readily and quickly identify cultivars using seeds and young leaves. Sixty individuals representing 7 radish cultivars were examined for RAPD marker polymorphism. Based on the polymorphism generated, 5 primers were selected, out of the 14��examined, to fingerprint the cultivars. The 5 primers produced a total of 52 fragments, 6 monomorphic and 46�polymorphic fragments, ranging in size from 206 to 2258 base pairs. A total and mean character difference matrix was calculated based on the RAPD data and a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA). Three DNA fingerprinting keys were developed for the 7 cultivars and 5 markers derived from 3 primers was the minimum required to distinguish cultivars. Results demonstrated that RAPD markers could be effectively used for the identification of radish cultivars.

Numerical taxonomy contributes to delimitation of Iranian and Turkish Hesperis L. (Brassicaceae) species

Phytotaxa ◽  
2018 ◽  
Vol 367 (2) ◽  
pp. 101 ◽  
Author(s):  
ATENA ESLAMI FAROUJI ◽  
HAMED KHODAYARI ◽  
MOSTAFA ASSADI ◽  
BARIŞ ÖZÜDOĞRU ◽  
ÖZLEM ÇETIN ◽  
...  
Keyword(s):  
Distance Matrix ◽  
Morphological Characters ◽  
Resolving Power ◽  
Group Method ◽  
Morphological Descriptors ◽  
Operational Taxonomic Units ◽  
Pair Group ◽  
Species Circumscription ◽  
Taxonomic Descriptions ◽  
Brassicaceae Species

Taxonomic descriptions of Iranian and Turkish Hesperis (Brassicaceae) species are generally insufficient and partly incomplete, which makes the species delimitation ambiguous. In order to clarify species circumscription, we scored 57 morphological descriptors (MDs) in 121 operational taxonomic units (OTUs) of Hesperis from Iran and Turkey and performed a multivariate analysis. The dendrogram was created from Gower’s distance matrix using Unweighted Pair Group Method with arithmetic mean (UPGMA) algorithm. The dendrogram clearly separates the 121 OTUs of Hesperis into five main phenons, which significantly deviate from the classical taxonomic treatment (sectional assignments) of the genus. Similar distinct delineation among the five phenons was revealed by a Principal Coordinate Analysis (PCoA), highlighting the resolving power of the multivariate analyses of quantitative and qualitative morphological characters. While there were significant variations among the OTUs for 57 MDs, the most distinctive morphological descriptors delimiting the phenons were estimated to be fruit, petal, stem, and leaf by a de-trended correspondence analysis (DCA). We also present a comparative discussion between the classical taxonomy and the delimitation of taxa revealed in our study.

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 The Diversity And Classification Of Intraspecies Of Gembolo (Dioscorea Bulbifera L.) Based On Morphological Character

2018 ◽  
Vol 73 ◽  
pp. 04022
Author(s):  
Andri Prasetia ◽  
Purnomo ◽  
Budi Setiadi
Keyword(s):  
Morphological Character ◽  
Leaf Shape ◽  
Similarity Index ◽  
Morphological Characters ◽  
Multivariate Statistical ◽  
Pair Group ◽  
Group I ◽  
Dioscorea Bulbifera ◽  
Phenetic Relationship ◽  
Special Region

Gembolo (Dioscorea bulbifera L.) is a dioecious, annual, herbaceous, climbing plants and has heart-shaped leaves. Gembolo has aerial tubers (bulbil) and main tuber that has irregular shapes, as well as many rough roots at the base of the stem. The purpose of this research is to know the phenetic relationship of the germplasm of Gembolo in Special Region of Yogyakarta based on morphological character. The results of this study are expected to provide information on intraspecies diversity, phenetic relationship and Gembolo distribution. Gembolo plant samples were taken from D.I Yogyakarta. The sample was observed based on the difference of morphological character, so the number of accessions obtained from D.I Yogyakarta could be determined. Morphological characters would be described and characterized to determine the Operational Taxonomic Units (OTU’s). Based on morphological character data, then the grouping analysis was done by grouping analysis method and the dendrogram was formed by the method of Unweighted Pair Group Methods using Arithmetic averages (UPGMA) using Multivariate Statistical Program (MVSP) software version 3.1pc. The results showed that gembolo had morphological variation in tuber shape, stem color, leaf shape, leaf base shape and leaf tip shape. Based on the morphological characters, 2 main groups with the value of similarity index of 62,8% was formed. Group I consisted of four accessions with a similarity value of 85%. Group II consisted of eight accessions with a similarity value of 75%. A high similarity based on the morphological character on gembolo accession caused the gembolo plants in Special Region of Yogyakarta did not vary.

