scholarly journals Morphometric and Genetic Variation in Three Populations of Indian Salmon (Polydactylus plebeius)

2013 ◽  
Vol 5 (3) ◽  
pp. 275-281
Author(s):  
Ramakrishnan THIRUMARAISELVI ◽  
Muthusamy THANGARAJ ◽  
Vellaichamy RAMANADEVI
Keyword(s):  
Univariate Analysis ◽  
Arithmetic Mean ◽  
Group Method ◽  
Morphometric Character ◽  
Clear Pattern ◽  
Arbitrary Primers ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Morphometric Analyses ◽  
The Status

Morphometric character analyses and RAPD was used to discriminate and ratify the status of three populations of Indian salmon, Polydactylus plebeius along the coromandel coast of India. Morphometric analyses showed a clear pattern of differentiation between the stocks and revealed the discreteness of two groups, southern stock (Pazhayar) and northern stock (Cuddalore). The univariate analysis of variance showed significant differences between means of the samples for most morphometric descriptors. A total of 1077 scorable bands were produced using all ten arbitrary primers in three populations. An un-weighted pair-group method with arithmetic mean (UPGMA) dendrogram was constructed based on genetic values to show the genetic relationship among the three populations. The genetic diversity (H) of P. plebeius in Cuddalore was more (0.0733 ± 0.0648) than Pazhayar (0.0609 ± 0.0416) and Vellar (0.0613 ± 0.0344) populations. All the three populations had significantly (p

scholarly journals GENETIC DIVERSITY OF Brassica rapa GERMPLASM OF KHYBER PAKHTUNKHWA PAKISTAN REVEALED BY MOLECULAR MARKERS

2019 ◽  
Vol 18 (6) ◽  
pp. 57-65
Author(s):  
Naushad Ali ◽  
Sardar Ali ◽  
Naqib Ullah Khan ◽  
Sohail Ahmad Jan ◽  
Malik Ashiq Rabbani ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Ssr Markers ◽  
Brassica Rapa ◽  
Arithmetic Mean ◽  
Group Method ◽  
Khyber Pakhtunkhwa ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Ssr Primers ◽  
Simple Sequence

A total of 96 indigenous Brassica rapa accessions were collected from different locations of Khyber Pakhtunkhwa, Pakistan. Simple Sequence Repeats (SSR) markers were used to identify the most diverse genotypes among the collected lots. Twenty six (26) different SSR primers were used for (genetic) variability among collected genotypes. These primers were selected from literature based on their previous results. These primers produced 135 scorable bands of which 75 were polymorphic, with an average of 55.5% polymorphic loci, and reflected the broader genetic background of the collected genotypes. An average 2.88 polymorphic bands with an average PIC value of 0.49 was recorded. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) divided all genotypes into three main groups. Group one contained three clusters, while group two and three had four and two clusters each. Based on the UPGMA dendrogram, genotypes collected from Kohat, Bannu, Swat and Haripur showed considerable amount of variation. From the present study, it is concluded that SSR markers can be proved as the best tool for the genetic variability of other local and exotic B. rapa genotypes.

Characterization of genotypes and genetic relationships of cili (Rosa roxburghii) and its relatives using RAPD markers

2004 ◽  
Vol 1 (2) ◽  
pp. 79-84
Author(s):  
Wen Xiao-Peng ◽  
Deng Xiu-Xin
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Arithmetic Mean ◽  
Group Method ◽  
Arbitrary Primers ◽  
Pair Group ◽  
Rosa Roxburghii ◽  
Widespread Interest ◽  
Unweighted Pair Group Method

