scholarly journals Evaluation of the genetic variability in bamboo using RAPD markers

2011 ◽  
Vol 49 (No. 1) ◽  
pp. 24-28 ◽  
Author(s):  
S. Nayak ◽  
G.R. Rout ◽  
P. Das
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Growth Habit ◽  
Floral Morphology ◽  
Genetic Relationships ◽  
Species Cluster ◽  
Wide Range ◽  
Bambusa Vulgaris ◽  
Bambusa Ventricosa ◽  
Taxonomic Studies

Classical taxonomic studies of the bamboos are based on floral morphology and growth habit, which can cause problems in identification due to erratic flowering. Identification and genetic relationships in 12 species of bamboo were investigated using random amplified polymorphic DNAs (RAPD) technique. Analysis started by using thirty 10-mer primers that allowed us to distinguish 12 species and to select a reduced set of primers. The selected primers were used for identification and for establishing a profiling system to estimate genetic diversity. A total of one hundred thirty seven distinct polymorphic DNA fragments (bands), ranging from 0.4–3.3 kb were amplified by using 10 selected primers. The genetic similar analysis was conducted based on presence or absence of bands, which revealed a wide range of variability among the species. Cluster analysis clearly showed two major clusters belonging to 12 species of bamboo. Two major clusters were further divided into three minor clusters. The species of Bambusa vulgaris and Bambusa vulgaris var. striata were the most closely related and formed the first minor cluster along with Bambusa ventricosa. The variety of Bambusa multiplex var. Silver stripe and Bambusa multiplex were very closely related and there was no variation with Bambusa ventricosa. Another minor cluster was obtained between Bambusa arundinacea, Cephalostachyum pergracil and Bambusa balcooa. The RAPD technique has the potential for use in species identification and genetic relationships between taxa and species of bamboo for breeding program.

Biochemical and Molecular Characterization of Bamboo Variants

2020 ◽  
Vol 27 (1) ◽  
pp. 50-55
Author(s):  
Bhaskar Jyoti Dey ◽  
◽  
Ashok Kumar Verma ◽  
Salil Kumar Tewari ◽  
Ashutosh Dubey ◽  
...  
Keyword(s):  
Growth Habit ◽  
Floral Morphology ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
The Other ◽  
Sds Page ◽  
Bambusa Nutans ◽  
Taxonomic Studies ◽  
Maximum Similarity

Classical taxonomic studies of the bamboos are based on floral morphology and growth habit, which can cause problems in identification due to erratic flowering. Identification and genetic relationships in 18 species of bamboo were investigated using SDS-PAGE and RAPD analysis. Protein profiles of 18 bamboo species revealed clear polymorphism which can be used to identify species. Dendrogram based on SDS-PAGE data separated 18 species into two major clusters with Bambusa nutans & B. polymorpha, Gigantochloa andamanica & Dendrocalamus longispathus, G. andamanica & D. gigangteus showed maximum similarity of 71.4% in each case while genotype B. tulda and B. nutans (10.4%) showed lowest similarity. On the other hand, RAPD analysis proved to be a better tool with 14.67 as an average number of bands per polymorphic primers. Dendrogram based on RAPD separated 18 species into 2 major clusters with D. membranaceous and B.multiplex showed maximum similarity of 83% while genotype D. asper and B. balcooa showed least similarity (10.6%).

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 Comparison of Genetic Diversity between Nuña and and Other Andean bean (Phaseolus vulgaris) Populations

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 544C-544
Author(s):  
James Nienhuis ◽  
Paul Skroch ◽  
Steve Beebe
Keyword(s):  
Genetic Diversity ◽  
Energy Efficiency ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Core Collection ◽  
Rapd Markers ◽  
Practical Consideration ◽  
Common Beans ◽  
Germplasm Bank ◽  
Wide Range

