scholarly journals Genetic diversity of Sterculia quadrifida in Kupang, Indonesia based on RAPD (Random Amplified Polymorphic DNA) markers

2020 ◽  
Vol 21 (7) ◽  
Author(s):  
Uslan Uslan ◽  
MADE PHARMAWATI
Keyword(s):  
Genetic Diversity ◽  
Geographical Distribution ◽  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Mixed Forest ◽  
Similarity Coefficient ◽  
Community Forest ◽  
High Genetic Diversity ◽  
Ctab Method

Abstract. Uslan, Pharmawat M. 2020. Genetic diversity of Sterculia quadrifida in Kupang, Indonesia based on RAPD (Random Amplified Polymorphic DNA) markers. Biodiversitas 21: 3407-3414. This study aims to determine the genetic diversity of Sterculia quadrifida R.Br. in Kupang based on RAPD markers. Samples of S. quadrifida were collected from the yard and community forest in Kupang City (Sub-districts of Oebobo, Kelapa Lima, Maulafa, and Alak) and mixed forest in the Kupang District (Sub-districts of Kupang Barat, Nekamese, Taebenu, and Fatuleu). DNA was isolated by the CTAB method and amplified by six RAPD primers (OPD-11, OPF-11, UBC-106, UBC-127, UBC-250, and OPB-04). The data were analyzed in the MVSP software using UPGMA method and Nei & Li similarity coefficient. Total of 131 DNA bands ranging from 250-1400 bp was obtained. Populations of S. quadrifida in Kupang were divided into two main clusters and 12 sub-clusters with. The highest genetic diversity was found in Kelapa Lima of 0.1050, while the lowest genetic diversity was found in S. quadrifida population in Fatuleu of 0.0305. The population of S. quadrifida in Kupang has high genetic diversity and also clustered based on their geographical distribution

scholarly journals Assessment of genetic diversity using DNA markers among Brassica rapa var. yellow sarson germplasm lines collected from Eastern Uttar Pradesh and Uttarakhand hills

2016 ◽  
Vol 8 (3) ◽  
pp. 1333-1340
Author(s):  
Harsha Harsha ◽  
Jitendra Kumar Meena ◽  
Ram Bhajan ◽  
Usha Pant ◽  
Mohammed Talha
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Principal Coordinate Analysis ◽  
Molecular Profile ◽  
Polymorphic Band ◽  
Germplasm Management ◽  
High Genetic Diversity

The genetic diversity and the relatedness among thirty-one germplasm lines of yellow sarson collected from eastern UP were evaluated using morphological characters and Random Amplified Polymorphic DNA (RAPD) markers. Molecular parameters, viz. A total number of bands, average polymorphic band, average percent polymorphism, average polymorphic information content (PIC), Jaccard’s similarity coefficient, Principal Coordinate Analysis (PCA) and dendrogram generated using RAPD markers. A total of 148 different polymorphic amplification products were obtained using 10 selected decamer primers. The Jaccard similarity coefficient ranged from 0.557-0.899. Maximum polymorphism detected was 100 %.The range of amplification was from 190bp to 9 kb. Some unique bands were also reported with different primers that can be used for the identification of particular accession. PYSC-11-11 and PYSC-11-36 genotypes showed a maximum number of unique loci of different size. 31 germplasm lines grouped into two major clusters I and II based on RAPD profiling. Morphological characterization was done on the basis of leaf, petal and beak characteristics. The similarity value among the germplasm lines ranged from 0.222 to 1.000 using morphological descriptors. The dendrogram generated grouped the germplasm accession into two major groups at 44% similarity value. The cluster analysis was comparable up to some extent with Principal Coordinate Analysis (PCA) of two and three-dimensional plots. The variability revealed by morphological and molecular profile were found to be non-comparable. This study indicated the presence of high genetic diversity among collected yellow sarson germplasm, which could be used for developing for breeding and germplasm management purposes.

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.

