The use of RAPD markers in Hordeum phylogeny

Genome ◽  
1996 ◽  
Vol 39 (4) ◽  
pp. 646-654 ◽  
Author(s):  
Elizabeth F. Marillia ◽  
Graham J. Scoles
Keyword(s):  
Molecular Markers ◽  
Key Words ◽  
Phylogenetic Relationships ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Tree Topology ◽  
Binary Matrix ◽  
Phylogenetic Studies ◽  
Cultivated Barley ◽  
Hordeum Species

The phylogenetic relationships among 39 wild Hordeum species, subspecies, and cultivated barley were investigated using RAPD markers as discriminating characters. Seventy-six RAPD fragments were generated using 12 single decameric primers of arbitrary nucleotide sequences. Amplification reactions resulted in fragments ranging in length between 200 and 2000 bp. Clearly resolved bands were scored for their presence or absence in a binary matrix. Amplified products were treated as independent characters to generate a phenogram using the NTSYS-PC package. Tree topology was generally found to be consistent with those based on morphological treatments. However, a few species like H. erectifolium, H. jubatum and, to a lesser extent, H. bulbosum occupied a position different from previous classifications. The results demonstrated that RAPD technology represents a useful and reliable tool for detecting polymorphism for phylogenetic studies. Key words : RAPD analysis, molecular markers, phylogenetic studies, Hordeum species, barley.

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.

Comparative analysis of genetic relationships in barley based on RFLP and RAPD markers

Genome ◽  
1997 ◽  
Vol 40 (5) ◽  
pp. 607-616 ◽  
Author(s):  
Enrico Noli ◽  
Silvio Salvi ◽  
Roberto Tuberosa
Keyword(s):  
Molecular Markers ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Hordeum Vulgare L ◽  
Cluster Analyses ◽  
Barley Cultivars ◽  
Length Polymorphisms ◽  
Different Types ◽  
Marker Class

Genetic relationships have seldom been analyzed with different types of molecular markers in order to compare the information provided by each marker class. We investigated genetic relationships among nine barley cultivars using separate cluster analyses based on restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNAs (RAPDs). Genomic DNA restricted with three enzymes and hybridized with 68 probes revealed 415 RFLPs (74.2% of all bands). Among the 128 primers used for RAPD analysis, 100 provided a reproducible profile, 89 of which revealed 202 polymorphic and 561 monomorphic bands (26.5 and 73.5%, respectively). A nonrandom distribution of 62 RAPDs with a tendency to cluster near centromeric regions was produced when these RAPDs were mapped using 76 doubled-haploid lines derived from a cross between two of the nine cultivars. The correlation between the RFLP and RAPD similarity matrices computed for the 36 pairwise comparisons among the nine cultivars was equal to 0.83. The dendrograms obtained by cluster analyses of the RFLP and RAPD data differed. These results indicate that in barley the information provided by RFLPs and RAPDs is not equivalent, most likely as a consequence of the fact that the two marker classes explore, at least in part, different portions of the genome.Key words: Hordeum vulgare L., genetic distance, molecular markers, cluster analysis.

scholarly journals Phylogenetic Relationships in Actinidia as Revealed by RAPD Analysis

2002 ◽  
Vol 127 (5) ◽  
pp. 759-766 ◽  
Author(s):  
Hongwen Huang ◽  
Zuozhou Li ◽  
Jianqiang Li ◽  
Thomas L. Kubisiak ◽  
Desmond R. Layne
Keyword(s):  
Phylogenetic Relationships ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Southern China ◽  
Morphological Characters ◽  
Southeastern China ◽  
Wide Range ◽  
Average Similarity ◽  
Taxonomic Uncertainty ◽  
Upgma Phenogram

Phylogenetic relationships within the Actinidia were investigated using randomly amplified polymorphic DNA (RAPD) markers. DNAs from 40 taxa, including 31 species encompassing all four sections and four series of the traditional subdivisions within the genus, were amplified using 22 preselected 10-mer oligonucleotide primers. A total 204 DNA bands were scored across the 40 taxa, of which 188 (92%) were polymorphic. A wide range of genetic similarity was observed among the taxa (0.13 to 0.61). The average similarity between varieties of the same species was 0.54, and between different species was 0.28, respectively. Although the phylogenetic analysis revealed a clear indication that section Leiocarpae was a monophyletic group, subdivisions of the other three traditional sections were poorly supported. The UPGMA phenogram showed that the majority of the species clustered into geographic subgroups in accordance with their natural distribution (the Yangtzi River, southeastern China, southern China and southwestern China). The intrageneric subdivisions of Actinidia appeared to be difficult, but some subdivisions could be explained by the geographic distribution of the species, particularly for species of Liang's sections of Maculatae and Stellatae. The phylogenetic relationships among several species with previous taxonomic uncertainty are also discussed on the basis of the RAPD data. The results of this study supplement our previous understanding of the Actinidia taxonomy based solely on morphological characters.