Nuñas are a type of common bean (Phaseolus vulgaris) that possess the unusual characteristic of popping or expanding their cotyledonary tissue when heated. Numerous landraces of nuña beans were domesticated in the Andean region of South America (Peru, Bolivia, and Ecuador) and have been grown and consumed in this region since antiquity. The practical consideration in the domestication of nuñas in the high Andes was likely due to the greater energy efficiency in cooking toasted vs. boiled seeds.The Phaseolus germplasm bank at CIAT (Centro Internacional de Agricultura Tropical) has developed a core collection of Andean beans that includes numerous nuña landraces. Based on the wide range of phaseolin types observed among nuña landraces, it has been hypothesized that nuñas may represent a greater source of genetic diversity compared to other landraces and cultivars of common bean. Eighty nuña accessions and 120 nonpopping common bean accessions were randomly sampled from the CIAT Andean germplasm core collection. The 200 accessions were characterized for 140 mapped RAPD markers. The objectives of our research were to 1) understand the genetic structure of nuña bean accessions relative to other Andean common beans, and 2) to measure the genetic distance and genetic diversity between nuña and other Andean bean populations.

scholarly journals Comparison of AFLPs, RAPD Markers, and Isozymes for Diversity Assessment of Garlic and Detection of Putative Duplicates in Germplasm Collections

2003 ◽  
Vol 128 (2) ◽  
pp. 246-252 ◽  
Author(s):  
Meryem Ipek ◽  
Ahmet Ipek ◽  
Philipp W. Simon
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Morphological Diversity ◽  
Mantel Test ◽  
Group Method ◽  
Aflp Analysis ◽  
Additional Tool ◽  
Germplasm Collections ◽  
Diversity Assessment

Garlic (Allium sativum L.) is an asexually propagated crop that displays much morphological diversity. Studies which have assessed garlic diversity with isozymes and randomly amplified polymorphic DNA (RAPD) markers generally agreed with the morphological observations but sometimes failed to discriminate clones. To discriminate among closely related garlic clones in more detail, we introduced amplified fragment-length polymorphism (AFLPs) to evaluate the genetic diversity and phenetic relatedness of 45 garlic clones and three A. longicuspis clones and we compared AFLP results with RAPD markers and isozymes. Three AFLP primer combinations generated a total of 183 polymorphic fragments. Although similarities between the clusters were low (≥0.30), some clones within the clusters were very similar (>0.95) with AFLP analysis. Sixteen clones represented only six different banding patterns, within which they shared 100% polymorphic AFLPs and RAPD markers, and likely are duplicates. In agreement with the results of other investigators, A. longicuspis and A. sativum clones were clustered together with no clear separation, suggesting these species are not genetically or specifically distinct. The topology of AFLP, RAPD, and isozyme dendrograms were similar, but RAPD and isozyme dendrograms reflected less and much less polymorphism, respectively. Comparison of unweighted pair group method with arithmetic averaging (UPGMA) dendrograms of AFLP, RAPD, and isozyme cluster analyses using the Mantel test indicated a correlation of 0.96, 0.55, and 0.57 between AFLP and RAPD, AFLP and isozyme, and RAPD and isozyme, respectively. Polymorphic AFLPs are abundant in garlic and demonstrated genetic diversity among closely related clones which could not be differentiated with RAPD markers and isozymes. Therefore, AFLP is an additional tool for fingerprinting and detailed assessment of genetic relationships in garlic.

Assessment of genomic diversity among wheat genotypes as determined by simple sequence repeats

Genome ◽  
2002 ◽  
Vol 45 (4) ◽  
pp. 646-651 ◽  
Author(s):  
M Ahmad
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Simple Sequence Repeats ◽  
Common Ancestor ◽  
Genetic Relationships ◽  
Genomic Diversity ◽  
Pedigree Information ◽  
Wheat Genotypes ◽  
Wide Range ◽  
Simple Sequence

