scholarly journals Random Amplified Polymorphic DNA (RAPD) Marker Variability between and within Gene Pools of Common Bean

1994 ◽  
Vol 119 (1) ◽  
pp. 122-125 ◽  
Author(s):  
Scott D. Haley ◽  
Phillip N. Miklas ◽  
Lucia Afanador ◽  
James D. Kelly
Keyword(s):  
Common Bean ◽  
Gene Pool ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Major Gene ◽  
Rapd Marker ◽  
Gene Pools ◽  
Navy Bean ◽  
Breeding Programs ◽  
Polymerase Chain

The objective of this study was to evaluate the degree of RAPD marker variability between and within commercially productive market classes representative of the Andean and Middle American gene pools of common bean (Phaseolus vulgaris L.). Six sets of near-isogenic lines were screened with oligonucleotide primers in the polymerase chain reaction-based RAPD assay. Simultaneous analyses with at least three sets of lines enabled us to score RAPD markers between the two major gene pools, races within the same gene pool, and different genotypes of the same race (within race). A “three-tiered” pattern of polymorphism was observed: between gene pools> between races> within races. The overall level of polymorphism between the Andean and Middle American gene pools was 83.4%. The overall level of polymorphism between races within the same gene pool was similar for Andean races (60.4%) and Middle American races (61.7%). The level of polymorphism between related commercial navy bean lines was 39.2% and between related commercial snap bean lines was 53.6 %. The inherent simplicity and efficiency of RAPD analyses, coupled with the number of polymorphisms detectable between related commercial genotypes, should facilitate the construction of RAPD-based genetic linkage maps in the context of populations representative of most bean breeding programs.

Genetic diversity of Colombian landraces of common bean as detected through the use of silver-stained and fluorescently labelled microsatellites

2011 ◽  
Vol 9 (01) ◽  
pp. 86-96 ◽  
Author(s):  
Lucy M. Díaz ◽  
Héctor F. Buendía ◽  
Myriam C. Duque ◽  
Matthew W. Blair
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Common Bean ◽  
Gene Pool ◽  
Major Gene ◽  
Gene Pools ◽  
Silver Stain ◽  
Fluorescent Marker ◽  
Fluorescent Markers

Colombia, situated at the northern end of the Andes mountains of South America and in proximity to Central America, is an important centre of diversity for common bean (Phaseolus vulgarisL.) that has a mix of cultivated germplasm from both major gene pools (Andean and Mesoamerican) for the species. Microsatellites are a useful marker system for analyzing genetic diversity of this crop and can be analyzed with manual (silver-stain) or automated (ABI) detection systems and using unlabelled or fluorescently labelled markers, respectively. The objectives of this research were to evaluate the genetic diversity of 92 Colombian landraces and gene pool controls with 36 fluorescent and 30 non-fluorescent microsatellite markers and to determine the extent of introgression between the Andean and Mesoamerican gene pools for this germplasm. A comparison of fluorescentversusnon-fluorescent marker systems was performed with 14 loci, which were evaluated with both methods; the fluorescent markers were found to be more precise than the non-fluorescent markers in determining population structure. A combined analysis of 52 microsatellites using the 36 fluorescent markers and 16 non-overlapping, silver-stained markers produced an accurate population structure for the Andean gene pool that separated race Nueva Granada and race Peru genotypes and clearly identified introgression between these races and the gene pools. The results of this research are important for the application of microsatellite markers to diversity analysis in common bean and for the conservation of landraces in Colombia and neighbouring countries of Latin America, where similar germplasm exists and where gene pool or race mixtures also occur.

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.

Development of a SCAR marker linked to the I gene in common bean

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1216-1219 ◽  
Author(s):  
M. Melotto ◽  
L. Afanador ◽  
J. D. Kelly
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Rapd Marker ◽  
Bean Common Mosaic Virus ◽  
Gene Pools ◽  
Phaseolus Vulgaris L ◽  
Breeding Programs ◽  
Heat Stable ◽  
Rapd Primer ◽  
I Gene

Two 24-mer SCAR primers (SW13) were developed from a previously identified 10-mer RAPD primer (OW13690) linked to the I gene, which conditions resistance to bean common mosaic virus (BCMV) in common bean. Linkage between SW13 and the I gene was tested in three F2 populations segregating for both SW13 and the I gene: N84004/Michelite (1.0 ± 0.7 cM), Seafarer/UI-114 (1.3 ± 0.8 cM), and G91201/Alpine (5.0 ± 2.2 cM). SW13 proved to be more specific and reproducible than the OW13690 RAPD marker. Using different heat-stable DNA polymerases, SW13 amplified a single 690-bp fragment linked to the I gene that more consistently permitted the identification of resistant plants. In addition, the presence of the I gene was detected using SW13 in genotypes originating from different gene pools of Phaseolus vulgaris L., indicating a broad utility of this marker for bean breeding programs. Key words : Phaseolus vulgaris, SCAR, RAPD, BCMV.

