scholarly journals Development of Molecular Markers Linked to Cladosporium fulvum Resistant Gene Cf-6 in Tomato by RAPD and SSR Methods

HortScience ◽  
2007 ◽  
Vol 42 (1) ◽  
pp. 11-15 ◽  
Author(s):  
Aoxue Wang ◽  
Fanjuan Meng ◽  
Xiangyang Xu ◽  
Yong Wang ◽  
Jingfu Li
Keyword(s):  
Molecular Markers ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Cladosporium Fulvum ◽  
Tomato Plants ◽  
Codominant Marker ◽  
Physiological Races ◽  
Sequence Characterized Amplified Region ◽  
Ssr Primers ◽  
Serious Disease

Leaf mold, caused by the fungus Cladosporium fulvum, is a serious disease of tomato. In the current study, the main physiological races of C. fulvum collected from three northeastern provinces of China were identified using a set of identification hosts. The results showed that the prevalent pathogenic physiological races were 1.2.3, 1.3, 3, 1.2.3.4, and 1.2.4. F1, F2, and BC1 tomato plants were obtained by crossing C. fulvum-resistant cultivar 03748 carrying the Cf-6 gene and susceptible cultivar 03036. Three 10-mer oligonucleotide random amplified polymorphic DNA (RAPD) primers and two simple sequence repeat (SSR) primers were selected for the further molecular marking analysis after 210 RAPD primers and 50 SSR primers were screened using the bulked segregate analysis method. The polymorphic DNA bands were amplified among parents, 10 F1 plants, 184 F2 plants including 145 resistant plants and 39 sensitive plants using three RAPD primers and two SSR primers so that three RAPD molecular markers and two SSR molecular markers linked to the Cf-6 loci were identified. Three RAPD markers were linked to the Cf-6 resistant locus separated with 8.7 cM, 20.3 cM, and 33.4 cM. Also, one RAPD codominant marker S374619/559 was found. The locations of the two SSR markers were 12.6 cM and 9.7 cM away from the Cf-6 locus. After cloning and sequencing two specific DNA fragments closely connected to the Cf-6 resistant and susceptible alleles respectively, in the RAPD codominant marker S374619/559 and one codominant sequence characterized amplified region marker S674619/559 was converted from RAPD marker S374619/559. In the RAPD marker S374619/559, the length difference of two specific fragments, 619-bp fragment and 559-bp fragment, is the result of one insertion (60 bp) in the 619-bp fragment. These markers will facilitate the selection of resistant tomato germplasm containing the Cf-6 gene and cloning of Cf-6 to breed new C. fulvum resistant tomato cultivars.

scholarly journals Characterization of genetic diversity of cactus species (Opuntia spp.) in Morocco by morphological traits and molecular markers

2017 ◽  
Vol 5 (2) ◽  
pp. 149-159 ◽  
Author(s):  
Y. El Kharrassi ◽  
M.A. Mazri ◽  
M.H. Sedra ◽  
A. Mabrouk ◽  
B . Nasser ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Morphological Traits ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Group Method ◽  
Rapd Primer ◽  
Opuntia Spp ◽  
Issr Primers

The genetic diversity within and among 124 accessions of Opuntia spp. collected from different regions of Morocco was assessed using morphological descriptors and molecular markers. Based on 10 morphological traits, the accessions were separated into 3 main clusters; each cluster was containing accessions from different regions and species. Polymerase chain reaction (PCR) was then performed on 22 accessions from different regions and species, with 10 inter-simple sequence repeat (ISSR) primers and one random amplified polymorphic DNA (RAPD) primer. ISSR primers produced 66 bands overall, 64 (96.9 %) of which were polymorphic while 6 bands were generated by the RAPD marker, all polymorphic. The polymorphic information content (PIC) values ranged from 0.62 to 0.97, with an average of 0.82. The dendrogram of genetic differences generated using the unweighted pair-group method using arithmetic averages (UPGMA) method showed 7 different clusters at a similarity of 0.76, which was confirmed by the principal component analysis (PCA). The main conclusion of our work is the high genetic similarity between Opuntia ficus indica and Opuntia megacantha species in Morocco. Our results will be useful for plant breeding and genetic resource conservation programs.

scholarly journals Genome Relationship among Nine Species of Millettieae (Leguminosae: Papilionoideae) Based on Random Amplified Polymorphic DNA (RAPD)

