A Study on the Genetic Variation in Licorice (Glycyrrhiza glabra) Iran  by Molecular DNA Markers (RAPD)

Thirty ecotypes of licorice (a medicinal plant) from all of Iran were collected and genetically evaluated. To assess the genetic diversity of licorice, genomic DNA was extracted using Winnepenninckx method (CTAB method). 12 random primers were used to perform PCR. All 12 primers showed obvious and repeatable bands. Totally, 1343 bands were produced. Bands size varied from 250 to 5000 bp. Percentage of polymorphism and polymorphic loci was 88.83% and 95.5%, respectively. The highest number of band was related to primer OPN-08 (band 188). The highest similarity between Esfaraien and Bojnourd ecotypes is equal to 0.647. Kermanshah and Orumieh ecotypes had the lowest similarity that was 0.3. Dendrogram divided 30 ecotypes into 5 groups in terms of genetic distance. Generally, surveying the variation in genotypes of licorice using RAPD marker showed that this marker can be useful in identifying the polymorphism, estimating the genetic distance, and managing germplasm.

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Molecular Analysis of Synedrela Nodiflora (L.) Gaertn. Resistance Against Fomesafen using RAPD Markers

Biosfera ◽

10.20884/1.mib.2015.32.1.290 ◽

2015 ◽

Vol 32 (1) ◽

pp. 11

Author(s):

Murni Dwiati ◽

Agus Hery Susanto

Keyword(s):

Genetic Variation ◽

Data Analysis ◽

Environmental Factors ◽

Genetic Distance ◽

Molecular Analysis ◽

Dna Markers ◽

Genomic Dna ◽

Rapd Markers ◽

Rapd Marker ◽

Synedrella Nodiflora

Both morphological and protein studies reveal that differences are observed between resistant Synedrella nodiflora against fomesafen and its susceptible wildtype. These are, however, more or less influenced by environmental factors, so that molecular analysis employing DNA markers is necessarily required. The methods involved total genomic DNA extraction using modified CTAB protocol following Doyle & Doyle (1990), RAPD marker amplification and visualization of RAPD markers prior to data analysis. Ten RAPD markers were used, but only seven of them showed polymorphism. Calculation of genetic distance and variation was carried out employing PopGen software.Based on the RAPD markers used in this study, it can be concluded that genetic distance between susceptible and resistant S. nodiflora is higher than that within susceptible samples supporting our previous morphological and protein data, although genetic variation among susceptible individuals seems to be significantly high.

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Analysis of Genetic Diversity of Indonesia Rodent Tuber (Typhonium flagelliforme Lodd.) Cultivars Based on RAPD Marker

KnE Life Sciences ◽

10.18502/kls.v2i1.133 ◽

2015 ◽

Vol 2 (1) ◽

pp. 139

Author(s):

Danny Laurent ◽

Nesti F. Sianipar ◽

Chelen _ ◽

Listiarini _ ◽

Ariandana Wantho

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Medicinal Plant ◽

Genetic Distance ◽

Genetic Information ◽

Rapd Marker ◽

Anti Cancer ◽

Cancer Agent

Rodent tuber (Typhonium flagelliforme Lodd.) is a plant from Araceae family. The plant has high medical potential as anti-cancer agent. The information regarding Indonesian rodent tuber’s genetic diversity is not available yet. Genetic information is very important for the development of rodent tuber as medicinal plant. In this research, genetic diversity and genetic distance of three Indonesian rodent tuber’s cultivars, from Bogor, Pekalongan, and Medan, were analyzed by using RAPD molecular markers. The data obtained was analyzed by NTsys software. Out of 16 primers used in the study, the 12 primers were found to be polymorphic. There were 83 bands of DNA obtained and 31 of them were polymorphic. Dendogram analysis of the three rodent tuber cultivars showed that these cultivars were clustered into two clusters. The first cluster consists of rodent tuber Bogor and Medan. The second cluster consists of rodent tuber Pekalongan. The coefficient of similarity ranged from 0.81 to 0.87. The highest coefficient of similarity was 0.87, which was detected between rodent tuber Pekalongan and Medan. The lowest coefficient of similarity was 0.81, which was detected between rodent tuber Bogor and Pekalongan. Among these three cultivars of rodent tuber, cultivar Bogor was exclusively different. Keywords: Indonesia-rodent tuber, genetic diversity, RAPD-marker

