scholarly journals Assessment of Genetic Relationships among Cultivated and Wild Pistachios (Pistacia vera L.) using Molecular Markers

2019 ◽  
Vol 27 (1) ◽  
pp. 37-46 ◽  
Author(s):  
Mohammad Aref Pourian ◽  
Davood Bakhshi ◽  
Ali Aalami ◽  
Hossein Hokmabadi
Keyword(s):  
Genetic Relationships ◽  
Genetic Erosion ◽  
Inter Simple Sequence Repeat ◽  
Group Method ◽  
Pistacia Vera ◽  
Wild Type ◽  
Persian Empire ◽  
Breeding Programs ◽  
Mean Values ◽  
Pair Group

Abstract Iran is one of the main diversity centers and origins of pistachios in the world. Pistachio cultivation spread first within the ancient Persian Empire and then moved gradually westward. Knowledge of the genetic relationships among wild and cultivated varieties of pistachio is important for the efficient utilization of the available germplasm resources. Three molecular marker strategies, namely, inter-simple sequence repeat (ISSR), inter-retrotransposon amplified polymorphism (IRAP), and retrotransposon microsatellite amplified polymorphism (REMAP), were used to study the genetic relationships among 35 pistachio accessions including 15 wild-type genotypes of Pistacia vera and 20 important cultivars from Iran. According to the results, high levels of polymorphism were observed for all three marker systems. REMAP and IRAP techniques had the higher mean values of genetic relationships parameters than ISSR technique. The results from this study showed that the 5′LTR2, Sukkula, Sukkula + UBC855, and 5′LTR2 + UBC811 primers were the most informative and could be used to evaluate the genetic relationships of pistachios accessions. Cluster analysis using the unweighted pair group method with arithmetic mean (UPGMA) properly separated the accessions and divided them into four main groups. The presence of most cultivated genotypes in a group indicates genetic erosion of cultivated pistachio in Iran. Wild-type genotypes of P. vera are located in different clusters indicating the high diversity of the genotypes. The results provide useful genetic information about wild pistachios in northeastern of Iran and indicate that the use of wild pistachios in breeding programs could be useful for generating new genotypes with interesting characters.

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 Identification of Sour Orange Accessions and Evaluation of Their Genetic Variability by Molecular Marker Analyses

HortScience ◽  
2006 ◽  
Vol 41 (1) ◽  
pp. 84-89 ◽  
Author(s):  
Mirko Siragusa ◽  
Fabio De Pasquale ◽  
Loredana Abbate ◽  
Nicasio Tusa
Keyword(s):  
Genetic Variability ◽  
Genetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Group Method ◽  
Sour Orange ◽  
Pair Group ◽  
Polymerase Chain ◽  
Relationship Of ◽  
Simple Sequence ◽  
Issr Primers

A collection of 18 accessions of sour orange (Citrus aurantium L.) coming from Sicily and other countries was investigated by two polymerase chain reaction (PCR)-based DNA marker technologies. Ten inter-simple sequence repeat (ISSR) primers and fifteen randomly amplified polymorphic DNA (RAPD) primers were used to identify and to evaluate the genetic variability and relationship of accessions. A total of 111 ISSR and 145 RAPD amplified fragments were used to estimate the Dice's coefficient of similarity for cluster analysis using a unweighted pair-group method using an arithmetic averaging (UPGMA) algorithm. The genetic relationships identified using ISSR and RAPD markers were highly concordant, such that the correlation between ISSR and RAPD genetic distance (GD) estimates was r = 0.93. The ISSR and RAPD analysis of 18 sour orange accessions found a high grade of genetic diversity in foreign accessions, while a low variability was detected in local accessions. Sicilian accessions could be grouped in two distinct clusters, including indistinctly plants from three origin regions. Some markers could be linked to the different growing areas. The ISSR and RAPD molecular reference system seems to be suitable for a fine identification of tightly related plants and the obtained results can form the basis for future setting up of Citrus rootstock genetic improvement projects.