AbstractCili (Rosa roxburghii Tratt), characterized by containing the highest vitamin C content among fruits and showing attractive senescence-retarding and cancer-preventing effects, has gained widespread interest. RAPD markers were applied to identify the seven genotypes of cili and to evaluate the genetic relationships within cili, as well as among its relatives. Sixteen arbitrary primers screened from 154 were adopted to analyse polymorphism in RAPD profiles for the 15 samples. A total of 137 RAPD bands ranging in size from 480 bp to 3.3 kb were obtained, among which 95 were polymorphic, covering 69.3% of the total bands obtained; and an average of 8.6 bands/primer was scored. The genotypes of cili and seedless cili could be identified efficiently by 14 genotype-specific bands, which were obtained from the polymorphic primers OPB-11, OPAF-16 and OPW-02. Additionally, using the unweighted pair group method with arithmetic mean, a dendrogram showing genetic relationships among the 15 samples was constructed based on cluster analysis of genetic distance. The possible origin of seedless cili and multiple-corolla cili is also discussed.

scholarly journals Molecular Characterization of Mulberry Accessions in Turkey by AFLP Markers

2008 ◽  
Vol 133 (4) ◽  
pp. 593-597 ◽  
Author(s):  
Salih Kafkas ◽  
Mustafa Özgen ◽  
Yıldız Doğan ◽  
Burcu Özcan ◽  
Sezai Ercişli ◽  
...  
Keyword(s):  
Fragment Length Polymorphism ◽  
Polymorphic Information Content ◽  
Arithmetic Mean ◽  
Fruit Color ◽  
Aflp Markers ◽  
Group Method ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Principle Coordinate Analysis

Mulberries (Morus L.) show a great deal of genetic variability and adaptability to various environments. There are more than 24 species of mulberries in cultivated and wild forms. In Turkey, three Morus species, M. alba L., M. nigra L., and M. rubra L., are grown. In this study, we attempted to characterize 43 Morus accessions originating from distinct regions of Turkey using fluorescent dye amplified fragment length polymorphism (AFLP) markers and capillary electrophoresis. The accessions belonged to M. alba, M. nigra, and M. rubra; M. alba consisted of white- and purple-fruited samples. Eight primer combinations generated a total of 416 bands, 337 of which were polymorphic (80.5%). Resolving powers of the AFLP primers ranged from 0.410 to 0.942 making a total of 5.015, whereas the polymorphic information content ranged from 0.662 to 0.898 with an average of 0.812. Unweighted pair-group method of arithmetic mean (UPGMA) clustering of the accessions showed three major groups representing M. nigra, M. rubra, and M. alba accessions. The M. alba group had two subgroups that were not correlated with fruit color. The UPGMA dendrogram of average taxonomic differences confirmed these results. The principle coordinate analysis demonstrated that M. nigra accessions had limited genetic variation. In conclusion, our study indicated that M. nigra and M. rubra are molecularly distinct from M. alba. Our results also suggest that M. nigra accessions having a low level of morphological variation are molecularly similar.

scholarly journals Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 890
Author(s):  
Zifeng Ouyang ◽  
Yimeng Wang ◽  
Tiantian Ma ◽  
Gisele Kanzana ◽  
Fan Wu ◽  
...  
Keyword(s):  
Group Method ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Important Data ◽  
Breeding Programs ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Medicinal Value ◽  
Genome Wide ◽  
Melilotus Albus

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

scholarly journals Caracterização Biométrica dos Caprinos da República de Cabo Verde

2019 ◽  
Vol 68 (263) ◽  
pp. 384-394
Author(s):  
L.C. Pires ◽  
T.M. Machado ◽  
J. de D. Fonseca ◽  
J.F. Fonseca ◽  
E. Pile ◽  
...  
Keyword(s):  
Arithmetic Mean ◽  
Group Method ◽  
Cabo Verde ◽  
Pair Group ◽  
Unweighted Pair Group Method