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Assessment of Genetic Diversity of Chili Cultivars Using RAPD Markers

Plant Tissue Culture and Biotechnology ◽

10.3329/ptcb.v22i2.14201 ◽

2013 ◽

Vol 22 (2) ◽

pp. 127-136

Author(s):

MM Uddin ◽

MI Khalil ◽

MS Haque ◽

MB Meah

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Plant Tissue ◽

Genomic Dna ◽

Rapd Markers ◽

Polymorphic Locus ◽

Random Amplified Polymorphic Dna ◽

Rapd Marker ◽

Genetic Identity ◽

Cluster 2

Random amplified polymorphic DNA (RAPD) assay was performed to estimate genetic polymorphisim in ten chili cultivars. Out of 12 primers four (OPA11, OPB03, OPB04 and OPB17) showed amplification of genomic DNA and generated 21 distinct score able bands of which 17 (80.95%) were polymorphic. The highest percentage (85.71) polymorphic locus was found in OPB03 while the lowest (66.67) in OPA11. The highest genetic distance was computed between Jamalpur Balujuri and Matal marich with the lowest genetic identity as against the lowest genetic distance between Hajari marich and Balujuri marich. The UPGMA dendogram indicated segregation of ten chili varieties and genotypes into two main clusters. Variety Bogra marich and Matal marich formed cluster 1 and Balujuri marich, Deshi marich, Jamalpuri balujuri, Bindu marich, Syloti, Hajari, Biroli city, and the genotype Ausadhebrara grouped in cluster 2. The result indicates the genetic diversity among the chili cultivars and RAPD marker could be used for improvement of chili varieties. DOI: http://dx.doi.org/10.3329/ptcb.v22i2.14201 Plant Tissue Cult. & Biotech. 22(2): 127-136, 2012 (December)

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Genetic Variation in Mutants of Chilli (Capsicum annum) Revealed by RAPD Marker

International Letters of Natural Sciences ◽

10.18052/www.scipress.com/ilns.11.1 ◽

2014 ◽

Vol 11 ◽

pp. 1-8

Author(s):

L. Mullainathan ◽

A. Sridevi ◽

S. Umavathi ◽

E. Sanjai Gandhi

Keyword(s):

Genetic Variation ◽

Untreated Control ◽

Genomic Dna ◽

Rapd Marker ◽

Slight Modification ◽

Chemical Mutagenesis ◽

Mutagenic Treatment ◽

Dna Damages ◽

Capsicum Annum ◽

Ctab Method

The present study was under taken in order to analyze the chemical mutagenesis on Chilli germplasm. In this regard, K1 variety of chilli was subjected to different mutagenic concentration for inducing mutagenesis. The M3 plants exposed to EMS and DES to produce clear difference from the untreated control, thus indicating that mutagenic treatment produce polymorphic regions in the chilli. For extraction of genomic DNA was adopted an improved protocol of CTAB method with slight modification. A total of ten primers were used to screen the polymorphism among the treated populations line tall, tall with chlorophyll deficient, leaf, flower, GMS and DNA damages in maturity mutants were analyzed with control. Out of ten primers, four primers (PGF02, PGF03, PGF04 AND OP107) were successfully amplified in all the samples used for this study. The successful primers were amplified in to 93 products showing an average of 9.3 bands

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Genetic analysis of silver-fir populations in the Beskids

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.2003.015 ◽

2011 ◽

Vol 72 (2) ◽

pp. 115-119 ◽

Cited By ~ 3

Author(s):