scholarly journals Genetic diversity within and among two-spotted spider mite resistant and susceptible common bean genotypes

2017 ◽  
Vol 109 (3) ◽  
pp. 517
Author(s):  
Zeinab YOUSEFI ◽  
Zahra TAHMASEBI ◽  
Mohammad Javad Erfani MOGHADAM ◽  
Ali ARMINIAN
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Ssr Markers ◽  
Rapd Markers ◽  
Spider Mite ◽  
Random Amplified Polymorphic Dna ◽  
Breeding Programs ◽  
Ssr Analysis ◽  
Two Spotted Spider Mite ◽  
Simple Sequence

<p>Two-spotted spider mite (<em>Tetranychus urticae </em><a title="Carl Ludwig Koch" href="https://en.wikipedia.org/wiki/Carl_Ludwig_Koch">C. L. Koch</a>, 1836), is one of the most destructive herbivores of common bean. Very little is known about the diversity among resistant sources in this crop. The present study was conducted to characterize 22 resistant and susceptible common bean genotypes by 8 Simple Sequence Repeats (SSRs) and 8 Random Amplified Polymorphic DNA (RAPD) markers. These SSR and RAPD primers produced 100 % and 81.8 % polymorphic bands. Based on RAPD fingerprints and SSR profiles, pairwise genetic similarity ranged from 0.0 to 0.857 and from 0.125 to 1, respectively. The resistant and susceptible common bean accessions were grouped together in the dendrograms generated from RAPD and SSR clustering analyses. The results indicate that RAPD and SSR analysis could be successfully used for the estimation of genetic diversity among genotypes. SSR markers could group genotypes according to their resistibility and susceptibility to the spotted spider mite but RAPD could not. Therefore, the SSR markers can facilitate the development of resistant common bean cultivars through breeding programs against <em>T. urticae</em>.</p>

Detection and Mapping of RAPD Markers Associated with QTL Affecting Seed Size and Shape in Common Bean

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 547b-547
Author(s):  
Soon O. Park ◽  
Dermot P. Coyne ◽  
Geunhwa Jung ◽  
E. Arnaud-Santana ◽  
H. Ariyarathne
Keyword(s):  
Linkage Group ◽  
Common Bean ◽  
Seed Size ◽  
Phenotypic Variation ◽  
Seed Weight ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Seed Shape ◽  
Seed Length ◽  
Ri Lines

Seed size is an important trait in common bean. The objective was to identify RAPD markers associated with QTL for seed weight, seed length, and seed height in a molecular marker-based linkage map in a recombinant inbred (RI) population from the common bean cross of the larger seeded (100 seed/39 to 47 g) PC-50 (ovate seed shape) × smaller seeded (100 seed/26 to 35 g) XAN-159 (flat rhomboidal seed shape). The parents and RI lines were grown in two separate greenhouse and two field (Wisconsin, Dominican Republic) experiments using a RCBD. Continuous distributions for seed weight, seed length, and seed height were observed for RI lines indicating quantitative inheritance. One to three QTLs affecting seed weight explained 17% to 41% of the phenotypic variation. Two to three QTLs for seed length explained 23% to 45% of the phenotypic variation. One to four QTL associated with seed height explained 17% to 39% of the phenotypic variation. A RAPD marker M5.850 in linkage group 3 was consistently associated with seed weight, seed length, and seed height in all experiments and explained 7% to 13% of the phenotypic variation for these traits. A seedcoat pattern morphological marker (C) in linkage group 1 was associated with seed weight and seed height in two greenhouse experiments.

scholarly journals Segregation for Resistance to Eastern Filbert Blight in Progeny of `Zimmerman' Hazelnut

2006 ◽  
Vol 131 (6) ◽  
pp. 731-737 ◽  
Author(s):  
China F. Lunde ◽  
Shawn A. Mehlenbacher ◽  
David C. Smith
Keyword(s):  
Rapd Markers ◽  
Chromosome Region ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Segregation Ratio ◽  
Enzyme Linked Immunosorbent Assay ◽  
Resistance Locus ◽  
Resistance Allele ◽  
Reciprocal Translocations ◽  
Eastern Filbert Blight

