Showing papers on "RAPD published in 2000"
TL;DR: The results suggest that RAPD can be a sensitive method for detection of genetic structuring according to the isolation-by-distance model, but also means that sampling strategies, as applied in individual studies, can seriously influence the resulting estimates of between-population diversity.
Abstract: A compilation of studies using RAPD markers for evaluating population differentiation resulted in 78 estimates of AMOVA-derived Φ ST and 31 estimates of Nei's G ST , as well as in 41 estimates of Nei's within-population diversity. In outcrossing taxa, estimates of between-population diversity were closely correlated with maximum geographic distance between sampled populations. A corresponding association was not found in selfing taxa. These results suggest that RAPD can be a sensitive method for detection of genetic structuring according to the isolation-by-distance model. However, it also means that sampling strategies, as applied in individual studies, can seriously influence the resulting estimates of between-population diversity. Other sampling strategies, like number of plants per population and number of scored polymorphic markers, do not seem to impart any serious artefacts. As previously verified with allozyme data, RAPD markers showed that long-lived, outcrossing, late successional taxa retain most of their genetic variability within populations. By contrast, annual, selfing and/or early successional taxa allocate most of the genetic variability among populations. Estimates for between- and within-population diversity, respectively, proved to be negatively correlated, as previously reported for allozyme data. The only major discrepancy between allozymes and RAPD markers concerns geographic range; within-population diversity was strongly affected by distributional range of the investigated species in the allozyme data but not in the RAPD data. Moreover, RAPD-based values for between-population diversity increased with increasing distributional range whereas the opposite has been reported in a large allozyme data compilation. Contrary to allozymes, RAPD marker-derived within-population diversity is probably therefore not a very good predictor of total species genetic diversity.
832 citations
TL;DR: Results show that each of the four techniques can on their own, individually identify each cultivar, but that techniques differ in the mean number of profiles generated per primer (or primer pair) per cultivar.
Abstract: Several DNA marker systems and associated techniques are available today for fingerprinting plant germplasm but information on their relative usefulness in particular crops is limited. The study investigated PCR based DNA fingerprinting in a set of 39 potato cultivars using RAPDs (20 primers), ISSRs (6 primers), AFLPs (2 primers) and SSRs (5 primer pairs). Results show that each of the four techniques can on their own, individually identify each cultivar, but that techniques differ in the mean number of profiles generated per primer (or primer pair) per cultivar, referred to as Genotype Index (GI). The order of merit based on this criterium and in this material was AFLPs (GI = 1.0), a multi-locus SSR (GI = 0.77),RAPDs (GI = 0.53), ISSRs (GI = 0.47) and single locus SSRs (GI = 0.36). Problems in relating banding patterns to individual loci and alleles for polyploid genomes, using these techniques as they are currently employed, are also discussed.
341 citations
TL;DR: Three randomly amplified polymorphic DNA markers species specific to the root-knot nematode species Meloidogyne arenaria, M. incognita and M. javanica respectively, were identified and the SCAR-PCR assay was successfully applied using DNA extracts from infested plant material.
Abstract: Three randomly amplified polymorphic DNA (RAPD) markers, OPA-12 420 , OPB-06 1200 and OPA-01 700 , species specific to the root-knot nematode species Meloidogyne arenaria , M. incognita and M. javanica respectively, were identified. After sequencing these RAPD-PCR products, longer primers of 18 to 23 nucleotides were designed to complement the terminal DNA sequences of the DNA fragments. This resulted in three pairs of species specific primers that were used to amplify the sequence characterised amplified regions (SCARs). The developed sets of SCAR primers were successfully used in straightforward, fast and reliable PCR assays to identify M. incognita , M. javanica and M. arenaria . The length variant SCAR markers can be amplified from DNA from egg masses, second stage juveniles and females. This species identification technique is therefore independent of the nematode's life cycle stage. Moreover the SCAR-PCR assay was successfully applied using DNA extracts from infested plant material. The method has potential to be optimised for routine practical diagnostic tests facilitating the control of these economically important pest organisms. Identification de Meloigyne incognita, M. javanica et M. arenaria au moyen de l'amplification de regions de sequences caracteristiques (SCAR) par une technique PCR - Trois marqueurs d'ADN polymorphique amplifiee au hasard (RAPD) OPA-12 420 , OPB-O6 1200 et OPA-OI 700 , respectivement specifiques des especes de nematodes Meloidogyne arenaria , M. incognita et M. javanica , ont ete identifies. Apres le sequencage de ces produits RAPD-PCR, les amorces les plus longues de 18 a 23 nucleotides ont ete choisies pour completer les sequences terminales d'ADN des fragments d'ADN. Cela a conduit a trois paires d'amorces specifiques de l'espece, utilisees pour amplifier les regions des sequences caracteristiques (SCAR). Les lots d'amorces SCAR mis au point ont ete utilises avec succes lors d'essais directs, rapides et surs pour identifier M. incognita , M. javanica et M. arenia . Les marqueurs peuvent etre amplifies a partir de l'ADN des masses d'oeufs, des juveniles de deuxieme stade ou des femelles. Cette technique d'identification specifique est donc independante des differents etats de developpement du nematode. De plus la technique SCAR-PCR a ete appliquee avec succes a l'ADN extrait du materiel vegetal infeste. Cette methode presente des potentialites d'amelioration permettant d'envisager des tests pratiques d'identification de routine, facilitant ainsi le controle de ces parasites economiquement importants.