Comparative analysis of diversity based on morpho-metric and molecular markers in chickpea over different environments

2018 ◽  
Author(s):  
Indu Rialch ◽  
Rama Kalia ◽  
H. K. Chaudhary ◽  
B. Kumar ◽  
J. C. Bhandari ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Agronomic Traits ◽  
Rapd Analysis ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Breeding Programme ◽  
Metric Traits

Ten morpho-agronomic traits and 80 random amplified polymorphic DNA (RAPD) molecular markers were used to survey genetic diversity in 25 chickpea genotypes. Analysis of variance revealed significant variability among different genotypes for morpho-metric traits. The cluster analysis done using morpho-metric traits grouped 25 genotypes into seven and six clusters in Environment I (Env. I) and Environment II (Env. II), respectively. Three genotypes viz., ICCV-96904, HPG-17, ICCV-95503 and L-HR-1 belonging to diverse clusters were identified divergent and may use in heterosis breeding programme. Of 80 random RAPD markers, 25 were found polymorphic. Three major clusters were identified using 25 polymorphic RAPD markers. The genetic similarity coefficient among genotypes ranged from 0.57 to 0.91. The average polymorphic information content (PIC) for 25 RAPD markers ranges from 0.12 to 0.40. D2-statistic, RAPD analysis and study of genotypes performance revealed sufficient genetic diversity among chickpea genotypes which would be useful in future breeding programme.

scholarly journals Genetic Similarity of Commerson’s Anchovy across Segara Anakan Cilacap Assessed Using Randomly Amplified Polymorphic DNA (RAPD) Markers

Jurnal Biota ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. 42-50
Author(s):  
Muhammad Khoerol Anam ◽  
Adi Amurwanto ◽  
Kusbiyanto Kusbiyanto ◽  
Hendro Pramono ◽  
M Husein Sastranegara ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Differences ◽  
Population Genetic Study ◽  
Randomly Amplified Polymorphic Dna ◽  
High Genetic Diversity ◽  
Impressive Result

Segara Anakan areas can be divided into three different regions according to their salinity. Salinity differences suggested that Commerson’s anchovy population in that area can be divided into three subpopulations due to genetic differences. Genetic differences among subpopulation can be assessed through a population genetic study using random amplified polymorphic DNA. This study aims to evaluate the genetic variation and differences of Commerson's anchovy (Stolephorus commersonnii) collected at three different water salinities in Segara Anakan estuary Cilacap Indonesia. Total genomic DNA was isolated using the Chelex method. Genetic diversity and differences were assessed using RAPD markers and were analyzed statistically using an analysis of molecular variance, as implemented in Arlequin software.  The results showed that high genetic diversity was observed within the subpopulations. However, no significant genetic differences were observed among subpopulations which indicate genetic similarity. A high number of offspring are likely to cause high genetic variation within subpopulations.  Adult and larvae migration is the cause of genetics similarity across Segara Anakan. Another impressive result is that water salinity did not affect the genetic characteristic of Commerson,s anchovy. Genetic similarity of Commerson’s anchovy indicates that Segara Anakan forms a single genetic conservation unit.

scholarly journals Molecular identification and genetic diversity in Hypericum L.: A high value medicinal plant using RAPD markers markers

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 393-405
Author(s):  
Dezhong Bi ◽  
Dan Chen ◽  
Majid Khayatnezhad ◽  
Zohreh Hashjin ◽  
Zifa Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characters ◽  
Mantel Test ◽  
High Genetic Diversity ◽  
Genetic Structure Of Populations ◽  
Geographical Distances ◽  
Species Adaptability ◽  
Hypericum Species