Simple sequence repeats (SSRs) have been used to examine the genomic diversity of wheat (Triticum aestivum L.) germplasm. Thirteen wheat genotypes of diverse origin were analyzed with 43 selected SSRs to provide uniform and maximum genome coverage. A total of 156 allelic variants were detected at 43 SSR loci, ranging from two to eight per locus with an average of 3.6. The polymorphic information content (PIC) values of the loci ranged from 0.10 (Xgwm264) to 0.89 (Xgwm471 and Xgwm577). Genetic similarities calculated from SSR data ranged from 30.1 ('Era' and 'Klasic') to 90.1 ('Neepawa' and 'Thatcher') between genotypes. UPGMA analysis based on genetic distance estimates produced three loose groupings that were generally consistent with available pedigree information. Cultivars 'Neepawa' and 'Thatcher' are closely related. Their genetic relationship was confirmed by the facts that they share a common ancestor and are clustered together. There were two different 'Era' genotypes, one used in the 'Otane' pedigree and one used in this study. None of the other genotypes had a close common ancestor indicating any close genetic relationships. Principal coordinate analysis also confirmed this pattern of genetic diversity. A wide range of genomic diversity was observed among all the genotypes, proving them to be prime candidates for selective breeding for specific traits and broadening the genetic base.Key words: simple sequence repeats, genetic diversity, Triticum aestivum, genetic similarity estimates, cluster analysis.

scholarly journals GENETIC DIVERSITY OF SABAH RICE CULTIVARS USING RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS

2020 ◽  
pp. 35
Author(s):  
Alvina Simon ◽  
Vijay Kumar Subbiah ◽  
Chee Fong Tyng ◽  
Noor Hydayaty Md Yusuf
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Random Amplification ◽  
Commercial Cultivars ◽  
Rice Samples ◽  
Staple Crop ◽  
Upland Condition ◽  
Insight Into

Rice is the most important staple crop in Malaysia and is cultivated all over the country, including the state of Sabah. The uniqueness of rice cultivation in Sabah lies in the type of rice itself, deriving mainly from local or non-commercial cultivars but with distinctive characteristics including long grains, aromatic properties, and drought tolerance. However, despite having these important agricultural traits, information on the genetic diversity of Sabah rice remains limited. Hence, the purpose of this study was to determine the genetic polymorphisms of Sabah rice using random amplification of polymorphic DNA (RAPD) markers. A total of 101 alleles were profiled, from which 94% were identified as polymorphic. Phylogenetic analysis grouped the rice samples into three clusters, with two clusters classifying the ability of rice to grow under different planting conditions, suitable for growth irrigate and upland condition. The first cluster was dominated by cultivars that could survive in wet (irrigated) areas, while the other featured those that were found in dry (upland) areas. Furthermore, two alleles, OPA-05-B2 and OPA-01-B11, were found to be unique to cultivars within the upland cluster and were thus proposed to be involved in dry environmental adaptation. The results of the present study provide an insight into the genetic relationships and diversity of Sabah rice.

scholarly journals Isolation and Characterization of 88 Polymorphic Microsatellite Markers in Kentucky Bluegrass (Poa pratensis L.)

HortScience ◽  
2010 ◽  
Vol 45 (11) ◽  
pp. 1759-1763 ◽  
Author(s):  
Josh A. Honig ◽  
Stacy A. Bonos ◽  
William A. Meyer
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Rapd Markers ◽  
Poa Pratensis ◽  
Morphological Characteristics ◽  
Kentucky Bluegrass ◽  
Ploidy Levels ◽  
Isolation And Characterization ◽  
Wide Range ◽  
Polymorphic Microsatellite

Kentucky bluegrass (Poa pratensis L.) is an important facultative apomictic temperate perennial grass species used for both forage and cultivated turf. Through apomixis, this species is able to propagate diverse and odd ploidy levels, resulting in many genetically distinct phenotypes. A wide range of diverse cultivars and accessions of kentucky bluegrass have been previously characterized based on common turf performance or morphological characteristics as well as by random amplified polymorphic DNA (RAPD) markers. Although previous characterization efforts have provided valuable information, the use of both morphological characteristics and RAPD markers for genetic diversity analysis has limitations. In the current report, we developed and characterized 88 novel microsatellite markers for kentucky bluegrass. Polymorphism for each marker was assessed in 265 kentucky bluegrass cultivars, experimental selections, collections, and hybrids. The number of alleles for individual microsatellites ranged from four to 81 with an average of 38.3 alleles per simple sequence repeat. These polymorphic microsatellite markers would be useful tools for investigating genetic diversity, creation of genetic linkage maps, assessment of levels of apomixis in cultivars and experimental varieties, and identification of aberrant progeny in apomictic kentucky bluegrass breeding programs.