328 citations
TL;DR: Middle American germplasm of common bean is more complex than previously thought, and contains diversity that remains to be explored for its practical value.
Abstract: More than 60% of common bean production worldwide is derived from cultivars of Middle American origin. Understanding the diversity of these will facilitate their use in genetic improvement. The objective of this study was to analyze a collection of 269 landraces of common bean (Phaseolus vulgaris L.) by correspondence analysis of random amplified polymorphic DNA (RAPD) data to determine the genetic structure of the Middle American gene pool of cultivated bean. One hundred eighty landraces originating in Mexico, the remainder in Central America and secondary centers of diversity within the Americas, and two checks were studied. DNA was extracted, RAPD reactions carried out, and polymorphic bands were scored as present or absent on the basis of 39 primers. Groups were formed which in part corresponded to races defined previously by morphological and agroecological criteria. However, tropical small-seeded Race M was composed of two groups: one largely Mexican that included most small-seeded black beans of upright plant habit, and one Central American with landraces of various seed colors. Most non-black small-seeded germplasm of Race M phenotype from secondary centers grouped with the Central American landraces, except for cream-seeded and purple-seeded accessions from Brazil. Races D and J could be distinguished and within races D and J further divisions could be recognized which were related to geographic origin. The more commercial Race D landraces formed a genetic group that was predominant in the western part of the Mexican highland plateau. Another Race D group was concentrated at the eastern extreme of the neovolcanic axis and was differentiated morphologically as well. Guatemalan germplasm contained accessions of climbing bean that did not group with any of the previously defined races and should be considered a separate race. Thus, Middle American germplasm of common bean is more complex than previously thought, and contains diversity that remains to be explored for its practical value.
280 citations
TL;DR: This result is interpreted as consistent with the presence of a single, exceptionally widespread clone of Japanese Knotweed in Britain, which must represent one of the world's largest vascular plants.
256 citations
TL;DR: There was a high level of genetic diversity in this population and that the genetic diversity was related to plant age, and some of the DAPG producers had the same genotype, which could be exploited in future screening programs for biocontrol agents.
Abstract: A Pseudomonas 2,4-diacetylphloroglucinol (DAPG)-producing population that occurred naturally on the roots, in rhizosphere soil of Zea mays and in the nonrhizosphere soil was investigated in order to assess the microbial diversity at five stages of plant growth. A total of 1,716 isolates were obtained, and 188 of these isolates were able to produce DAPG. DAPG producers were isolated at each stage of plant growth, indicating that the maize rhizosphere is colonized by natural DAPG producers throughout development. The frequency of DAPG producers was very low in the first stage of plant growth and increased over time. An analysis of the level of biodiversity of the DAPG producers at the species level was performed by comparing the AluI restriction patterns of the 16S ribosomal DNAs (rDNAs) amplified by PCR from 167 isolates. This comparison allowed us to cluster the isolates into four amplified rDNA restriction analysis (ARDRA) groups, and the main group (ARDRA group 1) contained 89.8% of the isolates. The diversity of the 150 isolates belonging to ARDRA group 1 was analyzed by the random amplified polymorphic DNA (RAPD) technique. An analysis of RAPD patterns by a molecular variance method revealed that there was a high level of genetic diversity in this population and that the genetic diversity was related to plant age. Finally, we found that some of the DAPG producers, which originated from all stages of plant growth, had the same genotype. These DAPG producers could be exploited in future screening programs for biocontrol agents.
231 citations
Journal Article•
TL;DR: A fast, simple, and reliable mini-prep method for the extraction of DNA from Gossypium species and cultivars has been developed, and it extracts DNA from one to three folded or nearly unfolded young leaves processed in a 1.5mL tube with 0.5 mL of extraction buffer.
