Morphological and molecular data to determine the origin and taxonomic status of Prosopis chilensis var. riojana (Fabaceae, Mimosoideae)

2003 ◽  
Vol 81 (9) ◽  
pp. 905-917 ◽  
Author(s):  
Soledad Vázquez-Garcidueñas ◽  
Ramón A Palacios ◽  
Jenny Segovia-Quiroz ◽  
Juan T Frías-Hernández ◽  
Victor Olalde-Portugal ◽  
...  
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Genetic Distances ◽  
Group Method ◽  
Sympatric Populations ◽  
Arithmetic Means ◽  
Genetic Characteristics ◽  
Genetic Traits ◽  
Prosopis Chilensis

This study analyzes the morphological and genetic characteristics of three sympatric populations of Prosopis from Argentina. Although morphological and geographical data suggest that Prosopis chilensis var. riojana is an interspecific hybrid of Prosopis chilensis var. chilensis and Prosopis flexuosa var. flexuosa, no correlation was found between morphological traits and genetic distances generated by random amplified polymorphic DNA - polymerase chain reaction (RAPD-PCR). Genetic similarity is greater among P. chilensis var. chilensis and P. flexuosa var. flexuosa than between either of these two taxa with P. chilensis var. riojana. Also, P. chilensis var. riojana has unique genetic markers that are absent from its putative parents. Additionally, dendrograms generated by unweighted pair group method with arithmetic means (UPGMA) and Neighbor-Joining clustering criteria group P. chilensis var. chilensis and P. flexuosa var. flexuosa apart from P. chilensis var. riojana. Possibilities for the lack of congruence between morphology and RAPD markers are discussed. The results obtained are insufficient to conclusively establish the origin of P. chilensis var. riojana; however, the morphological and genetic traits observed suggest this taxon is well differentiated from P. chilensis var. chilensis and P. flexuosa var. flexuosa.Key words: genetic distances, hybridization, morphology, Prosopis, RAPD, rare taxon.

Genetic Diversity Analysis of Salvadora Oleoides Decne: An Evergreen Dry Land Fruit Tree of Rajasthan, India

2021 ◽  
Author(s):  
Juleri M Upendra ◽  
Shari Nair ◽  
Satyawada R Rao ◽  
Harchand R Dagla
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Splice Junction ◽  
Genetic Distances ◽  
Climatic Conditions ◽  
Fruit Tree ◽  
Group Method ◽  
Dry Land ◽  
Intron Splice ◽  
Semi Arid

Abstract Genetic diversity of Salvadora oleoides Decne is analyzed by cumulative data of 10 Random Amplified Polymorphic DNA (RAPD), 10 Inter Simple Sequence Repeats (ISSR) and 7 Intron Splice Junction (ISJ) markers. The plant is an evergreen fruit tree and well distributed in semi-arid and sub-humid climatic conditions of Rajasthan, India. RAPD, ISSR and ISJ primers accounted for 84.4%, 85.3%, 85.9% polymorphism. Average 0.23 PIC is accounted for RAPD, ISSR and ISJ primers. The genetic similarity ranged between 0.42-0.89. Analysis of molecular variance (AMOVA) revealed higher variation (73%) at intra-population than inter-population (27%) level. Genetic distances based on Un-weighted Pair Group Method with Arithmetic mean (UPGMA) dendrogram and Principal Coordinate Analysis (PCoA) is correlated with physical distances or climatic conditions of Salvadora oleoides Decne in a semi-arid and sub-humid environment of Rajasthan. The present investigation may help in the understanding of gene flow systems between physical distances and environmental heterogeneity of the populations for better management of Salvadora oleoides Decne in the region.

The use of RAPD markers to distinguish among juniper and cedar cultivars

2000 ◽  
Vol 78 (5) ◽  
pp. 655-659 ◽  
Author(s):  
Tom Hsiang ◽  
Junbin Huang
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Unknown Origin ◽  
Genetic Distances ◽  
Group Method ◽  
Pair Group ◽  
Juniperus Chinensis ◽  
Juniperus Scopulorum ◽  
Close Relatives

Two species of Chamaecyparis and six cultivars each of Juniperus chinensis L. and Juniperus scopulorum Sarg. (Cupressaceae) were subjected to random amplified polymorphic DNA (RAPD) analysis using seven primers. Unweighted pair group method with averages (UPGMA) and principal component analyses of genetic distances between cultivars showed that 42 polymorphic RAPD bands could distinguish among all cultivars and properly group them by species and genera. Where the origin of a specific juniper cultivar is uncertain, analysis of genetic distance can pinpoint close relatives. For example, we were unable to trace the origin of J. chinensis 'Alps', and we initially thought it was a mislabeled J. chinensis 'Blue Alps'. However, we found 'Alps' to be closer to J. chinensis 'Fairview' and 'Mountbatten' than to 'Blue Alps'. Similarly, 'Wichita Blue' has an unknown origin, but it had the highest genetic similarity with 'Medora'.Key words: juniper, cedar, RAPD, cultivars, phylogenetics.

