Cluster analysis of karyotype similarity coefficients in Epimedium (Berberidaceae): insights in the systematics and evolution

In order to evaluate the genome evolution and systematics, karyotype analysis of mitotic metaphase chromosomes in 51 taxa of Epimedium and two species of Vancouveria was conducted. The 53 taxa were clustered, based on their karyotype similarity coefficients. Results showed that the 53 taxa studied were all diploid with 12 chromosomes (2n = 2x = 12). Each taxon had one pair of satellites located on pair I of homologous chromosomes. Moreover, the karyotype types of the 53 taxa studied were all type 1A or 2A of Stebbins. It can be concluded that the karyotypes between species are indeed very similar and the genome of Epimedium was conservative in evolution. The cluster analysis of karyotype similarity coefficients could provide valuable clues for the systematics and taxonomy of Epimedium. Results of the cluster analysis strongly supported the previous taxonomic division of E. subg. Rhizophyllum and E. subg. Epimedium. The results also showed that the interspecific relationship was closely correlated with geographical distribution in E. subg. Epimedium and the taxa native to east Asia had the highest genetic diversity in Epimedium. Finally, the origin of the modern geographical distribution of Epimedium was inferred. Results of the present study have significant scientific values in further studies on resource utilisation, taxonomy and phylogeny in Epimedium.

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Analysis of intra-population variability of bald cypress (Taxodium distichum L. Rich.) in seed stand near Backa Palanka using RAPD markers

Genetika ◽

10.2298/gensr1502571p ◽

2015 ◽

Vol 47 (2) ◽

pp. 571-580

Author(s):

Vladan Popovic ◽

Aleksandar Lucic ◽

Danijela Ristic ◽

Ljubinko Rakonjac ◽

Sabahudin Hadrovic ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Dna Markers ◽

Genetic Similarity ◽

Rapd Markers ◽

Rapd Analysis ◽

Genetic Distances ◽

Similarity Coefficients ◽

Bald Cypress ◽

Seed Stand

The analysis of Bald cypress genetic variability at the level of test trees was performed using RAPD (Random Amlified Polymorphic DNA) markers. RAPD analysis was performed on 20 test trees with 13 primers. A total of ten primers gave a clear picture while three primers amplified weakly. 60 is a total number of detected bands obtained by RAPD analysis with 10 selected primers, and the average number of bands is 6. Based on presence/absence of RAPD fragments among all 20 Bald cypress test trees were calculated similarity coefficients by Dice and they range from 0.73 to 1. Based on similarity coefficients was performed the cluster analysis and results were presented as a dendrogram. All 20 test trees were grouped into two sub-clusters. Test trees 1, 4 and 11 were grouped in the first sub-cluster while other test trees were grouped in the second sub-cluster. By analysis of relations within every sub-cluster and sub-sub-cluster the existence of genetic distances between observed test trees can be noticed. The greatest similarity is between test trees 2, 12, 15 and 18. The results of genetic similarity and distance between observed test trees indicate the overwhelming presence of genetic diversity.

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Assessment genetic diversity of einkorn genotypes (Triticum monococcum L.) by gliadin electrophoresis

Acta agriculturae Slovenica ◽

10.14720/aas.2020.116.2.1430 ◽

2020 ◽

Vol 116 (2) ◽

pp. 327

Author(s):

Gergana Nikolova DESHEVA ◽

Bozhidar KYOSEV ◽

Manol DESHEV

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Diversity Index ◽

Polyacrylamide Gel Electrophoresis ◽

Geographic Origin ◽

Seed Storage ◽

Storage Condition ◽

Similarity Coefficients ◽

Gliadin Patterns ◽

High Level

<p>The genetic diversity of gliadins in twenty two einkorn accessions preserved under long-term seed storage condition in the National gene bank of Bulgaria were evaluated, using acid polyacrylamide-gel electrophoresis (Acid-PAGE). In total, 64 polymorphic bands and 22 gliadin patterns were identified. Thirty four different mobility bands and 21 gliadin patterns were identified in the ω-gliadin zone, 12 bands and 16 patterns were noted in the γ-gliadins, 17 patterns and 12 mobility bands were found for β-gliadins and six bands with five different α -gliadin patterns were determined. The genetic diversity index (H) was the highest for ω-gliadins (0.950), followed by β-gliadins (0.924) and γ- (0.914), respectively and the lowest value was detected in α-gliadin patterns (0.120). Cluster analysis based on the UPGMA method and Nei and Li similarity coefficients classified all the genotypes into 3 main groups. No relationships between genetic diversity, geographic origin and the genotypes were observed. The results of cluster analysis justify the high level of genetic variation among investigated einkorn accessions.</p>

