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 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 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 Characterization Based on Rapd-Pcr in Cultured Strains of Clarias gariepinus (Siluriformes: Clariidae)

2020 ◽  
Vol 4 (2) ◽  
pp. 81-88
Author(s):  
Ola-Oladimeji Folasade Adesola ◽  
Michael Olufemi Awodiran ◽  
Victor Folorunso Olaleye ◽  
Joel Idowu Awopetu
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Polymerase ◽  
Clarias Gariepinus ◽  
Distance Matrix ◽  
Group Method ◽  
Fish Farms ◽  
Chain Reaction ◽  
Pair Group ◽  
Breeding Programmes ◽  
Polymerase Chain

The genetic polymorphisms of catfish populations collected from four fish farms in four Southwestern states of Nigeria were determined by Randomly Amplified Polymorphic DNA Polymerase Chain Reaction technique. This was to characterize the strains genetically and provide information on the studied catfish. Following standard procedures, polymerase chain reaction was performed by mixing 15 μl reaction mixture containing FIREPOL® Taq DNA polymerase, MgCl2, dNTPs, distilled water, dyes and glycerol, with 1.0 μl DNA sample of 16-week old C. gariepinus strains using OPA03, OPA04, OPC02, OPB08, OPC11, OPG16, OPG19 and OPA19 primers. A sum of 1708 loci having 3072 bands was amplified in all the samples. The RAPD analysis revealed significant genetic variability (P<0.05) among the four sampled populations. The unweighted pair group method with average (UPGMA) dendrogram based on Nei’s unbiased genetic distance matrix separated the Clarias gariepinus populations into two clades. The first clade was made up of populations from Ibadan and Abeokuta while the second clade consisted of populations from Ado-Ekiti and Ile-Ife. Thus, it is imperative to determine the genetic variation and population structure of the stocks of C. gariepinus in advance before commencing on breeding programmes.

scholarly journals Genetic Diversity in Aus Rice Genotypes using ILP Markers

2017 ◽  
Vol 20 (2) ◽  
pp. 13-19
Author(s):  
MA Siddique ◽  
M Khalequzzaman ◽  
MZ Islam ◽  
ESMH Rashid ◽  
MHK Baktiar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Distance Matrix ◽  
Group Method ◽  
Intron Length Polymorphism ◽  
Arithmetic Average ◽  
Pair Group ◽  
Conservation Genetic ◽  
Breeding Programmes ◽  
Rice Genotypes ◽  
Selection Of

Assessment of genetic diversity is essential for germplasm characterization, utilization and conservation. Genetic diversity of 31 Aus rice genotypes of Bangladesh was assessed using 11 ILP (intron length polymorphism) markers. A total of 28 alleles were detected and the number of alleles per locus varied from 2 (RI01779, RI05751, RI05304, RI03205, RI00299, RI05407) to 4 (RI05559). The PIC values ranged from 0.06 (RI05407) to 0.57 (RI05559) with an average of 0.33. PIC value revealed that RI05559 was the best ILP markers for the studied 31 Aus rice genotypes. The dendrogram from unweighted pair-group method with arithmetic average clustering classified the genotypes into five groups at a coefficient of 0.57. Two dimensional graphical views of Principal Coordinate Analysis (PCoA) revealed that the genotypes Kuchmuch, Kalo dhan, Aus dhan, Sadey aus, Chaina and Dighi bawalia were found far away from the centroid of the cluster and can be seslected as parents for further breeding programmes. Parangi and V3, Adubali and H1-2, Begunbichi and Hashikalmi had closest distance (0.000) in the distance matrix might have same genetic background. This information will be useful for the selection of genetically diversed parents and assist in trait development using genotypes in rice breeding programmes in future. The results provided some useful implications for establishment of sovereignty of Bangladeshi rice gene pool. It was also suggested that ILP markers could be very useful for the genetic study and breeding in rice.Bangladesh Rice j. 2016, 20(2): 13-19

Phenetic distinction between the dwarf yellow water-lilies: Nuphar microphylla and N. pumila (Nymphaeaceae)