scholarly journals Characterization of Induced Sugarcane Somaclones and their Sources Varieties Using Random Amplified Polymorphic DNA

2016 ◽  
Vol 25 (2) ◽  
pp. 223-229 ◽  
Author(s):  
Kuasha Mahmud ◽  
KM Nasiruddin ◽  
MA Hossain ◽  
L Hassan
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Sugarcane Varieties ◽  
Main Cluster ◽  
Pair Group ◽  
The Relationship ◽  
Linkage Distance

Sugarcane somaclones and their sources varieties were analyzed by RAPD molecular markers to check the variation at molecular level based on 1.4% agarose gel electrophoresis (AGE). Six RAPD primers generated 237 bands with average 39.5 varied from 15 to 63 with size ranging 145 - 1000 bp among the four sugarcane varieties and their 12 somaclones. Genetic diversity or polymorphism information content (PIC) value ranged from 0.39 to 0.50 for all loci across the 4 varieties and their 12 somaclones based on RAPD markers. Dendrogram based on linkage distance using unweighted pair group method of arithmetic means (UPGMA) based on 6 RAPD primers indicated segregation of the 4 sugarcane varieties and their somaclones into two main clusters at linkage distance 36. Variety Isd 39 was observed in main cluster C1 while its (Isd 39) somaclones and other varieties (Isd 37, Isd 38 and Isd 40) and also their somaclones were found in main cluster C2 having different sub-clusters. Theirfore, it may be concluded that RAPD markers can be used for identification of somaclonal variation and the relationship between sources varieties and their somaclones.Plant Tissue Cult. & Biotech. 25(2): 223-229, 2015 (December)

scholarly journals Description and analysis of genetic diversity among squash accessions

2009 ◽  
Vol 52 (2) ◽  
pp. 271-283 ◽  
Author(s):  
Athanasios L. Tsivelikas ◽  
Olga Koutita ◽  
Anastasia Anastasiadou ◽  
George N. Skaracis ◽  
Ekaterini Traka-Mavrona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Clustering Algorithm ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Molecular Data ◽  
Optimal Number ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group

In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also performed, revealing high level of polymorphism. To study the genetic diversity among the squash accessions, a clustering procedure using Unweighed Pair Group Method and Arithmetic Average (UPGMA) algorithm was also adopted. Two independent dendrograms, one for the morphophysiological and one for molecular data were obtained, classifying the accessions into two and three main clusters, respectively. Despite the different number of the clusters there were many similarities between these two dendrograms, and a third dendrogram resulting from their combination was also produced, based on Gower's distance and UPGMA clustering algorithm. In order to determine the optimal number of clusters, the upper tail approach was applied. The more reliable clustering of the accessions was accomplished using RAPD markers as well as the combination of the two different data sets, classifying the accessions into three significantly different groups. These groups corresponded to the three different cultivated species of C. maxima Duch., C. moschata Duch., and C. pepo L. The same results were also obtained using Principal Component Analysis.

Genetic Divergence Between South African Helcion Species and North-East Atlantic H. Pellucidum (Mollusca: Patellogastropoda)

1997 ◽  
Vol 77 (4) ◽  
pp. 1139-1150 ◽  
Author(s):  
L.I. Weber ◽  
D.R. Gray ◽  
A.N. Hodgson ◽  
S.J. Hawkins
Keyword(s):  
South African ◽  
Genetic Divergence ◽  
Genetic Relationships ◽  
Taxonomic Status ◽  
Genetic Distances ◽  
Group Method ◽  
Congeneric Species ◽  
East Atlantic ◽  
North East ◽  
The North

Allozyme electrophoresis was used to estimate the genetic divergence between three species of South African Helcion and the north-east Atlantic H. pellucidum (Patellidae). At a finer level the genetic relationships among South African Helcion were explored. Twenty-one loci were resolved for all the species. High values of expected heterozygosities (0·202–0·341) were found for the genus. Phenetic analysis (UPGMA (unweighted pair-group method with artihmetic averaging) and Distance Wagner Procedure) and cladistic parsimony methods (alleles as binary characters and loci as multistate unordered characters) agreed in showing the same topology for the tree which represents the genetic relationships among Helcion species. The north-east Atlantic H. pellucidum was the most divergent species showing high values of Nei's genetic distances (1·423–1·654) with its South African congeners. In the literature such values of genetic divergence have been associated with non-congeneric species. The degree of genetic divergence (0·351–0·615) found within the South African branch was characteristic for congeneric species. The results of this study supported the monophyletic condition of this branch, and showed H. pectunculus and H. pruinosus to be more closely related to each other than to H. dunkeri. Nevertheless, the monophyly of the genus Helcion is uncertain and therefore its taxonomic status was questioned. A possible independent origin for northern and southern hemisphere species of Helcion is considered.