Objetivou-se discernir populações caprinas de cinco ilhas da República de Cabo Verde (n=533) por meio de dados biométricos e análises estatísticas. Foram avaliadas 16 características de fêmeas adultas, através da estatística descritiva simples, análise de variância, teste de multicolinearidade, distância generalizada de Mahalanobis (D²) e algoritmo UPGMA (Unweighted Pair Group Method Arithmetic Mean). Após o teste de multicolinearidade foi identificada e descartada a variável profundidade torácica. As D² foram calculadas com base nas 15 medidas biométricas. O maior valor da D² foi entre as populações das ilhas do Fogo e São Nicolau (22,73), e a menor D² foi entre Santo Antão e São Vicente (3,71). O dendrograma a partir de 15 variáveis em cinco populações colocou as cabras da ilha de Fogo em ramo a parte das demais. Agruparam-se num ramo as cabras das ilhas de Santo Antão e São Vicente. Este resultado está de acordo com a distância geográfica entre as ilhas de Cabo Verde e o histórico recente de intercâmbio de animais entre elas.

scholarly journals Song Structure and Microgeographic Song Variation in Wedge-Tailed Sabrewings (Campylopterus Curvipennis) in Veracruz, Mexico

The Auk ◽  
2005 ◽  
Vol 122 (2) ◽  
pp. 593-607 ◽  
Author(s):  
Clementina González ◽  
Juan Francisco Ornelas
Keyword(s):  
Geographic Region ◽  
Arithmetic Mean ◽  
Floral Resources ◽  
Group Method ◽  
Complex Signals ◽  
Document Structure ◽  
Song Variation ◽  
Pair Group ◽  
Well Differentiated ◽  
Acoustic Variation

AbstractWe studied the songs of Wedge-tailed Sabrewings (Campylopterus curvipennis) in six localities from central Veracruz, Mexico, to document structure and variation within and between singing groups in the same geographic region. Wedgetailed Sabrewing songs were acoustically, structurally, and behaviorally complex, rivaling those of other taxa with complex signals. Songs of individual birds were composed of >45 well-differentiated and structurally complex syllables. We found 239 different syllable types across eight recorded singing groups of Wedge-tailed Sabrewings (∼20 syllable types per singing group), with the greatest versatility recorded in hummingbirds to date. The acoustic variation (15 variables) was summarized in three principal components (58% of acoustic variation), in which intragroup variability accounted for most of the observed variation. We found significant differences between and within groups in terms of syllable sharing (Jaccard’s similarity coefficient). Individuals generally shared >50% of syllable types within groups, whereas syllable sharing was <10% between individuals from different groups. The same microgeographic pattern was supported in a UPGMA (unweighted pair-group method with arithmetic mean) analysis where individual songs from each singing group clustered separately. However, songs recorded at the same location differed between seasons, which suggests that this species does not exhibit geographically distinct dialects that are consistent across time. The interplay among this species’ social system, distribution of its floral resources, and microgeographic and temporal variation of its song requires further research.

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 Filogenetik Human papillomavirus (HPV) tipe 6 dan tipe 11 pada penderita recurrent respiratory papillomatosis

2014 ◽  
Vol 44 (1) ◽  
pp. 52
Author(s):  
Lenny Buana Wuriningtyas ◽  
Dwi Reno Pawarti ◽  
Achmad Chusnu Romdhoni
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Arithmetic Mean ◽  
Recurrent Respiratory Papillomatosis ◽  
Open Reading Frame ◽  
Group Method ◽  
Cross Sectional ◽  
Reading Frame ◽  
Pair Group ◽  
Unweighted Pair Group Method