2004 ◽  
Vol 59 (11-12) ◽  
pp. 868-873 ◽  
Author(s):  
Laxmikanta Acharya ◽  
Arup Kumar Mukherjee ◽  
Pratap Chandra Panda
Keyword(s):  
Molecular Markers ◽  
Genetic Relationship ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Similarity Index ◽  
Morphological Characteristics ◽  
Genome Relationship ◽  
Tephrosia Purpurea ◽  
Constituent Species

Random amplified polymorphic DNA (RAPD) marker was used to establish intergeneric classification and phylogeny of the tribe Millettieae sensu Geesink (1984) (Leguminosae: Papilionoideae) and to assess genetic relationship between 9 constituent species belonging to 5 traditionally recognized genera under the tribe. DNA from pooled leaf samples was isolated and RAPD analysis performed using 25 decamer primers. The genetic similarities were derived from the dendrogram constructed by the pooled RAPD data using a similarity index, which supported clear grouping of species under their respective genera, inter- and intra-generic classification and phylogeny and also merger of Pongamia with Millettia. Elevation of Tephrosia purpurea var. pumila to the rank of a species (T. pumila) based on morphological characteristics is also supported through this study of molecular markers.

scholarly journals A DNA-Based Procedure for In Planta Detection of Fusarium oxysporum f. sp. phaseoli

2002 ◽  
Vol 92 (3) ◽  
pp. 237-244 ◽  
Author(s):  
Fernando M. Alves-Santos ◽  
Brisa Ramos ◽  
M. Asunción García-Sánchez ◽  
Arturo P. Eslava ◽  
José María Díaz-Mínguez
Keyword(s):  
Common Bean ◽  
Fusarium Oxysporum ◽  
Scar Marker ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
In Planta ◽  
Sequence Characterized Amplified Region ◽  
Polymerase Chain ◽  
Highly Virulent

We have characterized strains of Fusarium oxysporum from common bean fields in Spain that were nonpathogenic on common bean, as well as F. oxysporum strains (F. oxysporum f. sp. phaseoli) pathogenic to common bean by random amplified polymorphic DNA (RAPD) analysis. We identified a RAPD marker (RAPD 4.12) specific for the highly virulent pathogenic strains of the seven races of F. oxysporum f. sp. phaseoli. Sequence analysis of RAPD 4.12 allowed the design of oligonucleotides that amplify a 609-bp sequence characterized amplified region (SCAR) marker (SCAR-B310A280). Under controlled environmental and greenhouse conditions, detection of the pathogen by polymerase chain reaction was 100% successful in root samples of infected but still symptomless plants and in stem samples of plants with disease severity of ≥4 in the Centro Internacional de Agricultura Tropical (CIAT; Cali, Colombia) scale. The diagnostic procedure can be completed in 5 h and allows the detection of all known races of the pathogen in plant samples at early stages of the disease with no visible symptoms.

scholarly journals Development of Race-Specific SCAR Markers for Detection of Chinese Races CYR32 and CYR33 of Puccinia striiformis f. sp. tritici

Plant Disease ◽  
2010 ◽  
Vol 94 (2) ◽  
pp. 221-228 ◽  
Author(s):  
Baotong Wang ◽  
Xiaoping Hu ◽  
Qiang Li ◽  
Baojun Hao ◽  
Bo Zhang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Stripe Rust ◽  
Genomic Dna ◽  
Puccinia Striiformis ◽  
Random Amplified Polymorphic Dna ◽  
Scar Markers ◽  
Wheat Stripe Rust ◽  
Wheat Genotypes ◽  
Sequence Characterized Amplified Region ◽  
Wheat Leaves

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a devastating disease in China. Races CYR32 and CYR33 have been predominant in the recent P. striiformis f. sp. tritici population. To develop molecular markers for these races, initially 86 isolates, most of which were collected in 2007 throughout China, were tested on the set of wheat genotypes for differentiating Chinese P. striiformis f. sp. tritici races, and their genomic DNA were amplified with 94 random amplified polymorphic DNA (RAPD) primers. Twelve isolates were identified as CYR33, 14 as CYR32, and 60 as 13 other races. A 320-bp band was identified to be associated with CYR32 with primer S1271 (5′-CTTCTCGGTC-3′), and a 550-bp band was identified to be specific to CYR33 with primer S1304 (5′-AGGAGCGACA-3′). The two bands were cloned and sequenced. Based on the sequences, sequence characterized amplified region (SCAR) markers CYR32sp1/sp2 and CYR33sp1/sp2 were developed to differentiate CYR32 and CYR33, respectively, from other races. The SCAR markers were validated with DNA samples from wheat leaves inoculated with selected isolates from the 86 isolates and urediniospore DNA samples from an additional 63 isolates collected from 2006 to 2009. The detection of CYR32 and CYR33 with the SCAR markers was completely consistent with the results of the race identification with the set of differential wheat genotypes. Thus, the markers are highly reliable for identification of the two races.