scholarly journals Performance of salinity tolerance of F3 rice lines of BRRI dhan 29 × PBRC (STL-20) using RAPD markers

2019 ◽  
Vol 6 (2) ◽  
pp. 215-225
Author(s):  
Nazmul Islam Mazumder ◽  
Tania Sultana ◽  
Prtitish Chandra Paul ◽  
Dinesh Chandra Roy ◽  
Deboprio Roy Sushmoy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Salinity Tolerance ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Susceptible Variety ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Tolerant Line

Twenty six rice lines of PBRC (salt tolerant line-20) × BRRI dhan-29 were used to evaluate salinity tolerance at the seedling stage and tested for salt tolerance using RAPD markers. Salinity screening was done using hydrophonic system at the greenhouse following IRRI standard protocol. Among the studied line, ten were moderately salinity tolerant, nine susceptible and rest of the lines highly susceptible. For assessing genetic diversity and relationship of F3 rice lines including two parents were tested against PCR-based Random Amplified Polymorphic DNA (RAPD) technique using three arbitrary decamer primers; OPA02, OPC01, and OPC12. Selected three primers generated a total of 14 bands. Out of 14 bands, 12 bands (86.67%) were polymorphic and 2 bands (13.33%) were monomorphic. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters of the 28 rice genotypes. Most of the moderately tolerant lines and PBRC (STL-20) (tolerant variety) were grouped in same cluster due to lower genetic distance, while maximum susceptible along with BRRI dhan29 (susceptible variety) showed higher genetic distance with PBRC (STL-20) and moderately tolerant lines. This result indicates that the lines which formed grouped together, they are less diversed. On the other hand the lines remain in different clusters or different groups, are much diversed. Thus RAPD perform a potentially simple, rapid and reliable method to evaluate genetic diversity and molecular characterization as well. Res. Agric., Livest. Fish.6(2): 215-225, August 2019

scholarly journals Molecular characterization of oil seed Brassica using RAPD markers

2020 ◽  
Vol 55 (1) ◽  
pp. 1-8
Author(s):  
M Islam ◽  
A Habib ◽  
S Khan ◽  
S Akter ◽  
B Goswami ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Oil Seed ◽  
Pair Group ◽  
Brassica Spp ◽  
Breeding Programmes ◽  
High Level

Twelve varieties of oil seed Brassica spp. were characterized at molecular level using Random Amplified Polymorphic DNA (RAPD) primers to explore genetic diversity and to find out relationship among them. Twelve random primers used in the study generated 94 RAPD fragments and 53 (56.38%) of them were considered as polymorphic indicating high level of polymorphism within the materials. The size of amplified fragments ranged between 300-3000 bp. The values of pair-wise genetic distance ranged from 0.1613 to 0.5543. To find out phylogenetic relationships among the varieties, dendrogram based on Nei’s genetic distance was constructed using Unweighted Pair Group Method of Arithmetic Means (UPGMA) separating the 12 Brassica spp into two major clusters C1 and C2. This result will be useful for designing future breeding programmes for improvement of Brassica varieties. Bangladesh J. Sci. Ind. Res.55(1), 1-8, 2020

scholarly journals Identities and Relationships among Chinese Vegetable Brassicas as Determined by Random Amplified Polymorphic DNA Markers

1995 ◽  
Vol 120 (3) ◽  
pp. 548-555 ◽  
Author(s):  
Jianping Ren ◽  
James R. McFerson ◽  
Rugang Li ◽  
Stephen Kresovich ◽  
Warren F. Lamboy
Keyword(s):  
Chinese Cabbage ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Diversity Assessment ◽  
Wide Range ◽  
Chinese Vegetable ◽  
Vegetable Brassicas