scholarly journals Blueberry Cultivar Identification Using Random Amplified Polymorphic DNA and Sequence-characterized Amplified Region Markers

HortScience ◽  
2017 ◽  
Vol 52 (11) ◽  
pp. 1483-1489 ◽  
Author(s):  
Kang Hee Cho ◽  
Seo Jun Park ◽  
Su Jin Kim ◽  
Se Hee Kim ◽  
Han Chan Lee ◽  
...  
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Morphological Characters ◽  
Polymorphic Band ◽  
Group Method ◽  
Highbush Blueberry ◽  
United States Department ◽  
Scar Markers ◽  
Sequence Characterized Amplified Region ◽  
Pair Group

Blueberry cultivars have traditionally been identified based on the evaluation of sets of morphological characters; however, distinguishing closely related cultivars remains difficult. In the present study, we developed DNA markers for the genetic fingerprinting of 45 blueberry cultivars, including 31 cultivars introduced from the United States Department of Agriculture. We obtained 210 random amplified of polymorphic DNA (RAPD) markers using 43 different primers. The number of polymorphic bands ranged from three (OPG-10 and OPQ-04) to eight (OPR-16), with an average of five. A cluster analysis performed with the unweighted pair group method using arithmetic averages produced genetic similarity values among the blueberry cultivars ranging from 0.53 to 0.85, with an average similarity of 0.68. A dendrogram clustered the 45 blueberry cultivars into two main clusters, with a similarity value of 0.65. Cluster I consisted of four rabbiteye cultivars (Pink Lemonade, Alapaha, Titan, and Vernon) and the Ashworth northern highbush cultivar. Cluster II consisted of 31 northern highbush cultivars, eight southern highbush blueberry cultivars, and Northland half-highbush blueberry cultivar. Fifty five RAPD fragments selected were sequenced to develop sequence-characterized amplified region (SCAR) markers, resulting in the successful conversion of 16 of 55 fragments into SCAR markers. An amplified polymorphic band has the same size as the RAPD fragment or smaller according to the primer combinations in the 16 SCAR markers. Among these markers, a combination of 11 SCAR markers provided sufficient polymorphisms to distinguish the blueberry cultivars investigated in this study. These newly developed markers could be a fast and reliable tool to identify blueberry cultivars.

scholarly journals Assessment of Genetic Diversity in Cultivated Tomato (Solanum Lycopersicum L.) Genotypes Using Rapd Primers

2013 ◽  
Vol 21 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Saida Sharifova ◽  
Sabina Mehdiyeva ◽  
Konstantinos Theodorikas ◽  
Konstantinos Roubos
Keyword(s):  
Genetic Diversity ◽  
Rapd Analysis ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Arithmetic Mean ◽  
Similarity Coefficient ◽  
Group Method ◽  
Solanum Lycopersicum L ◽  
Pair Group ◽  
Upgma Cluster Analysis

Abstract Random Amplified Polymorphic DNA (RAPD) analysis was carried out on 19 Azerbaijan tomato genotypes, both cultivars and local populations. A total of 26 amplified products were revealed by 6 primers. The genetic similarity among evaluated genotypes ranged from 0.188 to 1.000. The lowest similarity was observed between cultivars ‘Azerbaijan’ and ‘Shakar’ (0.188), while the highest between ‘Elnur’ and ‘Garatag’ (1.000). The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis based on Jaccard’s similarity coefficient divided genotypes into four main groups. The first group was the largest and consisted of 12 genotypes, while the fourth group was the smallest consisted of 1 genotype only. The most polymorphic primer was OPB-18 that presented a genetic diversity index of 0.823, while the least informative was primer OPG-17 with an index of 0.349. The average genetic diversity calculated from RAPD data was 0.665.

scholarly journals Variation and Phenetic Relationship of Tobacco (Nicotiana tabacum L.) In Central Java and Yogyakarta Based on Morphological Characters

