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

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 Jaccard’s similarity coefficients. The genetic similarity among the tobacco genotypes calculated by using Jaccard’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 ‘Glustinusa Rasht’, 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.

scholarly journals Characterization of quince (Cydonia oblonga Mill.) cultivars using SSR markers developed for apple

2009 ◽  
Vol 15 (4) ◽  
Author(s):  
J. Halász ◽  
V. Hoffman ◽  
Z. Szabó ◽  
J. Nyéki ◽  
T. Szabó ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Bottleneck ◽  
The Self ◽  
Cydonia Oblonga ◽  
Allele Number ◽  
The World ◽  
Ssr Loci ◽  
A Minor

Quince (Cydonia oblongaMill.) is a minor fruit crop, which is primarily used for marmalade, jam and sauce.Very few quince cultivars are known all over the world and in many cases similar names are used for presumably different cultivars. The aim of the present study was to evaluate and characterize the genetic diversity of 36 quince cultivars and selections with SSR markers. Seven out of 8 SSR markers designed from apple sequences could successfully yield amplification also in quince cultivars. Number of alleles per locus ranged from 2 to 3 alleles. These allele numbers are quite low when compared to apple. It is supposed to be the consequence of a genetic bottleneck. In spite of the low allele number per locus, the 36 quince cultivars formed 30 different genotypes. The ratio of homozygosity was low, which might be coupled with the self-(in)compatibility phenotype of quinces. SSR markers proved unable to differentiate putatively closely related cultivars (e.g. ‘Bereczki’ and ‘Bereczki bôtermő’). In general, the level of polymorphism among the tested quince genotypes was much restricted due to the low allele number detected. However, it must be considered that the number of analysed SSR loci is not enough high to estimate the overall heterozygosity of the quince genome. Further experiments are needed and the SSR markers proved to be a reliable and useful tool for such analyses.

Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

2015 ◽  
Vol 3 (1) ◽  
pp. 1-11
Author(s):  
Rezq Basheer-Salimia
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Vitis Vinifera L ◽  
Similarity Matrix ◽  
Breeding Programs ◽  
Local Varieties ◽  
Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

scholarly journals Divergência genética entre acessos de mentrasto do Estado do Tocantins através de marcadores RAPD

2013 ◽  
Vol 4 (4) ◽  
pp. 290-298
Author(s):  
Elainy Martins Oliveira ◽  
Waldesse Oliveira Junior ◽  
Jaqueline Oliveira ◽  
Henrique Guilhon De Castro
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Geographic Location ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Ageratum Conyzoides ◽  
Genetic Studies ◽  
Low Degree ◽  
Medicinal Properties ◽  
Degree Of Association

Ageratum conyzoides (Asteraceae) is known in Brazil for its medicinal properties being mainly used as painkiller and anti-inflammatory. Due to the existence of few genetic studies for this species, this work aimed to characterize the genetic diversity among nine accessions from different sites at Tocantins state, to provide information about its genetic resources. Similarity coefficients obtained varied from 48% to 80%, result of amplification of 102 fragments, of which 72 (70.5%) were polymorphic. Groupment analysis allowed the differentiation in three groups. One of them was distinguished because it presented the highest similarity among all, being composed by ANA and NAT (80% similarity). In general, these data showed there is low degree of association between the geographic location of the accessions and the genetic distances. So, the collected accession ns in Tocantins state presented considerable genetic variability and the efficiency of RAPD markers for such characterization was here proven.

scholarly journals Genetic Divergence of Flax Genotypes (Linum Usitatissimum L.) Utilizing Microsatellite Markers

2017 ◽  
Vol 5 (1) ◽  
pp. 123-129 ◽  
Author(s):  
Sumita Nag ◽  
Jiban Mitra
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Linum Usitatissimum ◽  
Rank Correlation ◽  
Natural Fibre ◽  
Similarity Coefficients ◽  
Oilseed Crops ◽  
Linum Usitatissimum L ◽  
Ssr Primers ◽  
Ssr Loci