Fifty-two germplasm accessions of Chinese vegetable brassicas were analyzed using 112 random amplified polymorphic DNA (RAPD) markers. The array of material examined spanned a wide range of morphological, geographic, and genetic diversity, and included 30 accessions of Brassica rapa L. (Chinese cabbage, pakchoi, turnip, and broccoletto), 18 accessions of B. juncea (L.) Czern. (leaf, stem, and root mustards), and four accessions of B. oleracea L. ssp. alboglabra (Chinese kale). The RAPD markers unambiguously identified all 52 accessions. Nei-Li similarities were computed and used in unweighed pair group method using arithmetic means (UPGMA) cluster analyses. Accessions and subspecies were clustered into groups corresponding to the three species, but some accessions of some subspecies were most closely related to accessions belonging to other subspecies. Values for Nei-Li similarities suggest that Chinese cabbage is more likely to have been produced by hybridization of turnip and pakchoi than as a selection from either turnip or pakchoi alone. RAPD markers are a fast, efficient method for diversity assessment in Chinese vegetable brassicas that complements techniques currently in use in genetic resources collections.

Revalidation and redescription of Serranus knysnaensis Gilchrist, 1904, (Perciformes: Serranidae) with a new distribution record

Zootaxa ◽  
2021 ◽  
Vol 5057 (1) ◽  
pp. 99-113
Author(s):  
YONELA SITHOLE ◽  
ELAINE HEEMSTRA ◽  
MONICA MWALE
Keyword(s):  
Dna Barcode ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Genetic Distances ◽  
Valid Species ◽  
Eastern Atlantic Ocean ◽  
Coi Sequences ◽  
Morphological And Molecular Data ◽  
Gill Raker ◽  
Distribution Record

A southwestern Indian Ocean (SWIO) percoid fish Serranus knysnaensis Gilchrist, 1904, was long synonymised with the comber, Serranus cabrilla (Linnaeus, 1758), from the eastern Atlantic Ocean, Mediterranean and Black Sea. However, when the species was brought out of synonymy by Heemstra & Heemstra (2004), reasons for this decision were not given. This study aims to revalidate the present taxonomic status of S. knysnaensis using morphological and molecular assessments. The two species are distinguished by the number of circumpeduncular scales (26–34 in S. knysnaensis versus 34–38 in S. cabrilla) and total gill rakers (18–22 versus 22–24). Serranus knysnaensis is also distinct from S. novemcinctus Kner, 1864, the other SWIO species of Serranus, based on total gill raker counts (18–22 versus 31–35). Genetic analysis of mitochondrial DNA barcode (COI) sequences for 17 Serranus species revealed three closely-related monophyletic clusters corresponding to S. cabrilla, S. novemcinctus and S. knysnaensis that were supported (P <0.001) by species delimitation methods. Even though the genetic distances among the three species were the lowest in the genus (1.60−1.99%), these species may be ecomorphs or lineages that have only recently diverged from each other. These three species also have allopatric distributions and our morphological and molecular data thus confirm that S. knysnaensis is a valid species.  

scholarly journals Barrier to Gene Flow Between Eastern and Western Populations of Cronartium ribicola in North America

2000 ◽  
Vol 90 (10) ◽  
pp. 1073-1078 ◽  
Author(s):  
R. C. Hamelin ◽  
R. S. Hunt ◽  
B. W. Geils ◽  
G. D. Jensen ◽  
V. Jacobi ◽  
...  
Keyword(s):  
Gene Flow ◽  
New Mexico ◽  
North America ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Genetic Distances ◽  
Group Method ◽  
Cronartium Ribicola ◽  
Western North America ◽  
Pair Group

The population structure of Cronartium ribicola from eastern and western North America was studied to test the null hypothesis that populations are panmictic across the continent. Random amplified polymorphic DNA markers previously characterized in eastern populations were mostly fixed in western populations, yielding high levels of genetic differentiation between eastern and western populations (φst = 0.55; θ = 0.36; P < 0.001). An unweighted pair-group method, arithmetic mean dendro-gram based on genetic distances separated the four eastern and four western populations into two distinct clusters along geographic lines. Similarly, a principal component analysis using marker frequency yielded one cluster of eastern populations and a second cluster of western populations. The population from New Mexico was clearly within the western cluster in both analyses, confirming the western origin of this recent introduction. This population was completely fixed (Hj = 0.000; n = 45) at all loci suggesting a severe recent population bottleneck. Genetic distances were low among populations of western North America (0.00 to 0.02) and among eastern populations (0.00 to 0.02), indicating a very similar genetic composition. In contrast, genetic distances between eastern and western populations were large, and all were significantly different from 0 (0.07 to 0.19; P < 0.001). Indirect estimates of migration were high among western populations, including the number of migrants among pairs of populations (Nm > 1) between New Mexico and British Columbia populations, but were smaller than one migrant per generation between eastern and western populations. These results suggest the presence of a barrier to gene flow between C. ribicola populations from eastern and western North America.

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