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 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 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.

scholarly journals Genetic Diversity in Peach (Prunus persica L. Batch) Revealed by Randomly Amplified Polymorphic DNA (RAPD) Markers and Compared to Inbreeding Coefficients

1996 ◽  
Vol 121 (6) ◽  
pp. 1012-1019 ◽  
Author(s):  
Marilyn L. Warburton ◽  
Fredrick A. Bliss
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Prunus Persica ◽  
The United States ◽  
Genetic Distances ◽  
Pedigree Information ◽  
Sources Of Information ◽  
Similarity Coefficients ◽  
Breeding Lines ◽  
Inbreeding Coefficients

Previous studies of peach germplasm using pedigree information and isozyme polymorphism data have shown limited diversity in the U.S. gene pool. To further investigate the genetic diversity among peach cultivars grown in different regions of the United States, 94 RAPD markers were used to estimate the genetic distances among 136 cultivars. Of the 12 clusters formed in a dendrogram, the 90 U.S. cultivars and breeding lines and most of those from Europe and Latin America grouped to only three clusters, while the 23 peach entries from India, Pakistan, Russia, Okinawa, and China, as well as the almond cultivar used as an outgroup, were distributed among the other nine clusters. Therefore, the genetic diversity within temperate U.S. peach germplasm is quite limited, and to expand the variability, additional germplasm should be obtained, especially from Asia. Comparison of genetic similarity based on inbreeding coefficients with similarity coefficients based on the RAPD data produced a correlation of 0.395, which is comparable to values in similar investigations in other crops. Thus, similar conclusions can be drawn from these two sources of information. RAPD data are useful particularly when pedigree information is incomplete, there has been substantial selection within breeding populations, and a high proportion of alleles are identical in state but not by descent.

scholarly journals Genetic Diversity of Salvia Species Assessed by ISSR and RAPD Markers

2016 ◽  
Vol 44 (2) ◽  
pp. 431-436 ◽  
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. Nei’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.

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 Assessment of genetic diversity among surian Toona sinensis Roem in progenies test using random amplified polymorphic DNA markers

2018 ◽  
Vol 22 (1) ◽  
pp. 22
Author(s):  
Jayusman Jayusman ◽  
Muhammad Na’iem ◽  
Sapto Indrioko ◽  
Eko Bhakti Hardiyanto ◽  
ILG Nurcahyaningsih
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Management Strategies ◽  
Genetic Distances ◽  
Sampled Data ◽  
Toona Sinensis ◽  
The Mean ◽  
Individual Trees

Surian Toona sinensis Roem is one of the most widely planted species in Indonesia. This study aimed to estimate the genetic diversity between a number of surian populations in a progeny test using RAPD markers, with the goal of proposing management strategies for a surian breeding program. Ninety-six individual trees from 8 populations of surian were chosen as samples for analysis. Eleven polymorphic primers (OP-B3, OP-B4, OP-B10, OP-H3, OP-Y6, OP-Y7, OP-Y8, OP-Y10, OP-Y11, OP-Y14, and OP-06) producing reproducible bands were analyzed for the 96 trees, with six trees per family sampled. Data were analyzed using GenAlEx 6.3, NTSYS 2.02. The observed percentage of polymorphic loci ranged from 18.2% to 50%. The mean level of genetic diversity among the surian populations was considered to be moderate (He 0.304). Cluster analysis grouped the genotypes into two main clusters, at similarity levels of 0.68 and 0.46. The first two axes of the PCoA explained 46.16% and 25.54% of the total variation, respectively. The grouping of samples into clusters and subclusters did not correspond with family and their distances, but the grouping was in line with the genetic distances of the samples.

scholarly journals Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers

2021 ◽  
Vol 22 (6) ◽  
Author(s):  
Sri Ramadiana ◽  
Dwi Hapsoro ◽  
Rusdi Evizal ◽  
Kukuh Setiawan ◽  
Agus Karyanto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Breeding Program ◽  
Similarity Coefficients ◽  
Robusta Coffee ◽  
Genomic Dnas ◽  
Polymerase Chain ◽  
Group Ii ◽  
Group 1

Abstract. Ramadiana S, Hapsoro D, Evizal R, Setiawan K, Karyanto A, Yusnita. 2021. Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers. Biodiversitas 22: 3122-3129. This study aimed to estimate the genetic diversity among 24 clones of Robusta coffee from Lampung, Indonesia, by use of RAPD markers. The clones consisted of 18 local and 6 BP clones. These BP clones were developed from a breeding program of The Indonesian Coffee and Cocoa Research Institute. Genomic DNAs extracted from these clones were subjected to polymerase chain reaction and the amplified products were run using gel electrophoresis. Eleven random primers produced clear, reproducible, scorable bands. Fifty-four of 86 bands showed polymorphism and were used to construct a dendrogram based on UPGMA Jaccard's Similarity Coefficients. The genetic base of the population was narrow (average genetic similarity 68.4%), ranging from 26-93%. The genetic similarity of the local clones was higher than that of BP clones. The clones were clustered into five groups. Group 1 contained one clone (BP 534), while each of Group II-V contained more than one clone. The average genetic similarity of BP 534 to each clone of Group II-V was 41%. The genetic similarity of clones in Group II, III, IV, and V were 55.5%, 43.0%, 81.1%, and 80.1%, respectively. This research should be very useful for selecting parents in a breeding program to produce better clones of Robusta coffee.