Leon Mejnartowicz

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Analysis ◽

Abies Alba ◽

Genetic Distances ◽

Silver Fir ◽

Geographical Distance ◽

Polymorphic Loci ◽

Expected Heterozygosity ◽

Rare Alleles

Twenty-eight isozymic loci were studied in the Beskid Mts., in four populations of common silver-fir (Abies alba): one in Beskid Makowski (BM) and three populations in Beskid Sądecki (BS). Their genetic variation and diversity were analyzed, and Nei's genetic distances between the populations were calculated. The results show that the geographical distance between the BM population and the three BS populations is reflected in genetic distances. The BM population is clearly distinct from the others. It has the lowest genetic diversity (I = 0.42), percentage of polymorphic loci (%PoL = 64.29) and number of rare alleles (NoRa = 5). Besides, the BM population has the highest observed heterozygosity (Ho = 0.291), which exceeds the expected heterozygosity (He = 0.254), estimated on the basis of the Hardy-Weinberg Principle. On the contrary, BS populations are in the state of equilibrium, which is manifested, in similar values of He = 0.262 and Ho = 0.264.

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Measurement of Genetic Diversity of Chinese Seashore Paspalum Resources through Morphological and Sequence-related Amplified Polymorphism Analysis

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04700-19 ◽

2019 ◽

Vol 144 (6) ◽

pp. 379-386

Author(s):

Yan Liu ◽

Hailin Guo ◽

Yi Wang ◽

Jingang Shi ◽

Dandan Li ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Variation ◽

Genetic Distance ◽

Morphological Characteristics ◽

The United States ◽

Germplasm Resources ◽

Seashore Paspalum ◽

Chinese Germplasm

Seashore paspalum (Paspalum vaginatum) is a notable warm-season turfgrass. Certain germplasm resources are distributed in the southern regions of China. The objectives of this study were to investigate the genetic diversity and genetic variation of Chinese seashore paspalum resources. Morphological characteristics and sequence-related amplified polymorphism (SRAP) markers were used to assess genetic relationships and genetic variation among 36 germplasm resources from China and six cultivars from the United States. The results showed significant variation for 13 morphological characteristics among 42 tested seashore paspalum accessions, and that the phenotypic cv was, in turn, turf height > turf density > internode length > inflorescence density > leaf width > reproductive branch height > spikelet width > leaf length > spikelet number > inflorescence length > internode diameter > inflorescence width > spikelet length. According to the morphological characteristics and cluster analysis, 42 seashore paspalum accessions were divided into six morphological types. In total, 374 clear bands were amplified using 30 SRAP primer combinations; among these bands, 321 were polymorphic with 85.83% polymorphism. SRAP marker cluster analysis showed that 42 seashore paspalum accessions were grouped into seven major groups, with a genetic similarity coefficient ranging from 0.4385 to 0.9893 and genetic distance values ranging from 0.0108 to 0.8244. The high level of genetic diversity occurred among Chinese germplasm, and the genetic distance was relatively high between Chinese germplasm and cultivars introduced from the United States. The patterns in morphological trait variations and genetic diversity will be useful for the further exploitation and use of Chinese seashore paspalum resources.

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Genetic variation analysis of superior cotton varieties of Gossypium hirsutum through microsatellite markers

International Journal of Plant Biology ◽

10.4081/pb.2017.6996 ◽

2017 ◽

Vol 8 (1) ◽

Author(s):