Genus Hypericum (Guttiferae, Hypericoideae) is perennial, belonging to the Hypericaceae family, having 484 species in forms of trees, shrubs, and herbs, distributed in 36 taxonomic sections. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Hypericum genetic diversity. Therefore, we collected and analyzed six species from five provinces of Iran regions. Overall, seventy plant specimens were collected. Our aims were 1) to assess genetic diversity among Hypericum 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. H. dogonbadanicum depicted unbiased expected heterozygosity (UHe) in the range of 0.10. Shannon information was high (0.32) in H. perforaturm. H. dogonbadanicum showed the lowest value, 0.17. The observed number of alleles (Na) ranged from 0.22 to 0.53 in H. dogonbadanicum and H. elongaturn. Gene flow (Nm) was relatively low (0.87) in Hypericum. The Mantel test showed correlation (r = 0.45, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Hypericum 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 Hypericum species.

scholarly journals Genetic diversity of Lonicera L. (Caprifoliaceae) estimated by molecular markers and morphological characters

Genetika ◽  
2021 ◽  
Vol 53 (2) ◽  
pp. 651-662
Author(s):  
Xin Ma ◽  
Huailiang Tian ◽  
Haiou Xia ◽  
Z Zeenat
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characters ◽  
Mantel Test ◽  
High Genetic Diversity ◽  
Changing Environments ◽  
Genetic Structure Of Populations ◽  
Geographical Distances ◽  
Species Adaptability

Members of Lonicera are characterized by opposite, narrowly elliptic to obovate leaves, white, yellow, reddish, or purple-red corolla with capitate stigma and undulate calyx margin. In Flora Iranica, Wendelbo (1965) classified 19 species of the Lonicera into two subgenera (Chamaecerasus and Lonicera) and three sections, namely Isoxylosteum, Isika and Coeloxylosteum. The four studied species belong to subgenus Chamaecerasus and sections Isika and Coeloxylosteum. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Lonicera genetic diversity. Therefore, we collected and analyzed three species from 2 provinces regions. Overall, 45 plant specimens were collected. Our aims were 1) to assess genetic diversity among Lonicera 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. The Mantel test showed correlation (r=0.66, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Lonicera 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 Lonicera species.

scholarly journals Genetic Diversity between Yacon Landraces from Different Countries Based on Random Amplified Polymorphic DNAs

2011 ◽  
Vol 41 (No. 2) ◽  
pp. 73-78 ◽  
Author(s):  
L. Milella ◽  
J. Salava ◽  
G. Martelli ◽  
I. Greco ◽  
E.F. Cusimamani ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Relationship ◽  
Genetic Similarity ◽  
Morphological Traits ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Crop Germplasm ◽  
Relationship Of

Random amplified polymorphic DNA (RAPD) markers are widely used for evaluating the genetic relationship of crop germplasm. Five different landraces of yacon (Smallantus sonchifolius (Poepp. and Hendl.) H. Robinson; Asteraceae) collected in various countries and showing different morphological traits were investigated using a total of 61 decamer primers. A total of 282 RAPD markers were scored and 28.7% of them were polymorphic at least within landraces. RAPD markers generated by one primer (OBP14) discriminated between all landraces. Markers were used to calculate genetic similarity coefficient and to build a dendrogram representing the genetic relationship between analysed landraces. The results suggest that RAPD markers could be used as a reliable tool to perform fingerprinting studies in Smallantus sonchifolius genome. This is the first report on the use of RAPDs to evaluate genetic distance and to distinguish between different landraces in yacon.  

scholarly journals Assessment of genetic diversity in Tamarind (Tamarindus indica L. ) using random amplified polymorphic DNA markers

2015 ◽  
Vol 13 (1) ◽  
pp. 27-36 ◽  
Author(s):  
M Kumar ◽  
V Ponnuswami ◽  
C Rajamanickam ◽  
TL Preethi
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Molecular Level ◽  
Random Amplified Polymorphic Dna ◽  
Tamarindus Indica ◽  
Intrapopulation Diversity ◽  
Desirable Trait