2021 ◽  
Vol 3 (2) ◽  
pp. 73-79
Author(s):  
Agung Dwi Santoso ◽  
Purnomo Purnomo
Keyword(s):  
Nicotiana Tabacum ◽  
Similarity Index ◽  
Morphological Characters ◽  
Group Method ◽  
Similarity Coefficients ◽  
Leaf Venation ◽  
Central Java ◽  
Pair Group ◽  
Nicotiana Tabacum L ◽  
Micromorphological Characters

Tobacco (Nicotiana tabacum L.) is a plant used as a mixture of cigarettes, and recreational media especially for men. This study aimed to identify variations, and determine the relationship between tobacco cultivars in Central Java and Yogyakarta based on macromorphological and micromorphological characters. Sampling locations are determined by surveying locations in both regions. Tobacco samples found include 5 cultivars in Central Java namely 'Mantili', 'Uler Magetan', 'Garut', ‘Gober Boyolali’, 'Manila', and 3 cultivars in Yogyakarta namely 'Siluk', 'Java', and 'Virginia'. Characterization with 23 qualitative macromorphological characters including leaves, and stems, with 9 qualitative and quantitative micromorphological characters including trichome and stomata. Descriptive data analysis is done to obtain the typical character of each cultivar, followed by numerical analysis including scoring characters processed with MVSP (Multi Variate Statistical Package), clustering with UPGMA (Unweighted Pair Group Method with Averages), and calculation of similarity coefficients with Simple matching formula. The results showed variations in the macromorphological characters including the shape of the leaf lamina, the base of the leaf, the absence of leaf stalks, and type of leaf venation. Tobacco has anisositic stomata, and varies in terms of length, width, and density of stomata. Tobacco trichomes are glandular. The result dendrograms form two clusters (A and B) with the similarity index of each cluster above 0.80. Cultivars with close relationships such as 'Siluk'-'Java', and far relationship like 'Java'-'Manila'.

scholarly journals Genetic diversity and population structure of sugarcane (Saccharum spp.) accessions by means of microsatellites markers

2020 ◽  
Vol 42 ◽  
pp. e45088
Author(s):  
Hugo Zeni Neto ◽  
Luiz Gustavo da Mata Borsuk ◽  
Luiz Renato Frederico dos Santos ◽  
Henrique Sanches Angeli ◽  
Guilherme Souza Berton ◽  
...  
Keyword(s):  
Population Structure ◽  
Probabilistic Models ◽  
Similarity Coefficient ◽  
Group Method ◽  
Breeding Programs ◽  
Saccharum Spp ◽  
Pair Group ◽  
Industrial Yield ◽  
Degree Of Similarity ◽  
Simple Sequence

The success of sugarcane (Saccharum spp.) breeding programs depends on the choice of productive parent lines that have a high industrial yield and are genetically divergent. This study assessed the genetic divergence and population structure of sugarcane accessions that are the parents of the RB05 Series of the Sugarcane Breeding Program of Brazil. The DNA of 82 accessions was evaluated using 36 simple sequence repeat markers. The Jaccard similarity coefficient and Unweighted Pair Group Method with Arithmetic Mean clustering method were used to generate a cluster that was divided into 17 distinct groups derived from probabilistic models. The similarity coefficient used in both cases showed that the degree of similarity varied from 0.4716 (RB971551 x RB965586) to 0.9526 (RB936001 x SP89-1115), with a mean of 0.8536. This result demonstrates a high similarity between the 82 accessions and confirms Wright’s F statistic (0.125), which indicates moderate genetic variability. The less-similar crosses suggest that breeders seek a higher number of crosses using cultivar RB965586, highlighting the RB971551 x RB965586 and RB965586 x RB855511 crosses. The results demonstrate that crosses such as RB936001 x SP89-1115 and RB945954 x RB896342 should be avoided because of their high genetic similarity.

scholarly journals Molecular Characterization of Macrophomina phaseolina, the Incitant of Coleus forskohlii Revealed by RAPD Markers