Dede Nuraida ◽

Yusuf Abdurrajak ◽

Moh Amin ◽

Utami S. Hastutik

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Gossypium Hirsutum ◽

Microsatellite Markers ◽

Size Range ◽

Allele Frequencies ◽

Variation Analysis ◽

Ctab Method

This study was conducted in order to obtain information on genetic variation in populations rated as superior cotton (Gossypium hirsutum L.) varieties in Balittas Malang, Indonesia. The samples used 10 varieties of cotton Kanesia series and 2 other superior varieties that are LRA 5166 and ISA 205A. Indicators of genetic diversity are the number of alleles per locus, allele frequencies, and heterozygosity values. DNA was isolated from the leaves of 3- week-old seedlings using the CTAB method. Amplification was performed using 5 SSRs primer pairs of the JESPR series. The results showed five microsatellite loci, yielding 12 alleles with a size range of 80–500 bp, with an average number of alleles per locus of 4.60. The average values of heterozygosity of the five loci was high, at 0.71. Based on the number of alleles, allele frequencies and heterozygosity values, the genetic variation sampled in the superior cotton varieties studied here is quite high.

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Genetic diversity in wild and hatchery populations of stinging catfish (Heteropneustes fossilis Bloch) revealed by RAPD analysis

Journal of Bio-Science ◽

10.3329/jbs.v19i0.13005 ◽

2012 ◽

Vol 19 ◽

pp. 81-87

Author(s):

Md Nazrul Islam ◽

Abhishak Basak ◽

Dr Ashrafullah ◽

Md Samsul Alam

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Gene Diversity ◽

Similarity Index ◽

Heteropneustes Fossilis ◽

Wild Populations ◽

Polymorphic Loci

Context: DNA fingerprinting using genetic markers such as Random Amplification of Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP), microsatellite (Simple sequence repeat), Amplified Fragment Length Polymorphism (AFLP) etc. can be successfully used to reveal genetic variation within and among different populations. Objective: The aim of the present study was to assess genetic diversity in two wild and one hatchery populations of stinging catfish Heteropneustes fossilis by RAPD fingerprinting. Materials and Methods: A total of 90 live fish (H. fossilis), 30 from each source, were collected from a beel in Patuakhali, a beel in Jessore and Rupali Hatchery, Mymensingh. Genomic DNA was extracted from fin tissues. The concentration of DNA was estimated using a spectrophotometer. Fifteen decamer primers of random sequence from three kits (six from kit A, seven from kit B and two from kit C) (Operon technologies, Inc., Alameda, CA, USA) were screened on sub-samples of one randomly chosen H. fossilis DNA sample from the each population to test their suitability for amplifying RAPDs. The amplified products from each sample were separated by electrophoresis on 1.4% agarose gel containing ethidium bromide. The sizes of the bands were calculated using the software DNAFRAG and the sizes in base pair (bp) were used for identification of the bands (RAPD markers). The similarity index values (SI) between the RAPD fingerprint of any two individuals on the same gel were calculated from RAPD band sharing. Results: A total of 28 RAPD bands were obtained using four decamer random primers, among which 21 bands were polymorphic. The percentage of polymorphic loci, intra-population similarity indices and Nei's gene diversity values were 85.71%, 78.75 and 0.304±0.183 for Jessore population, 83.71%, 82.62 and 0.280±0.159 for Patuakhali population, 82.14%, 85.25 and 0.271±0.165 for Rupali hatchery population, respectively. The overall gene flow (Nm) among the populations was 5.755. The highest inter-similarity (Sij) was found between Patuakhali - Rupali hatchery populations. Among the three populations, the highest genetic distance (0.069) was found between Jessore and Patuakhali population. Considering polymorphic loci, intrapopulation similarity index and gene diversity the genetic variation in the Jessore population was higher than the other two populations. The genetic variation of the hatchery population was found to be lower than the two wild populations. Conclusion: The result of the present study can be used as baseline information regarding the genetic variation and population structure before undertaking any breeding programme. Study indicated that the genetic variation in the hatchery populations were slightly lower than those of the wild populations. DOI: http://dx.doi.org/10.3329/jbs.v19i0.13005 J. bio-sci. 19 81-87, 2011

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Genetic variation in populations of the endemic Achillea millefolium ssp. megacephala from the Athabasca sand dunes and the widespread ssp. lanulosa in western North America