scholarly journals Genetic relatedness of soybean genotypes based on agromorphological traits and RAPD markers

Genetika ◽  
2014 ◽  
Vol 46 (3) ◽  
pp. 839-854 ◽  
Author(s):  
Vesna Peric ◽  
Ana Nikolic ◽  
Vojka Babic ◽  
Aleksanda Sudaric ◽  
Mirjana Srebric ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quantitative Traits ◽  
Rapd Markers ◽  
Genetic Relatedness ◽  
Diversity Index ◽  
Genetic Relationships ◽  
Morphological Characters ◽  
Morphological Description ◽  
Modern Agriculture ◽  
Soybean Genotypes

Modern agriculture, breeding procedures, as well as competition among breeding institutions contribute to further reduction of already narrowed diversity of soybean commercial varieties. The objective of the study was to characterize eighteen soybean cultivars from three different breeding programs for agro-morphological traits and to reveal genetic diversity using molecular markers. Morphological description was performed with 13 qualitative and 9 quantitative traits. The genetic relationships were estimated using 21 RAPD markers. PIC was calculated for RAPD data, while the diversity of qualitative traits was described by Shannon genetic diversity index. Cluster analysis based on qualitative morphological characters showed clear separation of genotypes on the basis of their plant growth type. PC analysis performed for quantitative traits divided genotypes according to their maturity group. Grouping pattern based on molecular marker data was in agreement with pedigree of cultivars. A great similarity was found, primarily between the varieties under the same institution, and then among all examined varieties. Comparison of three methods in the assessment of diversity indicated that morphological markers might provide useful information in breeding process and allow classification by pedigree to some extent, but RAPD markers were found to be superior in assessing differences among genetically very similar genotypes.

Genetic diversity and phylogenetic relationships in Vigna Savi germplasm revealed by DNA amplification fingerprinting

Genome ◽  
2007 ◽  
Vol 50 (6) ◽  
pp. 538-547 ◽  
Author(s):  
M.V. Simon ◽  
A.-M. Benko-Iseppon ◽  
L.V. Resende ◽  
P. Winter ◽  
G. Kahl
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Dna Amplification ◽  
Maximum Parsimony Analysis ◽  
Sources Of Resistance ◽  
Cowpea Cultivars ◽  
Wide Range ◽  
Cultivated Species ◽  
Few Data

The pantropical genus Vigna (Leguminosae) comprises 7 cultivated species that are adapted to a wide range of extreme agroclimatic conditions. Few data are available on the relationships among these cultivated species or on their importance as sources of resistance against biotic and abiotic stresses. Therefore, we optimized DNA amplification fingerprinting (DAF) to estimate the genetic diversity within, and genetic relationships among, a representative core collection of cowpea, as compared with 16 accessions representing cultivars from 6 Vigna species. A set of 26 primers was selected from 262 tested random primers and used for the characterization of 85 Vigna accessions (6 V. angularis , 4 each of V. mungo and V. radiata , 2 V. umbellata , 1 V. aconitifolia , and 68 V. unguiculata ), with Phaseolus vulgaris subsp. vulgaris as outgroup. A total of 212 polymorphic bands were used for maximum parsimony analysis. Our results clearly distinguished Brazilian from African V. unguiculata genotypes. At the species level, V. angularis was the most related and V. radiata the most divergent species relative to V. unguiculata. DAF markers were also informative at the intraspecific level, detecting a large diversity between cowpea cultivars. The implications of the presented results for cowpea breeding programs are discussed.

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