Application of RAPD and ISSR markers to analyse molecular relationships in Grevillea (Proteaceae)

2004 ◽  
Vol 17 (1) ◽  
pp. 49 ◽  
Author(s):  
M. Pharmawati ◽  
G. Yan ◽  
I. J. McFarlane
Keyword(s):  
Phylogenetic Trees ◽  
Genetic Relationships ◽  
Initial Point ◽  
Morphological Characteristics ◽  
Issr Markers ◽  
Group Method ◽  
Pair Group ◽  
Molecular Relationships ◽  
Group B ◽  
Rapd And Issr

The potential of RAPD and ISSR markers to construct molecular relationships of Grevillea was evaluated with 23 RAPD and 12 ISSR primers. The 16 genotypes representing 12 species and 3 subspecies of Grevillea were sampled from the collection of the Mt Anann Botanic Garden, NSW. RAPD and ISSR assays generated a total of 401 RAPD and 280 ISSR fragments. High frequencies of polymorphisms, 99.39% for RAPD and 99.51% for ISSR, were detected by both markers. Three statistical approaches were employed to construct phylogenetic relationships from combined RAPD and ISSR data. Cluster analysis by the unweighted pair group method (UPGMA) of Jaccard's similarity and Neighbour-Joining analysis of total character difference generated dendograms with similar topology. Parsimony analysis also generated a tree that was in broad agreement with the two dendograms. The phylogenetic trees divided the Grevillea species studied into three groups. Group A consisted of G. buxifolia subsp. buxifolia, G. phylicoides and G. sphacelata. In group B, G. mucronulata was grouped together with G. montana, while G. diffusa, G. humilis, G. linearifolia, G. molyneuxii, G. oldei, G. sericea and G. speciosa formed group C. This molecular result was comparable to groupings suggested by a previous author (Makinson 2000) based on morphological characteristics. However, in contrast to the morphological taxonomy, molecular phylogeny suggests that G. oldei and G. speciosa belong to the same subgroup sensu Makinson (2000), whereas G. linearifolia and G. molyneuxii should not be placed in their originally suggested subgroups sensu Makinson (2000). The present study is the first published report on molecular relationships of Grevillea and can be considered as an initial point for further research on the genetic relationships and evolution of Grevillea.

Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

1996 ◽  
Vol 26 (8) ◽  
pp. 1454-1462 ◽  
Author(s):  
Naoki Tani ◽  
Nobuhiro Tomaru ◽  
Masayuki Araki ◽  
Kihachiro Ohba
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Phylogenetic Trees ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Group Method ◽  
Stone Pine ◽  
Arithmetic Means ◽  
Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

Genetic relatedness among cultivated and wild mulberry (Moraceae: Morus) as revealed by inter-simple sequence repeat analysis in China

2006 ◽  
Vol 86 (1) ◽  
pp. 251-257 ◽  
Author(s):  
Zhao Weiguo ◽  
Zhou Zhihua ◽  
Miao Xuexia ◽  
Wang Sibao ◽  
Zhang Lin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Pair Group ◽  
Simple Sequence

The genetic diversity of 27 mulberry (Morus spp.) genotypes mainly from China was investigated using inter-simple sequence repeat (ISSR) markers to assist in addressing breeding objectives and conserving existing genetic resources. Of the 22 primers screened, 15 produced highly reproducible ISSR bands. Using these 15 primers, 138 discernible DNA fragments were generated with 126 (91.3%) being polymorphic, indicating considerable genetic variation among the mulberry genotypes studied. Genetic similarity ranged from 0.6014 between Yu 2 and Yu 711 to 0.9493 between Cuizhisang and Dejiang 10. The phenetic dendrogram based on ISSR data generated by the unweighed pair group method with arithmetical averages (UPGMA) method grouped the 27 accessions into two major clusters: cluster I, cultivated mulberry species (M. multicaulis Perr., M. alba Linn., M. atropurpurea oxb., M. bombycis Kiodz., M. australis Poir., M. rotundiloba Kiodz., M. alba var. pendula Dipp., M. alba var. macrophylla Loud., and M. alba var. venose Delile.); and cluster II, wild mulberry species (M. cathayana Hemsl., M. laevigata Wall., M. wittiorum Hand-Mazz., M. nigra Linn., and M. mongolica Schneid.). Our molecular analyses agree with the existing morphological classification of Morus and clarify the genetic relationships among mulberry species. Key words: Morus L., genetic diversity, inter-simple sequence repeat, relatedness

scholarly journals Distinguishing grapefruit and pummelo accessions using ISSR markers