Abstract: A fast, simple, and reliable mini-prep method for the extraction of DNA from Gossypium species and cultivars has been developed. This small-scale method is cetyltrimethylammonium bromide (cTAB)-based, and it extracts DNA from one to three folded or nearly unfolded young leaves processed in a 1.5 mL tube with 0.5 mL of extraction buffer and homogenized by an electric drill. Compared with the macro-prep cTAB method, the improved mini-prep method is highly efficient and much cheaper in terms of time, chemical use, and labor input. Easily 200 samples per day can be processed by a single person. The DNA yield is greater (60 )g per 50-100 mg of fresh leaf tissue) than that obtained from the macroprep method (50 )g from 5 g of fresh leaf tissue) and it provides DNA for 3000 to 6000 polymerase chain reactions (PCRs). The DNA quality is sufficient for PCR-based and endonuclease restriction marker analysis. With the development of polymerase chain reaction (PCR) technology, molecular markers J. Zhang and J.McD. Stewart, 115 Plant Sci. Bldg., Dep. of Crop, Soil, and Environ. Sci., Univ. of Arkansas, Fayetteville, AR 72701. Received 10 Mar. 2000. *Corresponding author (jstewart@comp.uark.edu). Abbreviations: PCR, polymerase chain reaction; RAPD, random amplified polymorphic DNA; SSR, simple sequence repeat; AFLP, amplified fragment length polymorphism; RFLP, restriction fragment length polymorphism; cTAB, cetyltrimethylammonium bromide. 194 ZHANG & STEWART: ECONOMICAL, RAPID GENOMIC DNA EXTRACTION based on PCR soon found vast application in plant genetics and breeding (Lee, 1995). To accommodate the need for PCR-based markers, a rapid, simple, and reliable DNA preparation method is required to provide high quality and quantity DNA for the analyses. Although numerous DNA extraction methods for plants have been reported in the literature, the cTAB extraction method is used most often. The traditional macro-preparation of DNA usually requires from 0.5 to several grams of plant tissue, making it impractical to analyze individual plants during early seedling stage. Also, the methods are time consuming and laborious due to their multistep procedures. Furthermore, large amounts of hazardous chemical solvents are required. Modifications have been made for plant species such as cotton that are high in polysaccharides and polyphenols. The compounds form a sticky, brown gelatinous matrix during DNA preparation that interferes with DNA digestion and PCRs. These modified methods usually employ high salt concentrations to remove polysaccharides, and polyvinylpyrrolidone to bind polyphenols (Lodhi et al., 1994; Porebski et al., 1997). Ascorbic acid, emercaptoethanol, and activated charcoal were found to improve extracted DNA quality (Paterson et al., 1993; Bi et al., 1996). For PCR-based DNA markers used in markerassisted selection, a fast DNA extraction method is needed. A reliable method should meet the following criteria: (i) require only a small amount of tissue; (ii) involve simple procedures; (iii) use minimal number and amount of chemicals; (iv) yield high-quality DNA; and (v) yield large quantities of DNA. Many mini-prep methods for obtaining DNA have been developed that have included such modifications as no grinding, no centrifugation, and/or no liquid transfer.
223 citations
TL;DR: The objective of this research was to assess the relationship of 18 major ancestors of North American soybean germplasm with 87 plant introductions (PIs) that are potential new sources of genetic variation for soybean breeding programs.
Abstract: The genetic base of soybean [Glycine max (L.) Merr.] cultivars developed for North America is very narrow. This may threaten the ability of breeders to sustain improvement and increase vulnerability of the crop to pests. The objective of this research was to assess the relationship of 18 major ancestors of North American soybean germplasm with 87 plant introductions (PIs) that are potential new sources of genetic variation for soybean breeding programs. Genetic distances (GD) among the 105 genotypes analyzed were calculated from 109 polymorphic DNA fragments amplified with random oligonucleotide primers and simple sequence repeat (SSR) primer pairs. Two hierarchical clustering algorithms were combined with data resampling and multidimensional scaling (MDS) to evaluate relationships among the genotypes. Genetic distances ranged from 0.08 to 0.76, with a mean of 0.52. Genotypes were placed in 11 clusters on the basis of a consensus of the different methods utilized. Co-occurrence values calculated from the resampling iterations showed that the stability of clusters varied. The most stable grouping was among ancestors that corresponded with known relationships based on pedigree and maturity. Several groups of PIs are distinct from the majority of the ancestors. These genotypes may be useful to breeders wanting to utilize genetically diverse introductions in soybean improvement.
216 citations
TL;DR: Three different types of molecular markers, RAPD, AFLP and RFLP were used to measure genetic diversity among six genotypes of Cucumis melo L. showed the highest efficiency in detecting polymorphism.
Abstract: Three different types of molecular markers, RAPD, AFLP and RFLP were used to measure genetic diversity among six genotypes of Cucumis melo L. Each line represented a different melon genotype: Piel de Sapo, Ogen, PI161375, PI414723, Agrestis and C105. A number of polymorphic RAPD, AFLP and RFLP bands were scored on all materials and the genetic similarity measured. Clustering analysis performed with the three types of markers separated the genotypes into two main groups: (1) the sweet type, cultivated melons and (2) the exotic type, not cultivated melons. While the data obtained suggest that all three types of markers are equally informative, AFLPs showed the highest efficiency in detecting polymorphism.
214 citations
TL;DR: Six methods for subtyping of Campylobacter jejuni were compared and evaluated with a collection of 90 isolates from poultry, cattle, and sporadic human clinical cases as well as from a waterborne outbreak, finding fla-DGGE and serotypes were the least discriminative.
