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.

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.

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 Genetic variability in sugarcane (Saccharum spp. hybrid) genotypes through inter simple sequence repeats (ISSR) markers

2016 ◽  
Vol 8 (3) ◽  
pp. 1404-1409 ◽  
Author(s):  
Vivekanand P. Rao ◽  
Sanjay Singh ◽  
R. Chaudhary ◽  
M. K. Sharma ◽  
R.S. Sengar ◽  
...  
Keyword(s):  
Polymorphic Information Content ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Genomic Diversity ◽  
Group Method ◽  
Saccharum Spp ◽  
Arithmetic Average ◽  
Sugarcane Varieties ◽  
Pair Group ◽  
Simple Sequence

In the present study, 14 sugarcane (Saccharum spp. hybrid) genotypes were used for genomic diversity analysis based on nineteen inter simple sequence repeat (ISSR). These nineteen sets of ISSR markers generated a total of 164 discernible and reproducible bands including 109 polymorphic and 55 monomorphic bands. The unweighted pair group method with arithmetic average (UPGMA) analysis revealed three distinct clusters: I, II and III within the 14 genotypes. The polymorphic information content (PIC) value per locus ranged from 0.14 (UBC811) to 0.53 (ISSR1) locus with an average of 0.42 for all loci. The range of genetic distance or coefficient of similarity among sugarcane genotypes varied 0.14 - 0.78. The analysis of these similarities matrix revealed that greater similarity between CoS03234 and CoSe1424 (0.78), and lowest similarity between CoS03234 and Co0118 (0.14). The knowledge gained in this study would be useful to future breeding programs for increasing genetic diversity of sugarcane varieties and cultivars to meet the increasing demand of sugarcane cultivation for sugar and bio energy uses.

scholarly journals Phylogenetic Relationships among Selected Citrus Germplasm Accessions Revealed by Inter-simple Sequence Repeat (ISSR) Markers

1998 ◽  
Vol 123 (4) ◽  
pp. 612-617 ◽  
Author(s):  
Deqiu Fang ◽  
Robert R. Krueger ◽  
Mikeal L. Roose
Keyword(s):  
Phylogenetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Genetic Distances ◽  
Group Method ◽  
Sour Orange ◽  
Arithmetic Average ◽  
Pair Group ◽  
Citrus Germplasm ◽  
Group 5

ISSR markers were analyzed to study phylogenetic relationships among 46 Citrus L. accessions representing 35 species. A dendrogram based on the unweighted pair-group method, arithmetic average cluster analysis was constructed using a similarity matrix derived from 642 polymorphic ISSR fragments generated by 10 primers. These 46 accessions could be classified into five major groups: 1) C. indica Tan.; 2) C. maxima (Burm.) Merrill; 3) lemon [C. limon (L.) Burm.] or lime [C. aurantifolia (Christm.) Swingle] type accessions; 4) C. halimii B. C. Stone; and 5) sour orange (C. aurantium L.), mandarins and their hybrids. Group 5 was further divided into three subgroups. Although some previous work had grouped it with mandarins, C. indica appeared to be a distinct genotype or species that was not close to mandarins. C. tachibana Tan. grouped closely to mandarins. C. vulgaris Risso was not related to sour orange but was similar to accessions usually classified in the lime or lemon group. Sour orange and its hybrids, C. nippokoreana Tan., C. hanayu Hort. ex Shirai, C. sudachi Hort. ex Shirai, and C. yuko Hort. ex Tan. had close phylogenetic relationships with mandarins. Although the mandarin accessions studied were divergent in morphology, the genetic distances among them were relatively small. Relationships among these Citrus accessions revealed by ISSR markers were generally in agreement with previous taxonomic classifications.

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.

Inter Simple Sequence Repeat (ISSR) markers to assess genetic diversity and relatedness within strawberry genotypes

2008 ◽  
Vol 88 (2) ◽  
pp. 313-322 ◽  
Author(s):  
S. C. Debnath ◽  
S. Khanizadeh ◽  
A. R. Jamieson ◽  
C. Kempler
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Similarity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Breeding Lines ◽  
Pair Group ◽  
Simple Sequence

The goal of this study was to determine the level of genetic diversity and relatedness among 16 strawberry (Fragaria H ananassa Duch.) cultivars and 11 breeding lines developed in Canada, using Inter Simple Sequence Repeat (ISSR) markers. Seventeen primers generated 225 polymorphic ISSR-PCR bands. Cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) revealed a substantial degree of genetic similarity among the genotypes ranging from 63 to 77% that were in agreement with the principal coordinate (PCO) analysis. Geographical distribution for the place of breeding program explained only 1.4% of total variation as revealed by analysis of molecular variance (AMOVA). The ISSR markers detected a sufficient degree of polymorphism to differentiate among strawberry genotypes, making this technology valuable for cultivar identification and for the more efficient choice of parents in current strawberry breeding programs. Key words: Fragaria × ananassa, DNA fingerprinting, multivariate analysis, breeding, genetic similarity