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Statistical evaluation of chromosomes of some Lathyrus L. taxa growing in Turkey

Caryologia ◽

10.36253/caryologia-1124 ◽

2021 ◽

Author(s):

Bekir YILDIRIM ◽

Hasan GENÇ ◽

Mikail AÇAR ◽

Tolga ÇETİN

Keyword(s):

Cluster Analysis ◽

Statistical Analysis ◽

Correlation Analysis ◽

Statistical Evaluation ◽

Mitotic Metaphase ◽

Metaphase Chromosomes ◽

And Cluster Analysis

In this study, statistical analysis was performed on mitotic metaphase chromosomes of 26 Lathyrus taxa, four of which are endemic. According to the findings obtained as a result of analysis, taxa close to each other were determined. Chromosome characteristics were revealed based on the arm lengths of taxa. Based on these, ANOVA, correlation analysis, PCA and cluster analysis were performed to determine the chromosomal relationships between taxa. Morphological similarities of plant taxa and chromosomal statistics results may not be always parallel to each other. According to Cluster Analysis, especially L. hirsutus - L. odoratus, L. brachypterus subsp. haussknechtii - L. phaselitanus, L. stenophyllus - L. chloranthus, L. gorgoni var. gorgoni, - L. nissolia - L. pratensis, L. tuberosus - L. annuus taxa are closely related.

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Genetic diversity of Cucurbita moschata inbred lines selected from six different populations using HFO-TAG markers

Plant Omics ◽

10.21475/poj.13.02.20.2520 ◽

2020 ◽

pp. 86-93

Author(s):

Adel Ahmed Elshafei ◽

Abdullah Abdulrahman Alsadon ◽

Abdullah Abdulaziz Aldoss ◽

Talal Khaled Alateeq ◽

Talaat Hassan Solieman ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Saudi Arabia ◽

High Frequency ◽

Inbred Lines ◽

Cucurbita Moschata ◽

Similarity Coefficients ◽

Gene Markers ◽

Population Origin ◽

Different Populations

This study evaluated the genetic diversity among 18 inbred lines of Pumpkin (Cucurbita moschata) using HFO-TAG (high frequency oligonucleotide–targeting active gene) markers. The inbred lines were selected from six different populations in Saudi Arabia and Egypt according to genetic distance and population origin. A total of 132 alleles were detected. Sixteen HFO-TAG markers averaged 8.25 alleles per primer with 125 alleles showing polymorphisms that averaged 7.81 alleles per primer. A cluster analysis of the means of the HFO-TAG data created three groups with similarity coefficients between 0.34 and 0.74. In general, the 18 inbred lines were separated according to pedigree and population origin. Hybrids from the chosen inbred lines, S1 L-1 with E L-2, S1 L-2 with E L-3, and S1 L-3 with E L-1, may be the basis for improved hybridization programs and can be used in future hybridization program

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Genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm revealed by RAPD markers

Genome ◽

10.1139/g01-096 ◽

2001 ◽

Vol 44 (6) ◽

pp. 995-999 ◽

Cited By ~ 25

Author(s):

H I Amadou ◽

P J Bebeli ◽

P J Kaltsikes

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Geographic Origin ◽

Bambara Groundnut ◽

International Institute ◽

Tropical Agriculture ◽

Vigna Subterranea ◽

Ibadan Nigeria

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm using 25 African accessions from the collection in the International Institute for Tropical Agriculture, Ibadan, Nigeria. Fifty random decamer primers were screened to assess their ability to detect polymorphism in bambara; 17 of them were selected for this study. Considerable genetic diversity was found among the V. subterranea accessions studied. The relationships among the 25 accessions were studied by cluster analysis. The dendrograms showed two main groups of accessions mainly along the lines of their geographic origin. It is concluded that RAPD can be used for germplasm classification in bambara groundnut and hence for improving this crop.Key words: germplasm, PCR, RAPD, Vigna subterranea.