Abstract: Six methods for subtyping of Campylobacter jejuni were compared and evaluated with a collection of 90 isolates from poultry, cattle, and sporadic human clinical cases as well as from a waterborne outbreak. The applied methods were Penner heat-stable serotyping; automated ribotyping (RiboPrinting); random amplified polymorphic DNA typing (RAPD); pulsed-field gel electrophoresis (PFGE); restriction fragment length polymorphisms of the flagellin gene, flaA (fla-RFLP); and denaturing gradient gel electrophoresis of flaA (fla-DGGE). The methods were evaluated and compared on the basis of their abilities to identify isolates from one outbreak and discriminate between unrelated isolates and the agreement between methods in identifying clonal lines. All methods identified the outbreak strain. For a collection of 80 supposedly unrelated isolates, RAPD and PFGE were the most discriminatory methods, followed by fla-RFLP and RiboPrinting. fla-DGGE and serotyping were the least discriminative. All isolates included in this study were found to be typeable by each of the methods. Thirteen groups of potentially related isolates could be identified using a criterion that at least four of the methods agreed on clustering of isolates. None of the subtypes could be related to only one source; rather, these groups represented isolates from different sources. Furthermore, in two cases isolates from cattle and human patients were found to be identical according to all six methods.
190 citations
TL;DR: Molecular and morphological evidence led to recognition of two separate olive taxa in Macaronesia, to date included in ssp.
Abstract: Phylogenetic relationships in the Olea europaea complex and the phylogeography of 24 populations of the Macaronesian olive (O. europaea ssp. cerasiformis) were assessed by using three molecular markers: nuclear ribosomal internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR). Parsimony analysis of the ITS-1 sequences and Neighbour-joining (NJ) analyses of RAPD and ISSR banding variation revealed four major lineages in the O. europaea complex: (1) ssp. cuspidata; (2) ssp. cerasiformis from Madeira; (3) ssp. laperrinei; and (4) ssp. cerasiformis from the Canary Islands plus ssp. europaea. These results provide unequivocal support for two independent dispersal events of Olea to the Madeira and Canary Islands. Molecular and morphological evidence led to recognition of two separate olive taxa in Macaronesia, to date included in ssp. cerasiformis. NJ analyses of the combined RAPD and ISSR data suggest that the colonization of the Canaries by O. europaea may have followed an east to west stepping-stone model. An interisland dispersal sequence can be recognized, starting from the continent to Fuerteventura, Gran Canaria, Tenerife, La Gomera, and finally La Palma. High dispersal activity of the lipid-rich Olea fruits by birds in the Mediterranean region is congruent with multiple dispersal of olives to Macaronesia and successive colonization of the archipelagos. The observation of strong genetic isolation between populations of different islands of the Canary Islands suggests, however, that subsequent interisland dispersal and establishment has been very rare or may not have occurred at all.
TL;DR: These markers can be used for marker-assisted selection for ascochyta blight resistance in chickpea breeding programs, and to develop durable resistant cultivars through gene pyramiding.
Abstract: Ascochyta blight, caused by Ascochyta rabiei (Pass.) Lab., is a devastating disease of chickpea (Cicer arietinum L.) worldwide. Resistant germplasm has been identified and the genetics of resistance has been the subject of numerous studies. The objectives of the present study were to determine the genetics of resistance to ascochyta blight of chickpea and to map and tag the chromosomal regions involved using molecular markers. We used a set of 142 F 5:6 recombinant inbred lines (RILs) obtained from an interspecific cross of C. arietinum (FLIP84-92C, resistant parent) x C. reticulatum Lad. (PI 599072, susceptible parent). The RILs were scored for disease reactions in the field over 2 yr and were genotyped for polymorphic molecular markers [isozyme, random amplified polymorphic DNA (RAPD), and inter simple sequence repeat (ISSR)] in the laboratory. The disease was scored quantitatively and data were used for QTL analysis. A linkage map was established that comprised nine linkage groups containing 116 markers covering a map distance of 981.6 centimorgans (cM) with an average distance of 8.4 cM between markers. Two quantitative trait loci (QTLs), QTL-1 and QTL-2, conferring resistance to ascochyta blight, were identified which accounted for 50.3 and 45.0% of the estimated phenotypic variation in 1997 and 1998, respectively, and were mapped to linkage groups 6 and 1, respectively. Two RAPD markers flanked QTL-1 and were 10.9 cM apart while one ISSR marker and an isozyme marker flanked QTL-2 and were 5.9 cM apart. These markers can be used for marker-assisted selection for ascochyta blight resistance in chickpea breeding programs, and to develop durable resistant cultivars through gene pyramiding.
TL;DR: A simple method for isolation of genomic DNA from wild plants sampled in remote field areas is presented and is suitable for random amplified polymorphic DNA (RAPD) analysis of plant populations as well as for specific amplification of chloroplast DNA sequences.