Genetic diversity and relationships among Secale L. based on RAMP markers

2004 ◽  
Vol 1 (2) ◽  
pp. 73-78 ◽  
Author(s):  
Shang Hai-Ying ◽  
Zheng You-Liang ◽  
Wei Yu-Ming ◽  
Wu Wei ◽  
Yan Ze-Hong
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Group Method ◽  
Transitional Region ◽  
Arithmetic Average ◽  
Pair Group ◽  
Broad Leaf ◽  
Polymorphic Bands ◽  
High Level

AbstractGenetic diversity and relationships among 21 accessions of Secale L., including three species and 10 subspecies, were evaluated using RAMP markers. Forty-one out of 80 (50.5%) RAMP primers, which produced clear and polymorphic bands, were selected for PCR amplification of genomic DNA. A total of 446 bands were amplified from the 41 primers, and 428 of these bands (about 96%) were polymorphic. Three to 19 polymorphic bands could be amplified from each primer, with an average of 10.4 bands. The RAMP-based genetic similarity (GS) values among the 21 Secale accessions ranged from 0.266 to 0.658, with a mean of 0.449. A high level of genetic variation was found between or within the wild populations and the cultivars. Based on the GS matrix, a dendrogram was constructed using the unweighted pair group method with arithmetic average (UPGMA). All 21 accessions could be distinguished by RAMP markers. Clustering results showed that the genetic diversity of Secale based on RAMP markers was correlated with geographical distribution. Six rye cultivars, originating from Poland, Portugal, Mexico, Hungary, Armenia and Ukraine, were clustered into one group. The six countries are all located in the transitional region of broad-leaf forests between maritime and continental temperate zones, with narrow latitude span. In comparison, the other five cultivars from countries scattered over a region with large latitude span were distributed within different groups or subgroups. Genetic relationships based on RAMP markers had great deviation from the original taxonomy. Some subspecies of the same species were distributed within different groups, while some accessions of different species were closely clustered into one subgroup. These results suggest that RAMP markers could be an effective technique for detecting genetic diversity among Secale and give some useful information about its phylogenic relationships.

Genetic Diversity of an Alien Invasive Plant Mexican Sunflower (Tithonia diversifolia) in China

Weed Science ◽  
2012 ◽  
Vol 60 (4) ◽  
pp. 552-557 ◽  
Author(s):  
Jing Yang ◽  
Ling Tang ◽  
Ya-Li Guan ◽  
Wei-Bang Sun
Keyword(s):  
Genetic Diversity ◽  
Native Species ◽  
Invasive Plant ◽  
Genetic Relationships ◽  
Geographic Distance ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Chromosome Count ◽  
Group Method ◽  
Arithmetic Means

Mexican sunflower is a native species of North and Central America that was introduced into China early last century, but it has widely naturalized and become a harmful invasive plant in tropical and subtropical regions in South China. Inter-simple sequence repeat (ISSR) markers were employed to assess genetic diversity and variation in Mexican sunflower populations from China and neighboring regions. The karyotypes of populations were also studied. Our research showed high levels of genetic diversity in all populations. The lowest genetic diversity estimates were represented in two populations in Laos, suggesting prevention of new introductions into Laos is critical. Partitioning of genetic variance revealed that genetic variation was mostly found within populations, and unweighted pair group method with arithmetic means (UPGMA) analysis showed that the introductions into China and Laos were independent. There were no obvious correlations between genetic relationships and geographic distance of populations in China, consistent with the human associated dispersal history of Mexican sunflower. Previous cytological data and our chromosome count (2n = 34) and karyotype analysis showed chromosome stability among populations. The high levels of genetic diversity within invasive Mexican sunflower populations could be challenging for its management in China, and further expansion and potential negative effects on ecological systems of this plant should be monitored.

scholarly journals Discrimination among Cultivars of Cabbage Using Randomly Amplified Polymorphic DNA Markers

HortScience ◽  
2000 ◽  
Vol 35 (6) ◽  
pp. 1155-1158 ◽  
Author(s):  
Rogério L. Cansian ◽  
Sergio Echeverrigaray
Keyword(s):  
Rapd Markers ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Base Pairs ◽  
Arithmetic Average ◽  
Pair Group ◽  
Similarity Indices ◽  
Upgma Cluster Analysis ◽  
Group A

Randomly amplified polymorphic DNA (RAPD) markers were used to discriminate among 16 commercial cultivars of cabbage (Brassica oleracea L. Capitata Group). A set of 18 decamer primers was selected from 100 random sequences and used to characterize cultivars and to evaluate distances. The selected primers produced 105 (54%) polymorphic bands ranging in size from 100 and 2500 base pairs, out of a total of 195 bands, which allowed for discrimination of all cultivars. Similarity indices between cultivars were computed from RAPD data, and ranged from 0.72 to 0.87 with an average of 0.82. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis revealed two groups, one formed by two cultivars recommended for summer cropping, and the other by 14 cultivars. This large group was additionally divided into two subgroups. RAPD analysis provides a quick and reliable alternative for the identification of cabbage cultivars and for determination of the relationships among them.

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