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 Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 890
Author(s):  
Zifeng Ouyang ◽  
Yimeng Wang ◽  
Tiantian Ma ◽  
Gisele Kanzana ◽  
Fan Wu ◽  
...  
Keyword(s):  
Group Method ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Important Data ◽  
Breeding Programs ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Medicinal Value ◽  
Genome Wide ◽  
Melilotus Albus

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

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 Analysis of Genetic Variability Amongst Polyploid Genotypes of Pteris vittata L. From Various Geographic Locales of India

2021 ◽  
Vol 9 ◽  
Author(s):  
Jyoti Mathur ◽  
P. B. Khare ◽  
Apurva Panwar ◽  
S. A. Ranade
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Genomic Structure ◽  
Inter Simple Sequence Repeat ◽  
Pteris Vittata ◽  
Group Method ◽  
Bootstrap Analysis ◽  
Pair Group ◽  
Fern Species ◽  
Outgroup Taxon ◽  
Effective Multiplex Ratio

Pteris vittata L. is very common and a widely distributed species belongs to the family Pteridaceae. Various cytotypes from diploid to octaploid is available in this fern species. The present work has been carried out for genetic diversity in this fern both within and between the cytotypes. The molecular analysis at inter- as well as intra-species has been carried out with 57 accessions of P. vittata as well as of other species of Pteris with Microsorium punctatum considered as an out group taxon. For the present study 48 P. vittata (36 tetraploid and 12 pentaploid) and five of other species (four P. cretica, one P. pellucida, one P. tremula, one P. quadriaurita, and two P. ensiformis) accessions were used. The UPGMA (unweighted pair group method with arithmetic mean) dendrograms were generated for each method separately, as well as for all methods cumulatively, after a 1000 replicate bootstrap analysis. In order to determine the utility of each of the method, a comparative statistical assessment was done and marker index (MI), expected average heterozygosity, fraction of polymorphic loci and effective multiplex ratio (EMR) were calculated in case of each of the methods used in the present study. At the level of individual methods highest MI was obtained for directed amplification of minisatellites DNA (DAMD) method. Our findings of the present study concluded that out of the three methods Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat (ISSR), and Directed Amplification of Minisatellite DNA (DAMD), DAMD was the best in term of polymorphism and heterozygosity as scores exhibited highest MI. The different accessions of P. vittata collected from different phytogeographical regions falls into six groups. Out of six clusters, one cluster is of pentaploid cytotype, four clusters are of tetraploid cytotype and one for outgroup taxon (M. punctatum). The result thus showed that within tetraploid, heterozygosity with variable genomic structure exists.

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.

A search for diagnostic AFLP markers in Cichorium species with emphasis on endive and chicory cultivar groups

Genome ◽  
2000 ◽  
Vol 43 (3) ◽  
pp. 470-476 ◽  
Author(s):  
A M Kiers ◽  
T HM Mes ◽  
R van der Meijden ◽  
K Bachmann
Keyword(s):  
Wild Species ◽  
Genetic Relationships ◽  
Group Method ◽  
Specific Marker ◽  
Pair Group ◽  
Cultivar Groups ◽  
Average Analysis ◽  
Species Analysis ◽  
Cultivated Species ◽  
Unique Markers

The genus Cichorium consists of two widely cultivated species C. intybus (chicory) and C. endivia (endive) and four wild species, C. bottae, C. spinosum, C. calvum, and C. pumilum. A multivariate and an UPGMA (unweighted pair group method average) analysis based on AFLP (amplified fragment length polymorphism) markers were used to establish the genetic relationships among the species and cultivar groups of C. intybus and C. endivia. At the species level, the results correspond with previously obtained phylogenetic relationships in that C. bottae is the most divergent species, and C. intybus and C. spinosum, as well as C. endivia, C. pumilum, and C. calvum formed clusters. Based on the congruence between phylogenetic and genetic analyses, unique markers were expected for all species, however, hardly any specific marker was found except for C. bottae. The analysis of cultivar groups of C. intybus resembled the species analysis in two respects: (i) grouping of cultivars according to cultivar groups, and (ii) lack of markers unique to cultivar groups. In contrast to C. intybus, the cultivar series of C. endivia do not form distinct groups, which would reflect that crosses have been made among the various cultivar groups. The relationships among Cichorium species and cultivars will be useful for setting up a core collection of Cichorium, and stress the importance of inclusion of the wild species in the collection.Key words: Cichorium, AFLP, diagnostic markers, cultivar relationships, genetic resources.

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

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