Flax (Linum usitatissimum L.), stoods in position third, being the largest natural fibre crop and simultaneously one of the five preeminent oilseed crops in the world. SSR/microsatellite markers are extensively utilized for genetic diversity analysis and cultivar identification considering their myriad abundance, co-dominant inheritance, steep polymorphism, reproducibility, and comfort of assay by PCR. Ten microsatellites were amplified in 27 genotypes of Flax. The study was undertaken to assess the genetic diversity in flax and to select most diverse genotypes for future breeding program. Primer efficiency parameters were studied. The 10 SSR loci amplified a total of 41 alleles that were used for genetic analysis. Most primers have PIC value greater than 0.5 and the LU6 marker was highly polymorphic PIC = 0.95. Estimates of RP̅ were highest for the primer LU1 (0.68). The maximum MI was observed for the primer LU10 (3.56). The H and D ranged from 0.26 to 1.78 and 0.36 to 5.40, respectively. According to Spearman rank correlation, PIC and MI were most important parameters in assessing the efficiency of whole set of 10 SSR primers. Dendrogram was constructed using the genetic similarity coefficients using UPGMA. PCo-A was also performed in support. Genetic diversity in Flax was revealed at molecular level.

scholarly journals Development and characterization of microsatellite loci for Cedrela fissilis Vell (Meliaceae), an endangered tropical tree species

2014 ◽  
Vol 63 (1-6) ◽  
pp. 240-243 ◽  
Author(s):  
F. B. Gandara ◽  
E. V. Tambarussi ◽  
Alexandre Magno Sebbenn ◽  
E. M. Ferraz ◽  
M. A. Moreno ◽  
...  
Keyword(s):  
Genomic Library ◽  
Population Level ◽  
Fixation Index ◽  
Allele Number ◽  
Neotropical Tree ◽  
Expected Heterozygosity ◽  
Adult Trees ◽  
Ssr Loci ◽  
Polymorphic Microsatellite

Abstract The timber of the Neotropical tree Cedrela fissilis is used in construction, shipbuilding, carpentry and for medical purposes. In this study, polymorphic microsatellite (SSR) markers derived from an enriched genomic library were characterized using 120 adult trees from four different C. fissilis populations. No substantial genotypic linkage disequilibrium was detected among all possible pairs of SSR loci. The number of alleles per locus ranged from 2 to 20, the average allele number ranged from 8 to 9.7, depending on the population. The observed heterozygosity among the different SSR loci varied from 0.0 to 1.00 , the expected heterozygosity varied from 0.07 to 0.95 On the population level, the average observed and expected heterozygosities ranged from 0.50 to 0.63 and from 0.64 to 0.70, respectively. The average fixation index among populations ranged from 0.09 to 0.24. Thus, the SSR loci revealed high poly - morphism rates and can be used to study the genetic diversity,structure, mating system, and gene flow in C. fissilis.

scholarly journals Analysis of Genetic Diversity and Population Structure of Some Bangladeshi Rice Landraces and HYV

2012 ◽  
Vol 4 (3) ◽  
pp. 757-767 ◽  
Author(s):  
M. M. Hassan ◽  
A. K. M. Shamsuddin ◽  
M. M. Islam ◽  
K. Khatun ◽  
J. Halder
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Allele Number ◽  
Rice Landraces ◽  
Efficient Management ◽  
Ssr Loci ◽  
Pattern Of Variation ◽  
Rice Improvement