Genetic Diversity of Basil (Ocimum spp. - Lamiaceae) Based on RAPD Markers and Volatile Oil Constituents

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 492f-493
Author(s):  
Roberto F. Vieira ◽  
James E. Simon ◽  
Peter Goldsbrough ◽  
Antonio Figueira
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Volatile Oil ◽  
Essential Oil Composition ◽  
Oil Composition ◽  
Traditional Medicines ◽  
The Tropics ◽  
High Degree ◽  
First Time

Essential oils extracted from basil (Ocimum spp.) by steam distillation are used to flavor foods, oral products, in fragrances, and in traditional medicines. The genus Ocimum contains around 30 species native to the tropics and subtropics, with some species naturalized and/or cultivated in temperate areas. Interand intraspecific hybridization have created significant confusion in the botanical systematics of this genus. Taxonomy of basil (O. basilicum) is also complicated by the existence of numerous varieties, cultivars, and chemotypes within the species that do not differ significantly in morphology. In this study we are using RAPD markers and volatile oil composition to characterize the genetic diversity among the most economically important Ocimum species. We hypothesize that the genetic similarity revealed by molecular markers will more accurately reflect the morphological and chemical differences in Ocimum than essential oil composition per se. Preliminary research using five Ocimum species, four undetermined species, and eight varieties of O. basilicum (a total of 19 accessions) generated 107 polymorphic fragments amplified with 19 primers. RAPDs are able to discriminate between Ocimum species, but show a high degree of similarity between O. basilicum varieties. The genetic distance between nine species and among 55 accessions within the species O. americanum, O. basilicum, O. campechianum, O. × citriodorum, O. gratissimum, O. kilimandscharium, O. minimum, O. selloi, and O. tenuiflorum will be analyzed by matrix of similarity and compared to the volatile oil profile. This research will for the first time apply molecular markers to characterize the genetic diversity of Ocimum associate with volatile oil constituent.

Rediscovery of Rhacophorus yaoshanensis and Theloderma kwangsiensis at their type localities after five decades

Zootaxa ◽  
2018 ◽  
Vol 4379 (4) ◽  
pp. 484 ◽  
Author(s):  
WEICAI CHEN ◽  
XIAOWEN LIAO ◽  
SHICHU ZHOU ◽  
YUNMING MO ◽  
YONG HUANG
Keyword(s):  
Mitochondrial Dna ◽  
16S Rrna ◽  
Phylogenetic Relationships ◽  
New Record ◽  
Nature Reserve ◽  
Guangxi Province ◽  
Preliminary Assessment ◽  
Phylogenetic Studies ◽  
Pairwise Divergence ◽  
High Support

Rhacophorus yaoshanensis Liu & Hu, 1962 and Theloderma kwangsiensis Liu & Hu, 1962 were described by Liu & Hu (1962) based on two specimens and one specimen, respectively, from the Dayaoshan Ranges, Guangxi, China. Since these two species were described, no additional specimens have been collected from their type localities, presenting an issue for phylogenetic studies of the genera. Five decades later, we have rediscovered R. yaoshanensis and T. kwangsiensis from their type localities. In this paper, we re-describe the two species and conduct a preliminary assessment of their phylogenetic relationships using two mitochondrial DNA genes (12S and 16S rRNA). The results indicate with high support that R. yaoshanensis is closely related to Rhacophorus pinglongensis. Theloderma kwangsiensis is nested within Theloderma corticale, with only 0.0–0.6% pairwise divergence, a level typical of intraspecific variation. Based on both molecular and morphological analyses, we further confirm that T. kwangsiensis is a synonym of T. corticale. Shiwandashan National Nature Reserve, Guangxi Province, China, is a new record for T. corticale. 

Phylogenetic relationships of five morphological groups of hexaploid wheat (Triticum aestivum L. em Thell.) based on RAPD analysis

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 724-727 ◽  
Author(s):  
Wenguang Cao ◽  
G Scoles ◽  
P Hucl ◽  
R N Chibbar
Keyword(s):  
Hexaploid Wheat ◽  
Phylogenetic Relationships ◽  
Genetic Similarity ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Triticum Aestivum L ◽  
Similarity Coefficients ◽  
Morphological Classification ◽  
Wild Wheat

The genetic relationships among the five groups of hexaploid wheat: common, spelta, macha, vavilovii, and semi-wild wheat (SWW) are not clear. Random amplified polymorphic DNA (RAPD) analysis was used to assess phylogenetic relationships among these five morphological groups of hexaploid wheat. RAPD data were analyzed using the NTSYS-PC computer program to generate Jaccard genetic similarity coefficients. A dendrogram based on RAPD analysis grouped 15 accessions into five distinct clusters. These results are in agreement with those based on morphological classification, suggesting that common wheat is most closely related to SWW, followed by spelta, vavilovii, and macha.Key words: RAPD, macha, spelta, vavilovii, semi-wild wheat, phylogenetic relationships.