scholarly journals Genetic Diversity in Muscadine and American Bunch Grapes Based on Randomly Amplified Polymorphic DNA (RAPD) Analysis

1996 ◽  
Vol 121 (6) ◽  
pp. 1020-1023 ◽  
Author(s):  
Xianping Qu ◽  
Jiang Lu ◽  
Olusola Lamikanra
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
The United States ◽  
Average Genetic Distance ◽  
Separate Study ◽  
Randomly Amplified Polymorphic Dna ◽  
And Cluster Analysis ◽  
Grape Cultivars

Two morphologically distinct types of grapes belonging to the subgenera Euvitis and Muscadinia in the genus Vitis are cultivated in the United States. The former is commonly called bunch grapes while the latter is usually called muscadine. Genetic diversity among these grapes was investigated using RAPD markers. Sixteen grape cultivars, with parentage including V. rotundifolia Michx., V. vinifera L., and several American Vitis species, were used for the RAPD analysis. A total of 156 RAPD markers was produced from 19 random primers, over 90% of which was polymorphic among the muscadine and the bunch grapes. Polymorphisms were lower within each subgenus. Relationships between these two subgenera were estimated based on band-sharing and cluster analysis. The average genetic distance between the bunch and the muscadine grape cultivars was 0.45. The results based on DNA analysis agree with isozyme data obtained from a separate study, which demonstrated that muscadine grapes share very few common alleles with American bunch grapes and European grapes.

scholarly journals Genetic Variability of 21 Tea Genotypes [Camellia sinensis (L.) O. Kuntze] Based on RAPD Markers

2018 ◽  
Vol 5 (2) ◽  
pp. 77
Author(s):  
Budi Martono ◽  
Syafaruddin Syafaruddin
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Similarity ◽  
Binary Data ◽  
Rapd Markers ◽  
Group Method ◽  
Breeding Programs ◽  
Pair Group ◽  
Monomorphic Band ◽  
And Cluster Analysis

<em>Knowing the genetic diversity in the tea germplasms collection is one of important conditions for assembling new superior varieties. Information of genetic diversity can be obtained through analysis using RAPD molecular markers. The study aimed to determine the genetic diversity of 21 tea genotypes based on RAPD markers. The research was conducted in Integrated Laboratory, Seameo Biotrop, Bogor, from July to September 2013. Genomic DNA was isolated from 21 tea genotypes leaf samples, then amplified with primer OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, and OPD 08. Electrophoresis result was converted into binary data. The genetic similarity and cluster analysis calculation was done using NTSYS-pc version 2.10. In this research, 50 polymorphic bands (94,34%) and 3 monomorphic band (5,66%) were obtained. Cluster analysis based on Nei's genetic distance using the unweighted pair-group method with arithmatic (UPGMA) divided 21 tea genotypes into two groups at a genetic similarity value of 0,48. Group 1 consisted of 20 tea genotypes, while the second group comprised only a one genotype (Sin 27). The range of genetic similarity matrix was between 28%–92%, the lowest genetic similarity (28%) was found between GMB 4 and Sin 27 genotypes, while the highest (92%) was found between AS 2 and AS 1 genotypes. The information obtained can be utilized in breeding programs with the support of agronomic characters as well as in the conservation of tea germplasm.</em>

Study on genetic diversity of Castanopsis phuthoensis Luong in Phu Tho province, Vietnam by RAPD markers

2016 ◽  
Vol 14 (2) ◽  
pp. 237-243
Author(s):  
Nguyễn Văn Thọ ◽  
Lê Thị Mai Linh ◽  
Nguyễn Viễn ◽  
Phạm Quang Tiến
Keyword(s):  
Genetic Diversity ◽  
Tree Species ◽  
Dna Polymorphism ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Analysis ◽  
Dna Fragments ◽  
Similarity Coefficients ◽  
Rapd Pcr ◽  
Rapd Primer

Castanopsis phuthoensis Luong is an endemic tree species of Phu Tho province, only distributed narrowly in forest rehabilitation in two communes belonging to Doan Hung district with density of this species is very low, only from 3.1 to 11.1 trees per hectare. Diameter distributions of the species of number of trees is characterized by curve style with a peak in 20cm or 24cm diameter classes. As it is difficult to find the seedling in the nature, research on forest structure, relations between tree species and genetic diversity is very necessary to define method of conservation for this species. In this study, we used RAPD markers to study on genetic diversity of Castanopsis phuthoensis Luong. The random amplified polymorphic DNA (RAPD) based on the polymeraze chain reaction (PCR) detects nucleotide sequence polymorphism using a single 10mer of arbitrary nucleotided sequence. The RAPD technology has quickly gained widespread acceptance and application because it providesa tool for genetic analysis that have not previously benefited the use of molecular markers. In this study, ten random primers to analyse the genetic diversity of 15 Castanopsis phuthoensis Luong samples that were collected from Phu Tho province, Vietnam. 9 RAPD primers gave DNA polymorphism and 01 RAPD primer OPA20 gave not DNA polymorphism. In the analysis region 0.25-2 kb, there were 56 DNA fragments amplified and 34 DNA fragments were polymorphic. Genetic similarity coefficients of 15 Castanopsis phuthoensis Luong samples ranged from 0.55- 0.95. The phylogenetic tree of 15 samples are divided into two main groups. As results of RAPD-PCR analysis, these samples were collected from the homologous geographical locations and the genetic diversity of 15 samples is not high. Therefore, it is necessary to conserve the "Castanopsis phuthoensis Luong".

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