2010 ◽  
Vol 46 (No. 4) ◽  
pp. 170-177 ◽  
Author(s):  
A. Uzun ◽  
O. Gulsen ◽  
T. Yesiloglu ◽  
Y. Aka-Kacar ◽  
O. Tuzcu
Keyword(s):  
Citrus Fruit ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Citrus Paradisi ◽  
Arithmetic Average ◽  
Pair Group ◽  
Citrus Maxima ◽  
Group B ◽  
Citrus Hassaku

Grapefruit is the fourth economically most important citrus fruit in the world. In this research Inter-Simple Sequence Repeat (ISSR) markers were used to distinguish twenty-nine grapefruit (Citrus paradisi Macf.), five pummelo (Citrus maxima (Burm.) Merr.) and one Citrus hassaku Hort. Ex Tanaka accessions. Twelve ISSR primers produced a total of 100 fragments and 62 of them were polymorphic. The number of average polymorphic fragments per primer was 5.2. The mean polymorphism information content (PIC) was 0.37. The unweighted pair group method arithmetic average (UPGMA) analysis demonstrated that the accessions had a similarity range from 0.79 to 1.00. The accessions were separated into two main clusters; group A with five pummelos and group B with grapefruits. In the pummelo cluster, all pummelos were distinguished whereas in the grapefruit cluster some accessions were not clearly separated. There was a low level of variation in the grapefruits due to their mutation origin.

scholarly journals Isolation, Characterization, and Evaluation of Microsatellite Loci for Cultivar Identification in the Ornamental Pampas Grass Cortaderia selloana

2006 ◽  
Vol 131 (4) ◽  
pp. 499-505 ◽  
Author(s):  
Riaz Ahmad ◽  
Miki Okada ◽  
Jeffrey L. Firestone ◽  
Chris R. Mallek ◽  
Marie Jasieniuk
Keyword(s):  
Microsatellite Loci ◽  
Genetic Relationships ◽  
Morphological Characteristics ◽  
Clonal Plants ◽  
The United States ◽  
Bootstrap Support ◽  
Group Method ◽  
Genomic Libraries ◽  
Pair Group ◽  
Cortaderia Selloana

We isolated and characterized microsatellite loci in the ornamental pampas grass Cortaderia selloana (Schult. & Schult. f.) Asch. & Graebn. for purposes of identifying cultivars and assessing genetic relationships among cultivars. Small insert genomic libraries were enriched for dinucleotide (CT)n and (CA)n repeats. Ninety clones were sequenced of which 76% contained at least one microsatellite with a basic motif greater than six repeat units. Nine primer pairs amplified 10 polymorphic and putatively disomic loci, and were used to genotype 88 individuals representing 17 named cultivars and four selections. In total, 93 alleles were detected with a maximum of two to 19 per locus. Effective number of alleles varied from 1.3 to 9.5. Observed heterozygosity ranged from 0.07 to 0.81. The 10 microsatellite loci distinguished the majority of pampas grass cultivars. An unweighted pair group method with arithmetic mean (UPGMA) cluster analysis, based on proportion of shared alleles among individuals, revealed groups of cultivars corresponding to origin and morphological characteristics. With few exceptions, individuals of a single cultivar clustered together with moderate to strong bootstrap support (greater than 50%). Interestingly, `Pumila' from Europe and the United States formed separate clusters indicating independent origins. A large, diverse cluster with low bootstrap support consisted of selections and cultivars sold as seed, rather than potted or bare-root clonal plants. Primers designed for C. selloana amplified microsatellite loci in other Cortaderia Stapf species concordant with phylogenetic relationships among the species. Cross-amplification was 100% in C. jubata (Lemoine ex Carrière) Stapf; 77% in C. pilosa (d'Urv.) Hack. and C. rudiuscula Stapf; 66% in C. fulvida (Buch.) Zotov; and 55% in C. richardii (Endl.) Zotov and C. toetoe Zotov.

scholarly journals Phylogenetic relationships among the taxa of the genus Johrenia DC. (Apiaceae) from Turkey based on molecular method

2010 ◽  
Vol 17 (2) ◽  
pp. 113-120 ◽  
Author(s):  
Bekir Dogan ◽  
Ahmet Duran ◽  
Yavuz Bagci ◽  
Muhittin Dinc ◽  
Esra Martin ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Phylogenetic Relationships ◽  
Issr Markers ◽  
Arithmetic Mean ◽  
Group Method ◽  
Molecular Method ◽  
Pair Group ◽  
Plant Taxon ◽  
Molecular Relationships ◽  
Unweighted Pair Group Method