Evaluation of Genetic Diversity in Castor (Ricinus communis L.) using RAPD Markes

2011 ◽  
Vol 343-344 ◽  
pp. 981-987
Author(s):  
Feng Juan Li ◽  
Chang Lu Wang ◽  
Dong He ◽  
Ya Qiong Liu ◽  
Mian Hua Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Genetic Distance ◽  
Oil Content ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Ricinus Communis ◽  
Major Group ◽  
Ricinus Communis L ◽  
Polymorphic Bands

RAPD markers are used to study the genetic diversity of the main planting on 37 castor varieties widely cultivated in china according to the oil content and other characteristic of different castor varieties. Genetic distance of 37 Chinese castor varieties is studied by RAPD markers analysis. RAPD analysis shows that a total of 122 bands are amplified from random primers of 20 S series, including 71 polymorphic bands with polymorphic rate of 58.20%. 37 castor beans are divided into four major groups in the phylogenetic tree. One castor germplasm is included in1, 2, 3 groups respectively, and two sub-groups are included in the 4 major group.

Reaction of Hordeum species to the smut fungi Ustilago nuda and U. tritici

1987 ◽  
Vol 65 (10) ◽  
pp. 2024-2027 ◽  
Author(s):  
J. Nielsen
Keyword(s):  
Hordeum Chilense ◽  
Smut Fungi ◽  
New Hosts ◽  
Cultivated Barley ◽  
Ustilago Nuda ◽  
Hordeum Species ◽  
Eleven Species

Eleven species of Hordeum were tested for their reaction to Ustilago nuda (Jens.) Rostr. and U. tritici (Pers.) Rostr., the causes of the embryo-infecting loose smuts of cultivated barley and wheat, respectively. The species Hordeum chilense and H. depressum were resistant, while H. euclaston, H. halophilum, H. procerum, H. pusillum, and H. stenostachys were susceptible to both fungi. Hordeum muticum was susceptible only to U. nuda, while H. arizonicum, H. lechleri, and H. roshevitzii were susceptible only to U. tritici. The susceptible species are new hosts for these pathogens. It is proposed that these results, together with those of an earlier study, indicate that U. nuda evolved from U. tritici.

Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 201-210 ◽  
Author(s):  
F. N. Wachira ◽  
R. Waugh ◽  
W. Powell ◽  
C. A. Hackett
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Southeast Asia ◽  
Camellia Sinensis ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Systematic Assessment ◽  
Tree Crop ◽  
Taxonomic Relationships

Camellia sinensis is a beverage tree crop native to Southeast Asia and introductions have been made into several nonindigenous countries. No systematic assessment of genetic variability in tea has been done anywhere. In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and taxonomic relationships in 38 clones belonging to the three tea varieties, assamica, sinensis, and assamica ssp. lasiocalyx. Extensive genetic variability was detected between species, which was partitioned into between and within population components. Seventy percent of the variation was detected within populations. Analyses based on band sharing separated the three populations in a manner consistent with both the present taxonomy of tea and with the known pedigrees of some clones. RAPD analysis also discriminated all of the 38 commercial clones, even those which cannot be distinguished on the basis of morphological and phenotypic traits.Key words: genetic diversity, RAPDs, Camellia sinensis.

Morphological and phylogenetical analyses of pathogenic Hypomyces perniciosus isolates from Agaricus bisporus causing wet bubble disease in China

Phytotaxa ◽  
2021 ◽  
Vol 491 (2) ◽  
pp. 115-130
Author(s):  
CHUN-LAN ZHANG ◽  
ZHENG-WEN JIN ◽  
CAN SUN ◽  
ODESHNEE MOODLEY ◽  
JI-ZE XU ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Agaricus Bisporus ◽  
Morphological Characteristics ◽  
Pathogenicity Test ◽  
Test Results ◽  
Phylogenetic Studies ◽  
Group Ii

Hypomyces perniciosus is a destructive pathogen of Agaricus bisporus. The disease has been known to occur wherever A. bisporus is cultivated. Morphological characteristics have shown differences between reported isolates of H. perniciosus. However, clarification is needed to determine whether those isolates are the same species and an investigation of the phylogenetic relationships among them is warranted. Here, taxonomic and phylogenetic studies were carried out on 29 wet bubble disease pathogen isolates from China. Our analyses of the morphological characteristics and phylogenetic results support that they are the same H. perniciosus. Moreover, they are separated into two groups, groups ⅰ and groups ii. Pathogenicity test results inferred that group ii had weaker pathogenicity than group ⅰ. Consequently, we can deduce that wet bubble disease is still caused by H. perniciosus and isolates from two distinct groups.

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