1998 ◽  
Vol 76 (10) ◽  
pp. 1755-1762 ◽  
Author(s):  
Donald J Padgett
Keyword(s):  
Principal Components ◽  
Group Method ◽  
Water Lily ◽  
Closely Related Species ◽  
Operational Taxonomic Units ◽  
Pair Group ◽  
Univariate Statistics ◽  
Upgma Phenogram ◽  
Fruit Characters ◽  
Distinguishing Features

Nuphar pumila (Timm) DC. and Nuphar microphylla (Pers.) Fern. are morphologically similar yellow water-lily species that are often regarded as conspecific or recognized as varieties of Nuphar lutea (L.) Sm. This phenetic study analyzes 18 features of vegetative, floral, and fruit morphology scored from North American populations of N. microphylla and Eurasian populations of N. pumila. Morphological similarities among specimens were assessed by univariate statistics, clustering by the unweighted pair group method using arithmetic averages (UPGMA), and ordination by principal components analyses. Means for 17 of the 18 quantitative variables differed significantly between operational taxonomic units (OTUs) of the two species, and an UPGMA phenogram provided good separation of OTUs. Principal components analysis also provided reasonable separation of OTUs, indicating leaf and fruit characters as strong distinguishing features. Multivariate analyses indicate two similar, yet distinct, morphological entities. When coupled with qualitative features, geographical barriers, and putative physiological barriers, morphometric data support the taxonomic recognition of two closely related species. Both species are most closely related to the Japanese endemic Nuphar japonica DC.Key words: Nuphar, Nymphaeaceae, water-lily, taxonomy, phenetics.

Genomic variation and relationships in aerial yam (Dioscorea bulbifera L.) detected by random amplified polymorphic DNA

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 17-25 ◽  
Author(s):  
Juliane Ramser ◽  
Kurt Weising ◽  
Günter Kahl ◽  
Cristina López-Peralta ◽  
Rainer Wetzel
Keyword(s):  
Genetic Relatedness ◽  
Random Amplified Polymorphic Dna ◽  
Intraspecific Variability ◽  
Cesium Chloride ◽  
Morphological Characters ◽  
Genomic Variation ◽  
Group Method ◽  
Pair Group ◽  
Binary Character ◽  
Dioscorea Bulbifera

Random amplified polymorphic DNA (RAPD) markers were used to assess intraspecific variability and relationships in aerial yam (Dioscorea bulbifera L.). A total of 23 accessions from different geographic locations in Africa, Asia, and Polynesia were analyzed by 10 arbitrarily chosen GC-rich decamer primers. Using cesium chloride purified genomic template DNA, highly reproducible polymorphic fingerprints were generated by all 10 primers, resulting in a total of 375 informative characters. Only eight bands were monomorphic among all investigated accessions. A binary character matrix was generated by scoring for presence/absence of a band at a particular position, transformed into a matrix of pairwise distances using either the Jaccard or a simple matching coefficient, and analyzed by neighbour joining, UPGMA (unweighted pair group method with arithmetic averaging) cluster analysis, or split decomposition. All methods of data evaluation resulted in similar groupings that reflected the geographical origin of the samples. The African accessions formed a distinct isolated group, whereas Asian and Polynesian accessions proved to be more heterogeneous. With two exceptions (var. suavior and var. sativa), the RAPD data supported previous varietal classification based on morphological characters. Stepwise reduction of the number of evaluated characters did not affect branching patterns of the trees above a minimum threshold of 150. Key words : Dioscorea bulbifera, random amplified polymorphic DNA (RAPD), genetic variation, genetic relatedness.

scholarly journals Evaluation of genetic diversity in geranium (Geraniaceae) using RAPD marker

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 363-378
Author(s):  
Juan Yin ◽  
Majid Khayatnezhad ◽  
Abdul Shakoor
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Morphological Characters ◽  
Mantel Test ◽  
Group Method ◽  
Plant Resources ◽  
High Genetic Diversity ◽  
Pair Group ◽  
Genetic Structure Of Populations

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Geranium genetic diversity. Therefore, we collected and analyzed thirteen species from nine provinces. Overall, one hundred and twenty-five plant specimens were collected. Our aims were 1) to assess genetic diversity among Geranium species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and multidimensional scaling divided Geranium species into two groups. G. sylvaticum depicted unbiased expected heterozygosity (UHe) in the range of 0.11. Shannon information was high (0.38) in G. columbinum. G. sylvaticum showed the lowest value, 0.14. The observed number of alleles (Na) ranged from 0.25 to 0.55 in G. persicum and G. tuberosum. The effective number of alleles (Ne) was in the range of 1.020-1.430 for G. tuberosum and G. collinum. Gene flow (Nm) was relatively low (0.33) in Geranium. The Mantel test showed correlation (r = 0.27, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Geranium species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Geranium species.