In the present study, ISSR markers were employed to determine the phylogenetic relationships among the taxa of Johrenia. The genera Angelica and Xanthogalum were selected as outgroups. Unweighted pair group method with arithmetic mean (UPGMA) and Principal Coordinate Analyses were conducted to view the molecular relationships. Johrenia alpina, J. depauperatum and J. aurea are transferred to the genus Dichoropetalum. The infrageneric and intergeneric phylogenetic relationship among the Johrenia and Dichoropetalum genera are determined.Keywords: Johrenia; Dichoropetalum; Apiaceae; Taxonomy; ISSR; Turkey.DOI: 10.3329/bjpt.v17i2.6693Bangladesh J. Plant Taxon.17(2): 113-120, 2010 (December)

Genetic relationships among some Turkish Petrorhagia (Ser.) Link (Caryophyllaceae) taxa using ISSR markers

Phytotaxa ◽  
2016 ◽  
Vol 272 (2) ◽  
pp. 165 ◽  
Author(s):  
MUHİP HİLOOĞLU ◽  
İLHAM ERÖZ POYRAZ ◽  
İSMAİL POYRAZ ◽  
EBRU ATAŞLAR ◽  
EMEL SÖZEN
Keyword(s):  
Genetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Pair Group ◽  
Outgroup Species ◽  
Simple Sequence ◽  
Nei's Genetic Distance ◽  
Issr Primers

A study of the genetic relationships among Petrorhagia taxa from Turkey was carried out using inter-simple sequence repeat (ISSR) markers. A total of 409 amplified bands were obtained by 10 ISSR primers. The polymorphism ratio was high (100%) across 45 individuals representing nine Petrorhagia taxa (P. dubia, P. prolifera, P. pamphylica, P. peroninii, P. saxifraga, P. cretica, P. alpina subsp. alpina, P. alpina subsp. olympica, P. lycica) and was sufficient to distinguish each species. Statistical analyses were performed by using POPGENE, GenAlEx6, and PAUP. An unweighted pair-group method with arithmetic mean (UPGMA) dendrogram was constructed based on Nei’s genetic distance along with outgroup species (Velezia rigida) in MEGA4. The dendrogram shows two main clusters, the first one (Cluster-I) included only P. lycica, while the cluster-II contained all other taxa. Cluster-II can be grouped in two sub-clusters, with P. prolifera and P. saxifraga constituting a first sub-cluster, the other species (P. alpina subsp. alpina, P. alpina subsp. olympica, P. cretica, P. dubia, P. peroninii and P. pamphylica) being grouped in a second sub-cluster. Both PCoA and Neighbour-Net network analysis supported the dendrogram. The study showed that ISSR technique can be successfully used in species identification and determination of the genetic relationships between Petrorhagia species distributed in Turkey.

scholarly journals Application of ISSR Markers to Fingerprinting of Elite Cultivars (Varieties/Clones) From Different Sections of the Genus Populus L.

2006 ◽  
Vol 55 (1-6) ◽  
pp. 1-6 ◽  
Author(s):  
J. Gao ◽  
S. Zhang ◽  
L. Qi ◽  
Y. Zhang ◽  
C. Wang ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Molecular Techniques ◽  
Group Method ◽  
Arithmetic Average ◽  
Clear Cut ◽  
Pair Group

AbstractThe Inter-Simple Sequence Repeat (ISSR) was used in this study for genetic fingerprinting and identification of 28 important Populus L. (poplar) cultivars (varieties/ clones), and determination of the genetic relationships among these cultivars. These 28 cultivars belonged to sections Aigeiros, Tacahamaca, Leuce, Turanga, and hybrids between sections Aigeiros and Tacahamaca. Out of 27 ISSR primers tested, eight primers generated clear multiplex profiles. The best three primers produced 154 easily detectable fragments, 129 (84%) of which were polymorphic among the cultivars. Each of these 3 primers produced fingerprint profiles unique to each of the accessions studied, and thus could be solely used for their identification. Twenty-five markers, unique to 10 of the cultivars studied, were detected. These markers may be converted into cultivar-specific probes for identification purposes. Genetic relationships among the cultivars were evaluated by generating a similarity matrix based on the simple matching coefficient and the unweighted pair group method with arithmetic average (UPGMA) dendrogram. The results showed a clear-cut separation of cultivars among different sections of poplar, and were in agreement with the genealogy of the sampled cultivars. The present study shows that ISSR markers could generate abundant polymorphism, are reproducible, and are quick for characterization of poplar cultivars. In the future, the markers used in this study, in combination with other molecular techniques, could provide a useful panel of ISSR markers for largescale DNA fingerprinting of poplar cultivars and determination of the genetic relationships among these cultivars.