Determination of genetic variation is important to the plant breeders for development of high yielding variety. The aim of the current study was to investigate the genetic diversity of nine tamarind cultivars, out of nine four flowering cultivars using random amplified polymorphic DNA (RAPD) markers. Ten Random amplified polymorphic DNA (RAPD) primers were used to assess the genetic diversity in four flowering cultivars and five non-flowering of tamarind trees. The average genetic similarity level among the four flowering cultivars and five non-flowering accessions grouped into six clusters groups at 0.76%. RAPD profiles of all the tamarind were compared and a total of 58 scorable bands were produced with seven primers ranging from one for OPG-13 to twelve for OPA-R15. Genotypes which were morphological closely related were found to be unrelated at the molecular level. A sizeable amount of intrapopulation diversity recorded in the present study which can be utilized in hybridization programmes to efficiently introgress the desirable trait of interest.SAARC J. Agri., 13(1): 27-36 (2015)

scholarly journals Evaluation of RAPD markers for molecular identification of five bamboo genera from Indonesia

2019 ◽  
Vol 61 (4) ◽  
pp. 255-266
Author(s):  
◽  
Rini Hafzari ◽  
Tia Setiawati ◽  
Budi Irawan ◽  
Joko Kusmoro
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Similarity Coefficient ◽  
Bamboo Species ◽  
Base Pairs ◽  
Natural Genetic Variation ◽  
Molecular Genetic Diversity ◽  
Polymorphic Bands

Abstract Conservation of bamboos for future exploitation as fuel, fibre and as an ingredient for cosmetics depends on knowledge of its natural genetic variation. The study of molecular genetic diversity in bamboos will provide important information for its conservation. This article reports on the genetic diversity in 25 species representing five genera of bamboos found in Indonesia using Random Amplified Polymorphic DNA (RAPD) molecular markers. Out of 40 primers, 24 primers produced 1107 total bands and 86.21% of polymorphic bands across the 25 species. Sixteen bands were uniquely found in one species only and their presence or absence helped to define nine bamboo species. RAPD band sizes ranged from 162 to 2247 base pairs. A dendrogram based on the similarity coefficient of Dice divided the bamboo species into three big clusters. In conclusion, RAPD can capture the diversity among five different bamboo genera and has a great potential to be used in the study of genetic diversity in Indonesian bamboos.

scholarly journals Genetic variability in populations of Pilosocereus catingicola (Gürke) Byles & Rowley subsp. salvadorensis (Werderm.) Zappi (Cactaceae)

2020 ◽  
Vol 9 (8) ◽  
pp. e126985521
Author(s):  
Fabiana dos Anjos Barbosa ◽  
Alex da Silva Barbosa ◽  
Gláucia Diojânia Azevêdo Medeiros ◽  
Alberício Pereira de Andrade ◽  
Mailson Monteiro do Rêgo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Locus ◽  
Genetic Erosion ◽  
Jaccard Coefficient ◽  
Binary Matrix ◽  
High Genetic Diversity ◽  
Hierarchical Grouping ◽  
The Matrix ◽  
Ctab Method

Studies on genetic diversity of cacti are important to elucidate evolutionary events and ecological characteristics of populations vulnerable to genetic erosion. The objective of this study was to evaluate the genetic diversity among individuals of Pilosocereus catingicola subsp. salvadorensis occurring in three populations located in the Caatinga do Agreste region of Paraiba, using RAPD markers. For the extraction of DNA, tissues of the parenchyma and cladodium of the stem of the individuals were used by the 2% CTAB method and amplified using 05 primers. The obtained marks were converted into a binary matrix, from which the matrix of genetic dissimilarity was constructed using the arithmetic complement of the Jaccard coefficient and the construction of the dendrogram, by the UPGMA method. All markers tested amplified, being 82.4% polymorphic locus and 10.6% monomorphic for the Arara population; 84.4% polymorphic and 15.6% monomorphic for the Areial population, the Boa Vista population did not show monomorphism, resulting in 100% polymorphism. The averages of heterosigose observed (0.372, 0.492 and 0.135) show that there are genetic divergences within the populations. The primers used were effective in identifying polymorphism in the species. The populations evaluated in this study showed high genetic diversity, both within and between the population, originating fifteen groups among the 120 individuals from the UPGMA hierarchical grouping analysis, and it was possible to discriminate the populations.

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