Abstract: A simple method for isolation of genomic DNA from wild plants sampled in remote field areas is presented. The protocol combines NaCI/CTAB leaf preservation with sorbitol extraction of secondary compounds which often contain inhibitors of Taq DNA polymerase activity. The obtained DNA is suitable for random amplified polymorphic DNA (RAPD) analysis of plant populations as well as for specific amplification of chloroplast DNA sequences. The NaCI/CTAB leaf preservation is a powerful alternative to silica gel dryingbased preservation.
TL;DR: The RAPD method, used to detect DNA damage in the sublittoral macroalgae Palmaria palmata (Rhodophyta) exposed to both ambient and elevated irradiances of UV-B, may prove to be a valuable tool for investigating the specific effects of genotoxic agents upon marine algal populations.
TL;DR: The changes detected by RAPD-PCR and AFLP indicate that genetic drift occurs within H. pylori populations over the course of years of colonization of a single host.
Abstract: Helicobacter pylori isolates show greater genetic diversity than other bacterial species studied, but the basis for this phenomenon is unknown. Whether detectable genomic mutation appears within an H. pylori population during persistent colonization was investigated. Paired H. pylori populations obtained across 7- to 10-year intervals from 13 patients were characterized by use of methods including polymerase chain reaction (PCR) genotyping for cagA, vacA, iceA, recA, and IS605; random arbitrarily primed DNA (RAPD)-PCR and amplified fragment length polymorphism (AFLP) analysis; and ELISA, to determine Lewis phenotypes. Genotyping, including recA sequence analysis, revealed that initial and follow-up populations represented the same population in 11 patients (85%). Nevertheless, distinct dissimilarities were shown within each of these 11 pairs by both RAPD-PCR and AFLP analyses. During follow-up, Lewis-y levels, but not Lewis-x levels, decreased significantly. The changes detected by RAPD-PCR and AFLP indicate that genetic drift occurs within H. pylori populations over the course of years of colonization of a single host.
TL;DR: Somatic hybrids between potato and Solanum bulbocastanum, a wild diploid Mexican species, are highly resistant to late blight, caused by Phytophthora infestans, by noting randomly amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers that are closely linked to the resistance.
Abstract: Somatic hybrids between potato and Solanum bulbocastanum, a wild diploid (2n=2x=24) Mexican species, are highly resistant to late blight, caused by Phytophthora infestans. Both randomly amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers that are closely linked to the resistance have been noted by analysis of three different backcross-2 populations derived from two different somatic hybrids. With reference to previously published potato and tomato maps, resistance appears to be on the long arm of chromosome 8 and is flanked by RFLP markers CP53 and CT64. In a population of BC2 plants derived from a cross between the BC1 line J10lK6 [(S. tuberosum PI 203900+S. bulbocastanum PI 243510) ×Katahdin)]×Atlantic, late blight resistance cosegregated with RFLP marker CT88 and RAPD marker OPG02–625.
TL;DR: In this paper, the authors analyzed molecular and morphological data from individuals in a hybrid zone between two species of willows ( Salix sericea Marshall and S. eriocephala Michaux) and report the use of randomly amplified polymorphic DNA (RAPD), chloroplast DNA (cpDNA), and ribosomal DNA (rDNA) markers, as well as vegetative morphology and foliar chemistry data to identify individuals in terms of hybrid genealogy and to infer the direction and extent of backcrossing and introgression within the hybrid zone.
Abstract: Hybrid zones provide biologists with the opportunity to examine genetic and ecological interactions between differentiated populations. Accurate identification of hybrid genealogies is considered a necessary prerequisite to understanding observed patterns of hybridization‐related phenomena. We analysed molecular and morphological data from individuals in a hybrid zone between two species of willows ( Salix sericea Marshall and S. eriocephala Michaux) and report the use of randomly amplified polymorphic DNA (RAPD), chloroplast DNA (cpDNA), and ribosomal DNA (rDNA) markers, as well as vegetative morphology and foliar chemistry data to identify individuals in terms of hybrid genealogy and to infer the direction and extent of backcrossing and introgression within the hybrid zone. A novel version of a maximum likelihood estimate approach (developed for this study) was used to calculate hybrid index scores from RAPD marker data; this method produced results similar to those obtained using traditional arithmetic methods. Distribution of rDNA, cpDNA, and chemistry data were examined within the graphical context of RAPD‐based hybrid index score histograms and principal component analyses (PCA) on RAPD and morphology data. Seven of the 21 plants classified as S. eriocephala in the field were possible introgressants. Another plant presented an unequivocal example of backcrossed S. sericea chemistry and RAPD markers. Inter‐ and intraspecific chloroplast diversity found within the hybrid zone suggests both historic introgression (perhaps in a glacial refugium), and contemporary hybridization. Patterns of inheritance and expression within the hybrid zone suggest that morphological characters are often not expressed in a simple additive fashion, and problems associated with both morphological and molecular data are considered.
TL;DR: Despite the intraspecific origin of this map, it did not show any increase in length when compared to the high-density interspecific map of tomato, and was compared to other published interspecific maps of tomato.
Abstract: We have constructed a tomato genetic linkage map based on an intraspecific cross between two inbred lines of Lycopersicon esculentum and L. esculentum var. cerasiforme. The segregating population w...