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Genetic Diversity of Salvia Species Assessed by ISSR and RAPD Markers

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha44210391 ◽

2016 ◽

Vol 44 (2) ◽

pp. 431-436 ◽

Cited By ~ 6

Author(s):

Masoumeh YOUSEFIAZARKHANIAN ◽

Ali ASGHARI ◽

Jafar AHMADI ◽

Behvar ASGHARI ◽

Ali Ashraf JAFARI

Keyword(s):

Genetic Diversity ◽

Genetic Polymorphisms ◽

Genomic Dna ◽

Rapd Markers ◽

Genetic Relationships ◽

Genetic Variations ◽

Molecular Techniques ◽

Wild Populations ◽

Similarity Coefficients ◽

The World

The genus Salvia includes an enormous assemblage of nearly 1,000 species dispersed around the world. Due to possible threats to this genus, there is an immediate requirement to evaluate the diversity of its wild populations. ISSR and RAPD molecular techniques were used to evaluate the genetic relationships among twenty-one ecotypes of eight Salvia species. Amplification of genomic DNA using 23 primers (15 RAPD and eight ISSR) produced 280 bands, of which 91% were polymorphic. The results of marker parameters showed no clear difference between two marker systems. It was generally observed that both ISSR and RAPD markers had similar efficiency in detecting genetic polymorphisms with remarkable ability to differentiate the closely related ecotypes of Salvia. Neiâ€™s similarity coefficients for these techniques ranged from 0.48 to 0.98. Based on the results of clustering, PCoA and AMOVA, the genetic diversity between and within species was confirmed. So, conservation and domestication of the genus Salvia must be due to levels of genetic variations.

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Statistical analysis in support of maintaining a healthy traditional Siamese cat population

Genetics Selection Evolution ◽

10.1186/s12711-020-00596-w ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Arthur M. A. Pistorius ◽

Ineke Blokker

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Companion Animals ◽

Hereditary Diseases ◽

Small Scale ◽

Genetic Traits ◽

Inbreeding Coefficients ◽

A Value ◽

Siamese Cat ◽

Line Breeding

Abstract Background For many years, breeders of companion animals have applied inbreeding or line breeding to transfer desirable genetic traits from parents to their offspring. Simultaneously, this resulted in a considerable spread of hereditary diseases and phenomena associated with inbreeding depression. Results Our cluster analysis of kinship and inbreeding coefficients suggests that the Thai or traditional Siamese cat could be considered as a subpopulation of the Siamese cat, which shares common ancestors, although they are considered as separate breeds. In addition, model-based cluster analysis could detect regional differences between Thai subpopulations. We show that by applying optimal contribution selection and simultaneously limiting the contributions by other breeds, the genetic diversity within subpopulations can be improved. Conclusion In principle, the European mainland Thai cat population can achieve a genetic diversity of about 26 founder genome equivalents, a value that could potentially sustain a genetically diverse population. However, reaching such a target will be difficult in the absence of a supervised breeding program. Suboptimal solutions can be obtained by minimisation of kinships within regional subpopulations. Exchanging animals between different regions on a small scale might be already quite useful to reduce the kinship, by achieving a potential diversity of 23 founder genome equivalents. However, contributions by other breeds should be minimised to preserve the original Siamese gene pool.

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Genetic Diversity Assessment in Dolichos Bean (Lablab purpureus L.) Based on Principal Component Analysis and Single Linkage Cluster Analysis

Legume Research - An International Journal ◽

10.18805/lr-4561 ◽

2021 ◽

Author(s):

S.R. Singh ◽

S. Rajan ◽

Dinesh Kumar ◽

V.K. Soni

Keyword(s):