Latar belakang: Papiloma saluran pernapasan berulang (recurrent respiratory papillomatosis/RRP) merupakan neoplasma jinak laring terbanyak akibat infeksi HPV tipe 6 dan tipe 11. RRP merupakan masalah terkait agresivitas dan terapi. Analisis genetik digunakan untuk membedakan varian HPV tipe 6 dan tipe 11. Filogenetik mengevaluasi evolusi sequen DNA virus. Tujuan: Penelitian bertujuan mengidentifikasi sequen DNA dan menganalisis pohon filogenetik HPV tipe 6 dan tipe 11 pada papiloma saluran pernapasan berulang. Metode: Penelitian merupakan observasional deskriptif cross sectional. Analisis menggunakan data pembanding dari GenBank. Filogenetik disusun menggunakan metodeUPGMA (Unweighted Pair Group Method with Arithmetic Mean). Didapatkan 15 sampel jaringan papiloma. Dilakukan pemeriksaan PCR dan analisis sequen DNA. Hasil: Dari 15 sampel penelitian (12 laki-laki, 3 perempuan) didapatkan 9 isolat HPV tipe 6 (8 varian dan 1 subtipe) dan 4 isolat HPV tipe 11 (3 varian dan 1 subtipe). Terdapat mutasi titik yang mengakibatkan munculnya varian dan subtipe HPV tipe 6 maupun tipe 11. Kesimpulan: sequen DNA sampel berasal dari L1 ORF (Late 1 Open Reading Frame) yang merupakan kapsid mayor virus. Proses mutasi level gen berupa substitusi, insersi, dan delesi.Subtipe HPV tipe 6 dan tipe 11 yang ditemukan diperkirakan sebagai subtipe baru dan belum pernah dilaporkan sebelumnya. Lima varian HPV tipe 6 membentuk satu cabang tersendiri pada nomenklatur filogenetik yang sudah ada sehingga diajukan sebagai sublineage baru (sublineage C). Seluruh isolat HPV tipe 11 membentuk cabang pohon tersendiri dan diajukan sebagai sublineage baru (sublineage B).Kata kunci: HPV tipe 6 dan 11, variasi sequen DNA, pohon filogenetik HPV tipe 6 and 11. ABSTRACTBackground: Recurrent respiratory papillomatosis (RRP) is the most common laryngeal benign neoplasm caused by infection of HPV type 6 and 11. RRP is still a serious problem related to agresivity and therapy. Genetic analysis used to determine the variant of HPV type 6 or 11. Phylogenetic tree used to evaluate the evolution of viral DNA squence. Purpose: This study aimed to identify DNA squences and analyse the phylogenetic tree of HPV type 6 and 11 in RRP. Methods: this was a descriptive observational cross sectional study. Data analysis used GenBank database and phylogenetic tree was constructed usedUPGMA (Unweighted Pair Group Method with Arithmetic Mean). 15 papillomas biopsies from RRP patients subjected HPV typing using PCR dan DNA sequensing analysis. Result: From 15 patients with RRP (12 male, 3 female), there were 9 isolates HPV type 6 (8 variants, 1 subtype) and 4 isolates HPV type 11 (3 variants, 1 subtype). There was a point mutation in HPV type 6 and 11. Conclusion: L1 ORF (Late 1 Open Reading Frame) sequensials DNA samples was virus major capsid. There were mutational process at gene level (substitution, insertion, deletion). Subtype of HPV-6 and 11, might be new ones, and had not been reported yet. Five variants of HPV type 6 constructed a different lineage in phylogenetic and it is proposed to be C sublineage. All samples HPV type 11 proposed as B sublineage. Keywords: HPV type 6 and 11, DNA sequences variations, phylogenetic trees HPV type 6 and 11.

scholarly journals Genetic divergence among white-type acai palm accessions based on morpho-agronomic characters

2017 ◽  
Vol 52 (9) ◽  
pp. 751-760 ◽  
Author(s):  
Angela Maria de Sousa ◽  
Maria do Socorro Padilha de Oliveira ◽  
João Tomé de Farias Neto
Keyword(s):  
Genetic Divergence ◽  
Euclidean Distance ◽  
Multivariate Analyses ◽  
Arithmetic Mean ◽  
Group Method ◽  
Agronomic Characters ◽  
Germplasm Bank ◽  
Pair Group ◽  
White Type ◽  
Selection Of