TL;DR: Six discrete phylogenetic lineages were recently identified in Trypanosoma cruzi, on the basis of multilocus enzyme electrophoresis and random amplified polymorphic DNA (RAPD) characterisation, with characteristic patterns that were distinct in the six lineages.
TL;DR: A comparison between marker-assisted selection (MAS) and conventional greenhouse screening showed that the cost of MAS is about one-third less than that of the greenhouse test.
Abstract: The possibility of using random amplified polymorphic DNA (RAPD) markers previously mapped in the common bean PC50/XANI59 population to select for resistance to common bacterial blight (CBB) in different populations was examined. Two out of 02 selected RAPD markers were polymorphic in HR56 and W0633d, the parental lines used in this experiment. Cosegregation analysis of the two polymorphic markers and disease reaction in a recombinant inbred (RI) population derived from HR67/W1744d confirmed that one of the two RAPD markers, BC420900, was significantly associated with a major quantitative trait locus-conditioning resistance to CBB in HR67. This locus accounted for approximately 51) of the phenotypic variation. The RAPD marker was transformed into a sequence characterized amplified region (SCAR) marker and used for selection in a different population derived from ‘Envoy’/HR67. Prediction for resistance to CBB with the BC420.990 SCAR marker was 94.2% accurate in this population. A comparison between marker-assisted selection (MAS) and conventional greenhouse screening showed that the cost of MAS is about one-third less than that of the greenhouse test.
TL;DR: It was concluded that RAPD and microsatellites could be useful and powerful tools for assessing genetic variation and genetic relationships in tetraploid alfalfa.
Abstract: The level of random amplified polymorphic DNA (RAPD) and microsatellite variation present in four ecotypes and two varieties of alfalfa (lucerne) from Italian and Egyptian germplasm sources was evaluated. A sample of 100 plants from 10 populations was analysed by means of 41 RAPD markers and 37 simple sequence repeat (SSR) markers. Both molecular approaches revealed a high degree of genetic diversity within each of the cultivated populations and enabled each of the plants considered to be uniquely fingerprinted. The genetic relationships among plants and populations were analysed by computing AMOVA (analysis of molecular variance) and F ST analyses. RAPDs were able to separate the Italian populations from the Egyptian variety. SSRs allowed strong separation of the lour Italian alfalfa ecotypes. It was concluded that RAPD and microsatellites could be useful and powerful tools for assessing genetic variation and genetic relationships in tetraploid alfalfa.
TL;DR: At the highest levels of genetic similarity there was only partial agreement as to relationships between individual accessions when different markers were used, and the advisability of extrapolating to other sets of germplasm particularly of other crop species is discussed.
Abstract: We have examined the effectiveness of similar numbers of markers from four molecular marker systems (AFLP, isozymes, ISSR and RAPD) for revealing genetic diversity and discriminating between infraspecific groups of Oryza sativa germplasm. Each marker system classifies the germplasm into three major groups (most effectively with isozymes and AFLPs), but with differences (primarily with ISSR) between the precise classifications generated. However, at the highest levels of genetic similarity there was only partial agreement as to relationships between individual accessions when different markers were used. When variance was partitioned among and within the three subspecific groups, although the differences were not significant, greater variation was found among than within groups using AFLP and isozymes, with the reverse for RAPD and ISSR. Measurement of polymorphism using average heterozygosity and effective number of alleles gave similar results for each marker system. These results are discussed in relation to various genetic resources conservation activities, and the advisability of extrapolating to other sets of germplasm particularly of other crop species.
TL;DR: The results suggest that although limited genetic heterogeneity among F. tularensis strains was observed, this small variation is enough to validate the PCR methods used in this study and their combinations, because they can provide safe, useful, and rapid tools for the typing of F. Tularensis.
Abstract: In this study, we evaluated three PCR methods for epidemiological typing of Francisella tularensis: repetitive extragenic palindromic element PCR (REP-PCR), enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), and random amplified polymorphic DNA (RAPD) assay with both M13 and T3-T7 primers. The analysis was performed with 40 strains of F. tularensis isolated from hares, humans, ticks, and a vole. On the basis of the combination of REP, ERIC, and RAPD fingerprints, F. tularensis strains were divided into 17 genetic groups (designated A to Q), and one Francisella novicida strain was classified in group R. The F. novicida strain is of special concern, since previous genetic methods have been unable to clearly distinguish between F. tularensis and F. novicida. The F. tularensis isolates recovered from hares were included in groups A to J, M, and P; those recovered from humans were included in groups A, D, G, J, L, O, and N; those isolated from ticks were included in groups B and Q; and that recovered from a vole was in group K. The diversities calculated for the 40 F. tularensis isolates, according to Simpson's index, were 0.14 for REP-PCR, 0.52 for ERIC-PCR, 0.39 for RAPD assay with the M13 primer (RAPD/M13-PCR), and 0.65 for RAPD/T3-T7-PCR, and the diversity increased up to 0.90 when ERIC-PCR, RAPD/M13-PCR, and RAPD/T3-T7-PCR were combined. Our results suggest that although limited genetic heterogeneity among F. tularensis strains was observed, this small variation is enough to validate the PCR methods used in this study and their combinations, because they can provide safe, useful, and rapid tools for the typing of F. tularensis.