Genetic Diversity ◽

Principal Component Analysis ◽

Cluster Analysis ◽

Principal Component ◽

Component Analysis ◽

Single Linkage ◽

Pod Yield ◽

Diversity Assessment ◽

Single Linkage Cluster ◽

Linkage Cluster

Background: Dolichos bean occupies a unique position among the legume vegetables of Indian origin for its high nutritive value and wider climatic adaptability. Despite its wide genetic diversity, no much effort has been undertaken towards genetic improvement of this vegetable crop. Knowledge on genetic variability is an essential pre-requisite as hybrid between two diverse parental lines generates broad spectrum of variability in segregating population. The current study aims to assess the genetic diversity in dolichos genotypes to make an effective selection for yield improvement.Methods: Twenty genotypes collected from different regions were evaluated during year 2016-17 and 2017-18. Data on twelve quantitative traits was analysed using principal component analysis and single linkage cluster analysis for estimation of genetic diversity.Result: Principal component analysis revealed that first five principal components possessed Eigen value greater than 1, cumulatively contributed greater than 82.53% of total variability. The characters positively contributing towards PC-I to PC-V may be considered for dolichos improvement programme as they are major traits involved in genetic variation of pod yield. All genotypes were grouped into three clusters showing non parallelism between geographic and genetic diversity. Cluster-I was best for earliness and number of cluster/plant. Cluster-II for vine length, per cent fruit set, pod length, pod width, pod weight and number of seed /pod, cluster III for number of pods/cluster and pod yield /plant. Selection of parent genotypes from divergent cluster and component having more than one positive trait of interest for hybridization is likely to give better progenies for development of high yielding varieties in Dolichos bean.

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Molecular Characterization and Similarity Relationships among Flue-Cured Tobacco (Nicotiana tabacum L.) Genotypes Using Simple Sequence Repeat Markers

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha4027169 ◽

2012 ◽

Vol 40 (2) ◽

pp. 247

Author(s):

Soheila GHOLIZADEH ◽

Reza DARVISHZADEH ◽

Babak ABDOLLAHI MANDOULAKANI ◽

Iraj BERNOUSI ◽

Seyed Reza ALAVI ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Genetic ◽

Genetic Distances ◽

Similarity Coefficients ◽

Allele Number ◽

Nicotiana Tabacum L ◽

Ssr Loci ◽

Actual Degree ◽

Similarity Relationships

Characterization of genetic diversity has long been a major goal in tobacco breeding programs. Information on genetic diversity is essential for a rational use of genetic resources. In the present study, the genetic variation among 72 flue-cured tobacco genotypes was evaluated using microsatellite markers (SSRs). A set of 104 alleles was generated at 30 SSR loci. The mean number of alleles per locus (na) and the effective allele number (ne) were 3.467 and 2.358, respectively. The expected heterozygosity ranged from 0.29 to 0.75 with average of 0.54. Several methods were used to construct the similarity matrices and dendrograms. The co-phenetic correlation coefficient, which is a measure of the correlation between the similarities represented on the dendrograms and the actual degree of similarity, was calculated for each dendrogram. Among the different methods, the highest value (r=0.76368) was observed for the UPGMA created based on Jaccardâ€™s similarity coefficients. The genetic similarity among the tobacco genotypes calculated by using Jaccardâ€™s similarity coefficient ranged from 0.08 to 0.84, suggesting the presence of high molecular genetic variability among the studied tobacco genotypes. Based on UPGMA clustering method all studied flue-cured tobacco genotypes, except for â€˜Glustinusa Rashtâ€™, were placed in three distinct groups. We observed an obvious heterotic pattern in the studied flue-cured germplasm corresponding to genetic distances and classification dendrogram, which persuades exploitation of heterosis in flue-cured tobaccos.

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Analysis of genetic diversity in Cassia brewsteri with randomly amplified DNA fingerprints (RAFs)

Australian Systematic Botany ◽

10.1071/sb01012 ◽

2002 ◽

Vol 15 (2) ◽

pp. 237 ◽

Cited By ~ 2

Author(s):

David C. Cunningham ◽

Kerry B. Walsh ◽

Eric R. Anderson ◽

Dion K. Harrison ◽

Bernie J. Carroll

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Multidimensional Scaling ◽

Dna Fingerprints ◽

Similarity Coefficients ◽

Natural Distribution ◽

Amplification Profile

Genetic diversity in Cassia brewsteri (F.Muell.) F.Muell. ex Benth. was assessed with Randomly Amplified DNA Fingerprints (RAFs). Thirty accessions of C. brewsteri collected from throughout its natural distribution were analysed with three random decamer primers, along with three accessions of C. tomentella (Benth.) Domin and a single accession of each of C. queenslandica C.T.White and C. marksiana (F.M.Bailey) Domin. The three primers yielded a reproducible amplification profile of 265 scorable polymorphic fragments for the 35 accessions. These molecular markers were used to calculate Nei and Li similarity coefficients between each pair of individuals. A matrix of dissimilarity of each pair of individuals was examined by multidimensional scaling (MDS). The analysis supports the division of C. brewsteri into two subspecies and the suggestion that intergradation ofC. brewsteri and C. tomentella can occur where the distributions of these species meet.

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