Canadian Journal of Botany ◽

10.1139/b96-138 ◽

1996 ◽

Vol 74 (7) ◽

pp. 1138-1146 ◽

Cited By ~ 29

Author(s):

Brett G. Purdy ◽

Randall J. Bayer

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Gene Diversity ◽

Sand Dunes ◽

Achillea Millefolium ◽

Starch Gel Electrophoresis ◽

Widespread Species ◽

Polymorphic Loci ◽

Endemic Taxon ◽

Starch Gel

As part of an analysis of genetic diversity in endemic taxa of the Athabasca sand dunes in northern Saskatchewan, Canada, genetic variation was examined by starch gel electrophoresis in six populations of the endemic Achillea millefolium ssp. megacephala, and 13 populations of the closely related widespread taxon, A. millefolium ssp. lanulosa. Endemic populations had more alleles per locus, a higher percentage of polymorphic loci, and greater genetic diversity than did populations of the widespread taxon. At polymorphic loci, total gene diversity was comparable in both taxa, although within-population gene diversity was higher in the endemic taxon. Population differentiation (GST) was considerably lower in ssp. megacephala than in ssp. lanulosa, although GST values were reduced when the parameter was calculated separately for geographic subdivisions of the widespread taxon. Our results differ from previous studies in which the endemic is typically depauperate of genetic variation relative to related widespread species. We suggest that obligate sexual reproduction and the absence of long-term asexual reproduction may be one of a number of factors that help populations of ssp. megacephala maintain higher levels of genetic variation on the Athabasca sand dunes. Keywords: genetic variation, endemic, rare species, Athabasca sand dunes, Achillea millefolium.

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Going with the flow: analysis of population structure reveals high gene flow shaping invasion pattern and inducing range expansion of Mikania micrantha in Asia

Annals of Botany ◽

10.1093/aob/mcaa044 ◽

2020 ◽

Vol 125 (7) ◽

pp. 1113-1126

Author(s):

Achyut Kumar Banerjee ◽

Zhuangwei Hou ◽

Yuting Lin ◽

Wentao Lan ◽

Fengxiao Tan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Gene Flow ◽

Genetic Distance ◽

Range Expansion ◽

Mikania Micrantha ◽

High Gene Flow ◽

Genetic Pattern ◽

High Gene

Abstract Background and Aims Mikania micrantha, a climbing perennial weed of the family Asteraceae, is native to Latin America and is highly invasive in the tropical belt of Asia, Oceania and Australia. This study was framed to investigate the population structure of M. micrantha at a large spatial scale in Asia and to identify how introduction history, evolutionary forces and landscape features influenced the genetic pattern of the species in this region. Methods We assessed the genetic diversity and structure of 1052 individuals from 46 populations for 12 microsatellite loci. The spatial pattern of genetic variation was investigated by estimating the relationship between genetic distance and geographical, climatic and landscape resistances hypothesized to influence gene flow between populations. Key Results We found high genetic diversity of M. micrantha in this region, as compared with the genetic diversity parameters of other invasive species. Spatial and non-spatial clustering algorithms identified the presence of multiple genetic clusters and admixture between populations. Most of the populations showed heterozygote deficiency, primarily due to inbreeding, and the founder populations showed evidence of a genetic bottleneck. Persistent gene flow throughout the invasive range caused low genetic differentiation among populations and provided beneficial genetic variation to the marginal populations in a heterogeneous environment. Environmental suitability was found to buffer the detrimental effects of inbreeding at the leading edge of range expansion. Both linear and non-linear regression models demonstrated a weak relationship between genetic distance and geographical distance, as well as bioclimatic variables and environmental resistance surfaces. Conclusions These findings provide evidence that extensive gene flow and admixture between populations have influenced the current genetic pattern of M. micrantha in this region. High gene flow across the invaded landscape may facilitate adaptation, establishment and long-term persistence of the population, thereby indicating the range expansion ability of the species.

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