2012 ◽  
Vol 5 (1) ◽  
pp. 44-50 ◽  
Author(s):  
Chathuri Mudalige ◽  
ST Girisha ◽  
VB Raghavendra ◽  
MH Niranjan ◽  
K Ravikumar ◽  
...  
Keyword(s):  
Root Rot ◽  
Rapd Analysis ◽  
Macrophomina Phaseolina ◽  
Climatic Conditions ◽  
Similarity Coefficient ◽  
Group Method ◽  
Coleus Forskohlii ◽  
Severe Problem ◽  
Pair Group ◽  
Pathogenicity Tests

Coleus forskohlii belong to family lamiaceae is one of the commercial plants grown extensively in the country, the chemical found in the Coleus which has both medicinal application and gives great economy to the industrial organizations. Unfortunately, these plants are being highly succumbed to serious diseases like wilt and root rot caused by a fungus, hence the growers and industrialists are facing severe problem in safeguarding this crop in the field irrespective of the agro climatic conditions. Root rot disease, is one of the major diseases of Coleus forskohlii which, is caused by Macrophomina phaseolina, Pathogen variability was studied at both morphological and molecular level using cultural characteristics and Rapid Amplification of Polymorphic DNA (RAPD) analysis respectively. Totally thirty two isolates were isolated from roots of Coleus forskohlii. In RAPD 165 bands were obtained out of them 121 bands (73.3%) were polymorphic with a similarity coefficient of 0.48-0.66. Clusters analysis of RAPD data when Unweighted Pair Group Method with Arithmetic Mean (UPGMA) Tree constructed using NTSYS, it showed 6 groups. Among them two were major clusters and 4 were minor clusters with similarity coefficient 0.48-0.66. The pathogenicity of the isolates was tested on Coleus forskohlii plants. Analysis of the pathogenicity tests results revealed that the isolates grouped under two major clusters which were different from the one obtained using RAPD data. The results indicate that the data from RAPD analysis and Pathogenicity tests do not correlate with each other.DOI: http://dx.doi.org/10.3126/ijls.v5i1.5598 International Journal of Life Sciences Vol.5(1) 2011 44-50

Application of RAPD and ISSR markers to analyse molecular relationships in Grevillea (Proteaceae)

2004 ◽  
Vol 17 (1) ◽  
pp. 49 ◽  
Author(s):  
M. Pharmawati ◽  
G. Yan ◽  
I. J. McFarlane
Keyword(s):  
Phylogenetic Trees ◽  
Genetic Relationships ◽  
Initial Point ◽  
Morphological Characteristics ◽  
Issr Markers ◽  
Group Method ◽  
Pair Group ◽  
Molecular Relationships ◽  
Group B ◽  
Rapd And Issr

The potential of RAPD and ISSR markers to construct molecular relationships of Grevillea was evaluated with 23 RAPD and 12 ISSR primers. The 16 genotypes representing 12 species and 3 subspecies of Grevillea were sampled from the collection of the Mt Anann Botanic Garden, NSW. RAPD and ISSR assays generated a total of 401 RAPD and 280 ISSR fragments. High frequencies of polymorphisms, 99.39% for RAPD and 99.51% for ISSR, were detected by both markers. Three statistical approaches were employed to construct phylogenetic relationships from combined RAPD and ISSR data. Cluster analysis by the unweighted pair group method (UPGMA) of Jaccard's similarity and Neighbour-Joining analysis of total character difference generated dendograms with similar topology. Parsimony analysis also generated a tree that was in broad agreement with the two dendograms. The phylogenetic trees divided the Grevillea species studied into three groups. Group A consisted of G. buxifolia subsp. buxifolia, G. phylicoides and G. sphacelata. In group B, G. mucronulata was grouped together with G. montana, while G. diffusa, G. humilis, G. linearifolia, G. molyneuxii, G. oldei, G. sericea and G. speciosa formed group C. This molecular result was comparable to groupings suggested by a previous author (Makinson 2000) based on morphological characteristics. However, in contrast to the morphological taxonomy, molecular phylogeny suggests that G. oldei and G. speciosa belong to the same subgroup sensu Makinson (2000), whereas G. linearifolia and G. molyneuxii should not be placed in their originally suggested subgroups sensu Makinson (2000). The present study is the first published report on molecular relationships of Grevillea and can be considered as an initial point for further research on the genetic relationships and evolution of Grevillea.

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