TL;DR: Results of RAPD marker analysis suggest that 80 marker bands were adequate for assessing the genetic variation present in the accessions examined, and that, per band, lower coefficients of variation can be attained in the estimation of GD when using RAPDs compared to SSRs.
Abstract: 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 were important (p =0.01) in the detection of genetic differences. Estimators of GD were highly correlated (p 0.0001; rs = 0.64 to0.99) when comparisons were made between estimation methods within a particular marker system. Lower correlations (rs = 0.17 to 0.40) were detected (P > 0.001) between marker systems using any one estimator. The GD of the Conomon and Flexuosus accessions was significantly different (p> 0.001)from the mean GD of all the market classes examined. The mean GD (Jaccard's coefficient) among accessions of Ogen, Galia, Cassaba, Charentais, European shipper, and U.S. shipper groups was 0.11 ± 0.04, 0.33± 0.09, 0.21 ± 0.04, 0.26 ± 0.10, 0.17± 0.05 and 0.22 ± 0.08, respectively. Market classes were distinct (p > 0.001), such that GDs between Galia and other accessions were the largest(mean GD 0.34 to 0.35), and GDs between Ogen and other accessions were the smallest (mean GD 0.29 to 0.30). Contrasts between the U.S. shipper cultivar Top Mark and accessions within any market class was relatively large (mean GD = 0.42 ± 0.06). Empirical estimations of variances associated with each marker type in the accessions examined indicated that, per band, lower coefficients of variation can be attained in the estimation of GD when using RAPDs compared to SSRs. Nevertheless, the genetic relationships identified using these markers were generally similar. The disparity between the analyses of the two markers made may be related to the amount of genome coverage which is characteristic of a particular marker system and/or its efficiency in sampling variation in a population. Results of RAPD marker analysis suggest that 80 marker bands were adequate for assessing the genetic variation present in the accessions examined.
TL;DR: In the present study, 70 selected genotypes, representing variability for several morphological, physiological, and other characters, were studied for polymorphism employing random amplified polymorphic DNA (RAPD) assay with 48 oligonucleotide primers.
Abstract: Construction of a genetic linkage map is necessary to apply marker-assisted selection tools in a crop improvement program. Except for the recent studies from two laboratories, most of the previous studies have shown little or no DNA polymorphism in cultivated groundnut (Arachis hypogaea L.). In the present study, 70 selected genotypes, representing variability for several morphological, physiological, and other characters, were studied for polymorphism employing random amplified polymorphic DNA (RAPD) assay with 48 oligonucleotide primers. Of the 48 oligonucleotide primers only 7 (14.6%) yielded polymorphic amplification products. The total number of bands from the 7 primers was 408, of which 27 were polymorphic. Detection of polymorphism in cultivated groundnut opens up the possibility of development of its molecular map by judicious selection of genotypes that show DNA polymorphism. This approach will be useful for developing marker-assisted selection tools for genetic enhancement of groundnut for desirable traits.
TL;DR: A population genetic analysis of gene flow was conducted among 10 Aedes aegypti collections from seven cities along the northeastern coast of Mexico indicating that populations are isolated by distance and that free gene flow occurs among collections within 90-250 km.
Abstract: A population genetic analysis of gene flow was conducted among 10 Aedes aegypti collections from seven cities along the northeastern coast of Mexico. Four collections were made from Monterrey to examine local patterns of gene flow. Markers included 60 random amplified polymorphic DNA (RAPD) loci amplified by the polymerase chain reaction and single strand conformation polymorphism analysis of variation in a 387-basepair region of the NADH dehydrogenase subunit 4 from the mitochondrial DNA (mtDNA). Seven mitochondrial haplotypes were detected and phylogenetic analysis identified two well-supported clades. Regression analysis of geographic distances and pairwise FST estimated from RAPD markers indicated that populations are isolated by distance and that free gene flow occurs among collections within 90-250 km. Isolation by distance was not detected using mtDNA haplotypes. The Nuevo Laredo collection had unique RAPD and mtDNA haplotype frequencies and reduced heterozygosity suggesting that few mosquitoes established this population.
TL;DR: Results from this study corroborate the usefulness of AFLP markers for assigning inbreds into heterotic groups and revealing pedigree relationships among lines.