Eastern filbert blight (EFB), caused by the fungus Anisogramma anomala (Peck) E. Müller, is an important disease of european hazelnut (Corylus avellana L.) in the Pacific northwestern United States. In 1989, a chance seedling free of EFB was discovered adjacent to a severely diseased orchard near Troutdale, Ore. This selection, subsequently named `Zimmerman', was crossed with three susceptible selections. Based on morphological characters and incompatibility alleles, we speculated that `Zimmerman' (S1 S3) was a hybrid between `Barcelona' (S1 S2) and `Gasaway' (S3 S26). The three seedling populations were inoculated with spores of the pathogen in a greenhouse test and assayed by indirect enzyme-linked immunosorbent assay (ELISA) and by observation of canker incidence. The observed segregation fit a 3 resistant : 1 susceptible ratio in all three progenies, in contrast to the 1 : 1 ratio found when the resistant pollinizer `Gasaway' was crossed to susceptible genotypes. Random amplified polymorphic DNA (RAPD) marker UBC 152800 linked to the resistance gene in `Gasaway' co-segregated with the resistant phenotype in all three populations with 2%, 4%, and 6% recombination, respectively. Seed germination and transplanting records did not provide evidence of selection in favor of resistant seedlings. Pollen germination was 71% in `Gasaway', 29% in `Zimmerman', and 18% in `Barcelona', indicating possible selection at the gametophytic level. Subsequently 16 resistant seedlings of `Zimmerman' were crossed with the highly susceptible selection OSU 313.078. Segregation fit a 3 : 1 ratio in 14 of the 16 progenies, and showed a surplus of resistant seedlings in the other two. None showed a 1 : 1 segregation. Resistance co-segregated with two RAPD markers that flank the `Gasaway' resistance allele. To test allelism of resistance from `Gasaway' and `Zimmerman', VR 6-28 with resistance from `Gasaway' was crossed with `Zimmerman'. Eight resistant selections from this progeny were crossed with OSU 313.078. Five of the eight progenies segregated 3 : 1, two progenies segregated 1 : 1, and OSU 313.078 × OSU 720.056 gave only resistant offspring. The ratios indicate that OSU 720.056 is homozygous resistant and that `Zimmerman' and `Gasaway' share a common resistance allele. Reciprocal translocations have been reported in hazelnut cultivars, including `Barcelona', the leading cultivar in Oregon. `Zimmerman' appears to be a hybrid of `Barcelona' and `Gasaway', but because of cytogenetic abnormalities, `Zimmerman' may have inherited two copies of the chromosome region that contain the resistance locus and flanking RAPD markers. If the region containing the resistance were attached to two independent centromeres, a 3 : 1 segregation ratio for disease response and flanking markers would be expected, and we propose this as the most likely explanation. Resistance from `Gasaway' and `Zimmerman' has been called “immunity” or “complete resistance.” However, we noted a few seedlings with small cankers, nearly all of which lacked sporulating stromata. Flanking RAPD markers indicate that the resistance allele is present in these seedlings. Although not “immune” or “completely resistant,” `Gasaway' and `Zimmerman' transmit a very high level of resistance.

scholarly journals Genetic diversity of common bean (Phaseolus vulgaris L.) breeding collection in Serbia

Genetika ◽  
2019 ◽  
Vol 51 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Aleksandra Savic ◽  
Milka Brdar-Jokanovic ◽  
Miodrag Dimitrijevic ◽  
Sofija Petrovic ◽  
Milan Zdravkovic ◽  
...  
Keyword(s):  
Common Bean ◽  
Gene Pool ◽  
Gene Diversity ◽  
Principal Component ◽  
Molecular Data ◽  
Phenotypic Traits ◽  
Gene Pools ◽  
Vegetable Crops ◽  
Novi Sad

The characterization of 41 common bean cultivars and landraces from breeding collection of Institute of Field and Vegetable Crops, Novi Sad, Serbia, was done based on phenotypic traits and microsatellite markers. Phenotypic traits were chosen from Bioversity International descriptor list. In addition, main yield components were investigated. Analysis of phaseolin type revealed affiliation of cultivars and landraces to Mesoamerican or Andean gene pool. Cultivars and landraces demonstrated significant diversity level with regard to studied phenotypic traits. Identified variation showed high potential for developing new cultivars with desirable combination of traits. Principal component analysis based on phenotypic traits separated bean cultivars and landraces in two groups, which corresponded to Mesoamerican and Andean determined according to phaseolin type. Putative hybrids, with combination of traits between gene pools were also identified. Analysis of microsatellite data, using twenty-two SSR primer pairs, showed medium gene diversity in studied material. Microsatellite-based cluster analysis separated genotypes in two discrete clusters and several subclusters. No clear separation according to gene pool was found between the clusters, however grouping according to gene pool and patterns of phenotypic variation, following these gene pools, were observed within subclusters. Knowledge on detailed relationships of cultivars and landraces based on phenotypic and molecular data would facilitate identification of candidates for future breeding.