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 Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes

Genetika ◽  
2019 ◽  
Vol 51 (1) ◽  
pp. 137-146 ◽  
Author(s):  
Martin Vivodík ◽  
Zelmíra Balázová ◽  
Zdenka Gálová ◽  
Lenka Petrovicová
Keyword(s):  
Ricinus Communis ◽  
Polymorphic Information Content ◽  
Distance Matrix ◽  
Start Codon ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Genetic Distance Matrix ◽  
Functional Genetic Variation ◽  
Amplicon Size

In the present study, 111 castor genotypes were differentiated by the DNA fingerprinting patterns using 37 SCoT primers. The selected primers amplified DNA fragments across the 111 genotypes studied with the number of amplified fragments varying from 3 (SCoT 14) to 10 (SCoT 30 and SCoT 44) and the amplicon size varied from 100 to 3000 bp. Of the 246 amplified bands, 186 were polymorphic with an average of 5.03 fragments per primer. The percentage of polymorphic bands ranged from 57.14 % (SCoT 34) to 100.00 % (SCoT 28 and SCoT 33) with an average of 77.50%. The polymorphic information content (PIC) values varied from 0.372 (SCoT 14) to 0.818 (SCoT 30) with an average of 0.677. A dendrogram was constructed from a genetic distance matrix based on profiles of the 37 SCoT primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 111 diverse accessions of castor was clustered into two main clusters (1 and 2). The first cluster were subdivided into two subclusters (1a and 1b). Subclaster 1a contained 11 genotypes of castor and subclaster 1b contained 6 genotypes of castor. Subclaster 2 were subdivided into two subclusters (2a and 2b). Subclaster 2a contained 44 castor genotypes and subclaster 2b contained 50 castor genotypes. Results showed the utility of SCoT markers for estimation of genetic diversity of castor genotypes leading to genotype identification.

Evaluation of variability in five linseed (Linum usitatissimum L.) genotypes using agro‐morphological characters and RAPD analysis

2011 ◽  
Vol 1 (1) ◽  
pp. 43-47
Author(s):  
Towseef Mohsin Bhat ◽  
Rajdeep Kudesia ◽  
Manoj Kumar Srivastava ◽  
Sazada Sidiqqui
Keyword(s):  
Linum Usitatissimum ◽  
Rapd Analysis ◽  
Morphological Characters ◽  
Germination Percentage ◽  
Arithmetic Mean ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Linum Usitatissimum L ◽  
Pair Group ◽  
Number Of Leaves

Analysis of the extent and distribution of genetic diversity in crop plants is essential for optimizing sampling and breeding strategies. Morphological characters and Randomly amplified polymorphic DNA (RAPD) was used to estimate genetic variability among 5 genotypes of linseed (Linum usitatissimum L). Selected four RAPD primers generated 140 bands, 80 of which were found to be polymorphic. All the primers produced polymorphic amplification products, however the extent of polymorphism varied with each primer .The percentage of polymorphism generated by primer was OPG‐03 (85.029%), OPH‐12(45.94%), OPC‐02(45.94%) and OPG‐18(64.28%). Great variation among morphological characters viz., root length, stem diameter, number of leaves, germination percentage and radicle length was observed. UPGMA (Unweighted Pair Group Method with Arithmetic Mean) dendrogram obtained from cluster analysis using Jaccard’s similarity coefficient resulted into three clusters. Cluster1 comprised of two genotypes (Jawhar and saharda), cluster II also comprised of two genotypes (T‐397 and KL‐1) and cluster III consisted of only one genotype Garima, which was interesting to observe that the Garima was distinct from all other four experimental varieties and sole constituent of cluster III. All the genotypes could be discriminated from one another using combined profiles of 4 primers.

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