Abstract: A set (if 51 elite maize (Zea mays L.) inbred lines representative of the early-maturing European flint and dent heterotic groups were assayed for amplified fragment length polymorphisms (AFLP) markers using eight primer combinations. Our main objectives were to (i) investigate the amount of variation for AFLP markers in these materials, (ii) examine the usefulness of AFLP markers for assigning inbred lines to heterotic groups, and (iii) compare the genetic similarity (GS) based on AFLP markers with Malecot's coancestry coefficient (f) based on pedigree data and with GS estimates based on restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNA (RAPD) data. The eight AFLP primer combinations yielded 462 polymorphic bands. GS estimates calculated from AFLP data ranged between 0.38 and 0.77 between unrelated (f=0) pairs of lines. All flint and dent inbreds showed a smaller mean GS to lines from the other heterotic group than to unrelated lines from the same heterotic group. For lines of mixed origin, the difference in mean GS to flint lines and to dent lines was consistent with the expected genomic proportions from each heterolic group determined on the basis of pedigrees. Principle coordinate analysis of GS estimates resulted in a separate grouping of flint and dent lines. Correlations between f and GS estimates were substantially higher for RFLPs and AFLP markers than for RAPDs. Correlations of GS estimates based on different marker systems were closest between RFLP and AFLP markers both for related (J > 0) and unrelated (f=0) pairs of flint and dent lines. Results from this study corroborate the usefulness of AFLP markers for (i) assigning inbreds into heterotic groups and (ii) revealing pedigree relationships among lines.
TL;DR: From the analysis of results, it appears the majority of mango cultivars originated from a local mango genepool and were domesticated later.
Abstract: SummaryDNA-based RAPD (Random Amplification of Polymorphic DNA) markers have been used extensively to study genetic relationships in a number of fruit crops. A wide genetic diversity exists in the mango fruit in India. Present day commercial cultivars originated mainly from this subcontinent. In this study, 18 commercial mango cultivars, traditionally grown in western, southern, northern and eastern parts of India, were selected to assess genetic relatedness. Total genomic DNA was extracted and subjected to RAPD analysis using 30 arbitrary 10-mer primers. Of these, 27 primers amplified mango genomic DNA. None of these primers produced unique band pattern for each cultivar. RAPD data were used to calculate a squared Euclidean distance matrix, and based on this cluster analysis was done using a minimum variance algorithm. Cluster analysis clearly showed two groups—the first consisting of western, northern and eastern mango cultivars and the second group consisting of southern cultivars. From the analysis of...
TL;DR: The narrow genetic base of the greengram cultivars revealed in the present analysis emphasises the need to exploit the large germplasm collections having diverse morphoagronomic traits in cultivar improvement programs.
Abstract: Greengram [Vigna radiata (L.) Wilczek], also known as mung bean, widely cultivated in a large number of countries, is an important pulse crop of Asia and is considered one of the ancestral species of the genus Vigna. Since yields of greengram have remained low across subtropical and tropical Asia, it is important to estimate genetic diversity in existing cultivars in order to see if the lack of genetic variability might be a constraining factor. In this study, 32 Indian cultivars of greengram were subjected to random amplified polymorphic DNA (RAPD) analysis using 21 decamer primers. A total of 267 amplification products were formed at an average of 12.71 per primer with an overall polymorphism of 64%. The extent of polymorphism was moderate to low. Jaccard similarity coefficient values ranged from 0.65 to 0.92. The cluster analysis resulted in mainly three clusters revealing greater homology between cultivars released from the same source. The results of principal components analysis also substantiated this conclusion. The close genetic similarity between the cultivars could be explained due to the high degree of commonness in their pedigrees. The narrow genetic base of the greengram cultivars revealed in the present analysis emphasises the need to exploit the large germplasm collections having diverse morphoagronomic traits in cultivar improvement programs.
TL;DR: Analysis of genetic structure of the populations of the blacklip abalone Haliotis rubra of Victoria, Australia revealed that a Point Cook population sampled from within the semi-enclosed Port Phillip Bay was distinct from two other central zone populations.
Abstract: We investigated the utility of three polymerase chain-reaction (PCR)-based DNA molecular markers in analysing genetic structure of the populations of the blacklip abalone Haliotis rubra (Leach) of Victoria, Australia The DNA markers included 84 randomly amplified polymorphic DNA (RAPD) bands amplified using six random primers, two minisatellites, GHR (putative growth-hormone-gene-repeat) and MIPR (putative mollusca-insulin-like peptide-gene-repeat), and three microsatellites, RUBGT1 [containing (GT)n repeats], RUBCA1 [containing (CA)n repeats] and RUBGACA1 [containing (GACA)n repeats] All three types of DNA markers revealed significant subdivision in the H rubra populations along the coastline This is postulated as being related to the abalone's relatively short pelagic period and limited dispersion Further analysis revealed that a Point Cook population sampled from within the semi-enclosed Port Phillip Bay was distinct from two other central zone populations (Apollo Bay and Cape Schanck) The genotypes of microsatellites indicated excessive homozygotes across all the populations at all three microsatellite loci, and possible causes such as larval recruitment pattern and asynchronous spawning are discussed The excessive homozygotes recorded for the three microsatellite loci contrast with those observed in the minisatellite loci GHR and MIPR, the heterozygosities of which were at Hardy–Weinberg equilibrium