scholarly journals Associating Molecular Markers with Virus Resistance to Classify Sweetpotato Genotypes

2005 ◽  
Vol 130 (3) ◽  
pp. 355-359 ◽  
Author(s):  
M. Mcharo ◽  
D. LaBonte ◽  
R.O.M. Mwanga ◽  
A. Kriegner
Keyword(s):  
Molecular Markers ◽  
Qtl Analysis ◽  
Ipomoea Batatas ◽  
Rapd Markers ◽  
Dna Marker ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Multivariate Techniques ◽  
Accuracy Rates

Molecular markers linked to resistance to sweetpotato chlorotic stunt closterovirus [SPCSV (genus Crinivirus, family Closteroviridae)] and sweetpotato feathery mottle virus [SPFMV (genus Potyvirus, family Potyviridae)] were selected using quantitative trait loci (QTL) analysis, discriminant analysis and logistic regression. Eighty-seven F1 sweetpotato [Ipomoea batatas (L.) Lam.] genotypes from a cross of `Tanzania' and `Wagabolige' landraces were used to generate DNA marker profiles for this study. Forty-five of the clones were resistant to SPCSV while 37 were resistant to SPFMV. A combination of 232 amplified fragment length polymorphism (AFLP) markers and 37 random amplified polymorphic DNA (RAPD) markers obtained were analyzed to determine the most informative markers. All three statistical procedures revealed that AFLP marker e41m33.a contributed the greatest variation in SPCSV resistance and RAPD marker S13.1130 accounted for most of the variation in SPFMV resistance. The power of discriminant and logistic analyses is that you do not need a parent-progeny population. An evaluation of these two models indicated a classification and prediction accuracy rates of 96% with as few as four markers in a model. Both multivariate techniques identified one important discriminatory marker (e44m41.j) for SPCSV and two markers (e41m37.a and e44m36.d) for SPFMV that were not identified by QTL analysis.

scholarly journals Identification of Raspberry Cultivars by Sequence Characterized Amplified Region DNA Analysis

HortScience ◽  
1998 ◽  
Vol 33 (1) ◽  
pp. 140-142 ◽  
Author(s):  
Jean-Guy Parent ◽  
Danièle Pagé
Keyword(s):  
Rapd Markers ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Rubus Idaeus ◽  
Scar Markers ◽  
Certification Program ◽  
Red Raspberry ◽  
Sequence Characterized Amplified Region

Five polymorphic random amplified polymorphic DNA (RAPD) markers for 13 red raspberry (Rubus idaeus L.) and two purple raspberry (R. idaeus L. × R. occidentalis L.) cultivars were cloned and their termini sequenced. Sequence-specific 24-mer primer pairs were synthesized as extended RAPD primers and used in sequence characterized amplified region (SCAR) DNA analysis. All primer pairs generated polymorphic SCAR markers of the original RAPD marker sizes and length variants. Markers from four of the primer pairs could be easily scored and were adequate to identify the raspberry cultivars of the certification program of the province of Quebec.

scholarly journals A Molecular Marker Correlated with Selected Virulence Against the Tomato Resistance Gene Mi in Meloidogyne incognita, M. javanica, and M. arenaria

2001 ◽  
Vol 91 (4) ◽  
pp. 377-382 ◽  
Author(s):  
Jianhua Xu ◽  
Takashi Narabu ◽  
Takayuki Mizukubo ◽  
Tadaaki Hibi
Keyword(s):  
Resistance Gene ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Nucleotide Polymorphisms ◽  
Sequence Characterization ◽  
Sequence Characterized Amplified Region ◽  
Major Species ◽  
Wide Range ◽  
Meloidogyne Spp