Abstract: The objective of this work was to quantify the genetic divergence among accessions of white-type acai palm, through morpho-agronomic characters. The accessions belong to the active acai palm germplasm bank of Embrapa Amazônia Oriental. Thirteen characters were evaluated in 26 accessions, originated from six municipalities in the state of Pará, Brazil. The data were subjected to deviance and multivariate analyses, based on the average Euclidean distance, and were grouped by Tocher’s method and the unweighted pair group method with arithmetic mean (UPGMA). The accessions differed for eight characters. The distances among accessions ranged from 0.64 to 2.62, with an average of 1.36, and four groups were formed by Tocher’s method and two by the UPGMA. Seven major components explained 88.03% of the variation, whose graphic dispersion showed the tendency of forming four groups. The characters weight of 100 fruits, number of rachillae per bunch, and fruit yield per bunch contributed the most to the divergence, and the accessions from the municipalities of Breves, Curralinho, and Limoeiro do Ajuru were the most divergent. Therefore, the accessions of white acai palm show strong divergence and variability, which favor the selection of desirable individuals.

Genetic diversity among INERA-Mulungu (DR Congo) Musa spp. germplasm and their relatedness to those in Tanzania using numerical taxonomy

2012 ◽  
Vol 11 (1) ◽  
pp. 50-61 ◽  
Author(s):  
D. B. Nzawele ◽  
C. L. Rweyemamu ◽  
A. P. Maerere
Keyword(s):  
Democratic Republic ◽  
Multivariate Analyses ◽  
Democratic Republic Of Congo ◽  
Arithmetic Mean ◽  
Group Method ◽  
Similarity Coefficients ◽  
Dr Congo ◽  
Pair Group ◽  
Data Points ◽  
Southern Highland

Bananas and plantains (Musa spp.) constitute staple food for over 20 million people in Democratic Republic of Congo (DRC). Since 1960, DRC is considered as a secondary centre of plantain diversification with few unknown accessions kept in the INERA-Mulungu genebank. Through similarity coefficients, cluster (unweighted pair group method with arithmetic mean, single, complete, sequential, agglomerative, hierarchical and nested design/clustering procedure) and/or multivariate analyses, numerical morpho-taxonomy has established that this diversity is composed of 37 different accessions. Each accession expressed 98 characters among the 401 possible character states, thus providing 39,298 feature patterns (data points). The 98 characters included 32 vegetative and 66 male and female inflorescences. The accessions were clustered into three genomic groups (AAA, AAB and AABB). Subjective classification ascertained nine subgroups: AAB-Silk, AAB-Pome, AAB-Plantain, AABB-Pisang Awak, AAA-Cavendish, AAA-Ibota, AAA-Gros Michel, AAA-Green-Red and AAA-Lujugira-Mutika. Three subgroups were further divided into nine clone sets which consisted of: Dwarf and Giant Cavendish, French and Horn Plantains, and Musakala, Nfuuka, Nakitembe, Nakabululu and Beer/Mbidde within Lujugira-Mutika. Numerical morpho-taxonomy effectively indicated a relationship between the DRC and Tanzania's Musa diversity. For example, the accessions ‘Kamaramasengi’ and ‘Isangi’ were found to be similar to ‘Kisukari’ (AAB-Silk) and ‘Ngego I’ (AAB-French) common in the Tanzanian Southern Highland. Likewise, the accessions Kimalindi-fupi, Kimalindi-ndefu and Jamaica of Tanzania were duplicates of Bakurura (Kigurube), Cavendish of Butuza and Gros Michel in DRC, respectively. Moreover, numerical morpho-taxonomy confirmed the pedigree of AAB-Prata (Cibwalo) in FHIA 17 and FHIA 23 and the closeness of the ancestors of Yangambi Km5 and Gros Michel. Furthermore, numerical morpho-taxonomy established AA-Mshale malembo as one of the AAA-Lujugira-Mutika parents. Molecular investigations are finally required to confirm the genomes.

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