Information on the patterns of genetic variation and population structure is essential for rational use and efficient management of germplasms. It helps in monitoring germplasm and can also be used to predict potential genetic gains. Therefore, in the present study genetic diversity of 59 rice genotypes were assessed using 8 simple sequence repeat (SSR) primers. By the DNA profiling, a total of 114 alleles were detected. Allele number per/locus ranged from 9 to 27, with an average of 14.25. Average polymorphism information content (PIC) value was 0.857 with lowest 0.767 to highest 0.857. Mean gene diversity over all SSR loci was 0.870 with a range from 0.792 to 0.948. Fst values for each locus varied from 0.071 to 0.262. Genetic distance between the variety pair ranged from 0.33 to 1.0. The lowest genetic distance was found between Rajashili and Kumragori (2). Cluster and principal coordinate analysis (PCoA) analysis revealed similar pattern of variation. Marker RM11300 was found most polymorphic and robust among the accessions and can be widely used for rice germplasm characterization. The exclusive variability and unique feature of germplasm found in this study can be a gateway for both domestic and global rice improvement.© 2012 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved.doi: http://dx.doi.org/10.3329/jsr.v4i3.10416 J. Sci. Res. 4 (3), 757-767 (2012)

scholarly journals Genetic variation of Indian potato (Solanum tuberosum L.) genotypes using chromosomal and RAPD markers

2010 ◽  
Vol 10 (3) ◽  
pp. 238-246 ◽  
Author(s):  
Anath Bandhu Das ◽  
Iswar Chandra Mohanty ◽  
Dawanidhi Mahapatra ◽  
Suprava Mohanty ◽  
Ashutosh Ray
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Solanum Tuberosum L ◽  
Chromosome Analysis ◽  
Genetic Distances ◽  
Chromosome Length ◽  
Similarity Coefficients ◽  
Varietal Improvement ◽  
And Cluster Analysis ◽  
4C Dna Content

Genetic diversity in thirty Indian potatoes were analyzed employing karyotype, genome size and RAPD markers. Chromosome analysis revealed 2n = 4x = 48 except cv. K. Chandramukhi (2n = 4x + 2 = 50). Total genomic chromosome length and chromosome volume varied from 21.14µm in cv. K. Pukhraj to 31.91µm in cv. MS/89-60 and 14.31µm³ in cv. MS/92-1090 to 33.16µm³ in cv. JW-160 respectively. 4C DNA content was significantly varied from 3.640 pg (~891 Mbp) in cv. MS/92-1090 to 11.12 pg (~2747 Mbp) in cv. K. Chandramukhi. RAPD revealed 131 amplified DNA fragments (300 to 2200 bp) with 79 unique bands (7 to 71% polymorphism) among the genotypes. Similarity coefficients (ranged from 0.29 to 0.93) and cluster analysis reflected the expected trends in relationships of the full and half-sib potato genotypes. Genetic distances obtained from a dendrogram could help breeders to choose the diverse parents for a breeding program aimed at varietal improvement.

scholarly journals Assessment of Genetic Diversity and Population Structure of Tunisian Barley Accessions (Hordeum vulgare L.) Using SSR Markers

2020 ◽  
Vol 73 (4) ◽  
Author(s):  
Salem Marzougui ◽  
Mohamed Kharrat ◽  
Mongi Ben Younes
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Polymorphic Information Content ◽  
Hordeum Vulgare L ◽  
Software Analysis ◽  
Average Value ◽  
Allele Number ◽  
Cultivar Development ◽  
Principal Coordinates ◽  
Ssr Loci

In barley breeding programs, information about genetic dissimilarity and population structure is very important for genetic diversity conservation and new cultivar development. This study aimed to evaluate the genetic variation in Tunisian barley accessions (<em>Hordeum</em><em> </em><em>vulgare </em>L.) based on simple sequence repeat (SSR). A total of 89 alleles were detected at 26 SSR loci. The allele number per locus ranged from two to five, with an average of 3.4 alleles per locus detected from 32 barley accessions, and the average value of polymorphic information content was 0.45. A cluster analysis based on genetic similarity was performed, and the 32 barley resources were classified into five groups. Principal coordinates (PCoA) explained 12.5% and 9.3% of the total variation, and the PCoA was largely consistent with the results of cluster separation of STRUCTURE software analysis. The analysis of genetic diversity in barley collection will facilitate cultivar development and effective use of genetic resources.

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

Genetika ◽  
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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