Root-knot nematodes of the genus Meloidogyne are economically important pathogens of a wide range of crops. The tomato resistance gene Mi typically confers resistance to the three major species, M. incognita, M. javanica, and M. arenaria. However, virulent populations completely overcoming the Mi resistance still occur. In an attempt to develop molecular markers for virulence against Mi and gain insights into the genetic relationships among virulent populations of different species and origins, random amplified polymorphic DNA (RAPD) analyses of laboratory-selected virulent, field virulent, and avirulent populations of M. incognita, M. javanica, and M. arenaria were carried out. A RAPD marker, specific for selected virulent populations, was identified, and subsequently, converted to a sequence characterized amplified region (SCAR). Sequence characterization of the SCAR locus showed that alleles from laboratory- and field-selected virulent populations were highly similar to each other and clearly different from alleles from natural virulent and avirulent populations. This result suggests that the genetic mechanism for virulence against Mi may be similar among selected virulent populations of the three Meloidogyne spp., but different between selected and natural virulent populations. Based on the nucleotide polymorphisms at the SCAR locus, codominant and dominant polymerase chain reaction-based markers were developed enabling rapid diagnosis of selected virulent genotypes in M. incognita, M. javanica, and M. arenaria.

scholarly journals 050 Comparative Analysis of Cultivated Melon Groups (Cucumis melo L.) using Random Amplified Polymorphic DNA and Simple Sequence Repeat Markers

HortScience ◽  
2000 ◽  
Vol 35 (3) ◽  
pp. 397B-397
Author(s):  
Jack E. Staub ◽  
Gennaro Fazio ◽  
Thomas Horejsi ◽  
Yael Danin-Poleg ◽  
Noa Reis ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Estimation Methods ◽  
Sequence Repeat ◽  
Ssr Primers ◽  
Nei's Distance ◽  
Highly Correlated ◽  
Simple Sequence

Random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers were used to characterize genetic relationships among 46 accessions in two C. melo L. subsp. melo (Cantalupensis, Inodorus) and subsp. agrestis (Conomon and Flexuosus) groups. Genetic distance (GD) estimates were made among and between accessions in four melon market classes [Galia, Ogen, Charentais, and Shipper (European and U.S. types)] of Cantalupensis, one market class of Inodorus (Cassaba and Honey Dew), one accession of Conomon, and one accession of Flexuosus by employing three GD estimators; simple matching coefficient, Jaccard's coefficient, and Nei's distance-D. Differences detected among 135 RAPD bands and 54 SSR bands (products of 17 SSR primers) were used to calculate GD. Band polymorphisms observed with 21 RAPD primers and 7 SSR primers was important in the detection of genetic differences. Estimators of GD were highly correlated (P > 0.0001; rs = 0.64 to 0.99) when comparisons were made between estimation methods within a particular marker system. Lower correlations (P > 0.001; rs = 0.17 to 0.40) were detected between marker systems using any one estimator. The GD of the Conomon and Flexuosus accessions was significantly different from the mean GD of all the market classes examined, and market classes were distinguishable from each other. Although lower coefficients of variation can be attained in the estimation of GD when using RAPDs compared to SSRs, the genetic relationships identified using these markers were generally similar. Results of RAPD marker analysis suggest that 80 marker bands were adequate for assessing the genetic variation present in the accessions examined.

scholarly journals 049 Development of Molecular Markers Linked to High Pigment (hp) and Dark Green (dg) Loci in Tomato

HortScience ◽  
1999 ◽  
Vol 34 (3) ◽  
pp. 449D-449
Author(s):  
Yiping Zhang ◽  
John R. Stommel
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Tomato Fruit ◽  
Rapd Marker ◽  
Ripe Fruit ◽  
Total Carotenoids ◽  
Breeding Programs ◽  
Immature Fruit ◽  
Sequence Characterized Amplified Region ◽  
Allele Specific ◽  
Dark Green

The carotenoids have an important influence on tomato fruit quality and enhance the fruit contribution to human nutrition. Expression of the high pigment (hp) locus in tomato results in increased total carotenoids and increased efficiency of utilization of the polyenes. A similar mutant, dark green (dg), contains higher level of chlorophyll in immature fruit and results in darker red pigmentation, both externally and internally in ripe fruit. Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) analyses were performed using two pairs of near isogenic lines (NILs) designed to be isogenic at the hp and dg loci. Sixty-four AFLP primer pairs and more than 1000 RAPD 10-mer primers were screened for polymorphism between each pair of the NILs. One RAPD marker was identified to be linked to the hp gene, and two AFLP primer pairs showed polymorphic fragments which distinguished the dg NILs. The markers identified in this study will be converted to allele specific SCAR (sequence characterized amplified region) markers, which are more useful in marker-assisted selection breeding programs.

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