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Genetic Distances ◽  
Table Grape ◽  
Group Method ◽  
Molecular Characteristics ◽  
Table Grapes ◽  
Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

scholarly journals Genetic Relationships Among Representatives of Dasypyrum, Secale and Triticum Species Revealed with RAPD and ISSR Markers

2014 ◽  
Vol 42 (2) ◽  
pp. 420-430
Author(s):  
Agnieszka GRADZIELEWSKA ◽  
Mirosław TYRKA ◽  
Justyna LESNIOWSKA-NOWAK ◽  
Justyna NAZARUK
Keyword(s):  
Gene Diversity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Genetic Distances ◽  
Fixation Index ◽  
Triticum Species ◽  
The Difference ◽  
Bridge Species ◽  
Differentiation Gene ◽  
Rapd And Issr

In this study the genetic similarity among Dasypyrum, Secale andTriticum species with RAPDs and ISSRs was analyzed. To show a level of similarity between the species, 12 populations of Dasypyrum (11 D. villosum and 1 D. breviaristatum), together with 12 accessions belonging to 3 Secale species and 12 accessions from 4 Triticum species were used. Genetic distances (GD) and bootstrap values were calculated and PCA analysis was conducted to present the relationships among the species. To estimate the genetic structure among and inside genera, as well as population differentiation, gene diversity (He), total genetic variation (Ht) and Wright’s fixation index (Fst) were computed. The highest values were found in Triticum, within which Ht was equal to 0.332±0.023 and Fst was 0.42. It confirmed that the material studied was highly differentiated. Both systems found Dasypyrum more related with Triticum, as compared to Secale. With RAPDs, genetic distance (GD) between Triticum and Dasypyrum was 0.435, respectively 0.460 for Secale vs Dasypyrum. In the case of ISSRs these values were 0.374 and 0.407, respectively. Despite the fact that the difference between the two GD indices was insignificant, one should not exclude the possibility of successful hybridization of Dasypyrum and Secale, especially when using bridge species.

scholarly journals Assessment of Genetic Relationships among Philodendron Cultivars Using AFLP Markers

2004 ◽  
Vol 129 (5) ◽  
pp. 690-697 ◽  
Author(s):  
Pachanoor S. Devanand ◽  
Jianjun Chen ◽  
Richard J. Henny ◽  
Chih-Cheng T. Chao
Keyword(s):  
Genetic Similarity ◽  
Near Infrared ◽  
Genetic Relationships ◽  
Aflp Markers ◽  
Group Method ◽  
Limited Information ◽  
Similarity Coefficients ◽  
Arithmetic Average ◽  
Ornamental Foliage Plants ◽  
Pair Group

Philodendrons (Philodendron Schott) are among the most popular tropical ornamental foliage plants used for interior decoration. However, limited information is available on the genetic relationships among popular Philodendron species and cultivars. This study analyzed genetic similarity of 43 cultivars across 15 species using amplified fragment length polymorphism (AFLP) markers with near infrared fluorescence labeled primers. Forty-eight EcoR I + 2/Mse I + 3 primer set combinations were screened, from which six primer sets were selected and used in this investigation. Each selected primer set generated 96 to 130 scorable fragments. A total of 664 AFLP fragments were detected, of which 424 (64%) were polymorphic. All cultivars were clearly differentiated by their AFLP fingerprints, and the relationships were analyzed using the unweighted pair-group method of arithmetic average cluster analysis (UPGMA) and principal coordinated analysis (PCA). The 43 cultivars were divided into five clusters. Cluster I comprises eight cultivars with arborescent growth style. Cluster II has only one cultivar, `Goeldii'. There are 16 cultivars in cluster III, and most of them are self-heading interspecific hybrids originated from R.H. McColley's breeding program in Apopka, Fla. Cluster IV contains 13 cultivars that exhibit semi-vining growth style. Cluster V has five cultivars that are true vining in morphology, and they have lowest genetic similarity with philodendrons in other clusters. Cultivated philodendrons are generally genetically diverse except the self-heading hybrids in cluster III that were mainly developed using self-heading and semi-vining species as parents. Seven hybrid cultivars have Jaccard's similarity coefficients of 0.88 or higher, suggesting that future hybrid development needs to select parents with diverse genetic backgrounds.

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