Segregation of random amplified polymorphic DNA markers and strategies for molecular mapping in tetraploid alfalfa

Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 844-851 ◽  
Author(s):  
K. F. Yu ◽  
K. P. Pauls
Keyword(s):  
Chromosome Segregation ◽  
Dna Markers ◽  
Rapd Markers ◽  
Molecular Mapping ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Female Parent ◽  
Linkage Groups ◽  
Double Reduction ◽  
Chromatid Segregation

An F1 population was used to analyze the inheritance of random amplified polymorphic DNA (RAPD) markers in tetraploid alfalfa. Of the 32 RAPD markers that were used for a segregation analysis in this study, 27 gave ratios that are consistent with random chromosome and random chromatid segregation at meiosis. However, among all of the RAPD markers (121) that were screened in this study, only one example of a double reduction, that is typical of chromatid segregation, was observed. These results indicate that random chromosome segregation is likely the predominant but not the exclusive mode of inheritance for tetraploid alfalfa. χ2 analyses of cosegregation for RAPD marker pairs derived from the female parent revealed nine linkages that fell into four linkage groups. The recombination fractions among linked marker pairs ranged from 1 to 37%. These are the first molecular linkage groups reported in tetraploid alfalfa. In addition, various strategies for molecular mapping in the tetraploid alfalfa genome are proposed that should be of interest to plant breeders who are planning to use molecular markers for alfalfa or other tetraploid species.Key words: RAPD markers, tetraploid alfalfa, segregation, linkage groups.

Inheritance of random amplified polymorphic DNA markers in an interspecific cross in the genus Stylosanthes

Genome ◽  
1993 ◽  
Vol 36 (1) ◽  
pp. 50-56 ◽  
Author(s):  
Kemal Kazan ◽  
John M. Manners ◽  
Don F. Cameron
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Interspecific Cross ◽  
Parental Origin ◽  
Chain Reaction ◽  
Stylosanthes Hamata ◽  
Polymerase Chain

The inheritance of random amplified polymorphic DNA (RAPD) markers generated via the polymerase chain reaction amplification of genomic DNA sequences in an F2 family of an interspecific cross between Stylosanthes hamata and S. scabra was investigated. An initial comparison between the parental species, S. hamata cv. Verano and S. scabra cv. Fitzroy, demonstrated that 34% of detected RAPD bands were polymorphic. Of 90 primers tested, 35 showed relatively simple and reliably scorable polymorphisms and were used for segregation analysis. Sixty F2 individuals were scored for the segregation of 73 RAPD markers and 55 of these markers fit a 3:1 ratio. Segregation of eight other RAPD markers deviated significantly from a 3:1 ratio. There was no bias in the inheritance of RAPD markers regarding parental origin of the segregating RAPD markers. Linkage analysis revealed 10 linkage groups containing a total of 44 RAPD loci. Another 10 RAPD markers (7 of maternal origin) that were polymorphic between the parents did not segregate in the F2 population. One of the maternally inherited RAPD bands hybridized to chloroplast DNA. Analysis of RAPD loci by DNA hybridization indicated that mainly repeated sequences were amplified. These data indicate that RAPDs are useful genetic markers in Stylosanthes spp. and they may be suitable for genetic mapping.Key words: genetic mapping, molecular markers, polymerase chain reaction, Stylosanthes hamata, Stylosanthes scabra.

The genetic make-up of the European landraces of the common bean

2011 ◽  
Vol 9 (2) ◽  
pp. 197-201 ◽  
Author(s):  
S. A. Angioi ◽  
D. Rau ◽  
L. Nanni ◽  
E. Bellucci ◽  
R. Papa ◽  
...  
Keyword(s):  
Common Bean ◽  
Gene Pool ◽  
Chloroplast Microsatellites ◽  
Gene Pools ◽  
Mesoamerican Gene Pool ◽  
Hybridization Event ◽  
South Eastern Europe ◽  
Andean Type ◽  
The Common ◽  
African Sample

Here, we present a brief overview of the main studies conducted on the common bean (Phaseolus vulgaris L.) in Europe and other countries outside its centres of origin. We focus on the proportions of the Andean and Mesoamerican gene pools, and on the inter-gene pool hybridization events. In Europe, for chloroplast microsatellites, 67% of European germplasm is of Andean origin. Within Europe, interesting trends have been seen; indeed, the majority of the Andean type is found in the three macro-areas of the Iberian Peninsula, Italy and central-northern Europe, while, in eastern and south-eastern Europe, the proportion of the Mesoamerican type increased. On a local scale, the contribution of the Mesoamerican type is always low. On other continents, various situations are seen using different markers: in China and Brazil, the Mesoamerican gene pool prevails, while in an African sample, overall, both gene pools are equally represented, with differences in individual countries. The frequency of European bean genotypes deriving from at least one hybridization event was 44% with an uneven distribution. Interestingly, hybrids tend to have intermediate seed size in comparison with ‘pure’ Andean or Mesoamerican types. On other continents, very few hybrids are found, probably because of the different marker systems used.

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