Showing papers on "RAPD published in 2002"
TL;DR: An overview of the details of the ISSR-PCR technique and its application in genetics and plant breeding in a wide range of crop plants is provided.
Abstract: Summary Inter simple sequence repeat (ISSR)-PCR is a technique, which involves the use of microsatellite sequences as primers in a polymerase chain reaction to generate multilocus markers. It is a simple and quick method that combines most of the advantages of microsatellites (SSRs) and amplified fragment length polymorphism (AFLP) to the universality of random amplified polymorphic DNA (RAPD). ISSR markers are highly polymorphic and are useful in studies on genetic diversity, phylogeny, gene tagging, genome mapping and evolutionary biology. This review provides an overview of the details of the technique and its application in genetics and plant breeding in a wide range of crop plants.
880 citations
TL;DR: This work describes a Bayesian method that allows direct estimates of FST from dominant markers and illustrates the method with a reanalysis of RAPD data from 14 populations of a North American orchid, Platanthera leucophaea.
Abstract: Molecular markers derived from polymerase chain reaction (PCR) amplification of genomic DNA are an important part of the toolkit of evolutionary geneticists. Random amplified polymorphic DNA markers (RAPDs), amplified fragment length polymorphisms (AFLPs) and intersimple sequence repeat (ISSR) polymorphisms allow analysis of species for which previous DNA sequence information is lacking, but dominance makes it impossible to apply standard techniques to calculate F-statistics. We describe a Bayesian method that allows direct estimates of FST from dominant markers. In contrast to existing alternatives, we do not assume previous knowledge of the degree of within-population inbreeding. In particular, we do not assume that genotypes within populations are in Hardy-Weinberg proportions. Our estimate of FST incorporates uncertainty about the magnitude of within-population inbreeding. Simulations show that samples from even a relatively small number of loci and populations produce reliable estimates of FST. Moreover, some information about the degree of within-population inbreeding (FIS) is available from data sets with a large number of loci and populations. We illustrate the method with a reanalysis of RAPD data from 14 populations of a North American orchid, Platanthera leucophaea.
459 citations
TL;DR: Bulk analyses of RAPD and ISSR PCR markers provides a quick, reliable and highly informative system for DNA fingerprinting and also permit to establish genetic relationships which agree with, by other means, known origin of the cultivars.
Abstract: The potential of bulk analyses of RAPD and ISSR-PCR markers for fingerprinting purposes was evaluated using ten RAPD and ten ISSR primers. The phylogenetic relationships of 16 barley cultivars from different countries, and all having a known pedigree, were analysed using 353 PCR markers (125 RAPDs and 228 ISSRs). The band profiles generated were reproducible in spite of the different DNA extractions, PCR techniques, electrophoretic methods and gel scorings used. The RAPD primer S10 and four ISSR primers (811, 820, 835 and 881) were both able to distinguish all cultivars. A strong and quite linear relationship was observed between Resolving Power (Rp) of a primer and its ability to distinguish genotypes. The dendrograms obtained using these two molecular markers are in agreement with their known origin, showing clusters that separate very well the spring/winter and six-rows/two-rows cultivars. Thus, bulk analyses of RAPD and ISSR PCR markers provides a quick, reliable and highly informative system for DNA fingerprinting and also permit to establish genetic relationships which agree with, by other means, known origin of the cultivars.
344 citations
TL;DR: The vaginal flora of most participants was dominated by a single RAPD type, but five of them harbored two RAPD types representing two different species or strains, and Lactobacillus iners has not previously been reported as one of the predominant LactOBacillus species in the vagina.
Abstract: Species of the Lactobacillus acidophilus complex are generally considered to constitute most of the vaginal Lactobacillus flora, but the flora varies between studies. However, this may be due to difficulties in identifying the closely related species within the L. acidophilus complex by using traditional methods and to variations in the vaginal status of the participants. Two hundred two isolates from the vaginal fluids of 23 Swedish women without bacterial vaginosis, as defined by the criteria of Nugent et al. (R. P. Nugent, M. A. Krohn, and S. L. Hillier, J. Clin. Microbiol. 29:297-301, 1991), were typed by randomly amplified polymorphic DNA (RAPD) analysis and identified to the species level by temporal temperature gradient gel electrophoresis, multiplex PCR, and 16S ribosomal DNA sequencing. The vaginal flora of most participants was dominated by a single RAPD type, but five of them harbored two RAPD types representing two different species or strains. The most frequently occurring species were Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii. L. iners has not previously been reported as one of the predominant Lactobacillus species in the vagina.
330 citations
TL;DR: Increasing use of carbapenems and ciprofloxacin (selective pressure) as well as clonal dissemination might have contributed to the wide spread of PDRAB in this hospital.
Abstract: The rapid emergence (from 0% before 1998 to 6.5% in 2000) of pandrug-resistant Acinetobacter baumannii (PDRAB) was noted in a university hospital in Taiwan. To understand the epidemiology of these isolates, we studied 203 PDRAB isolates, taken from January 1999 to April 2000: 199 from 73 hospitalized patients treated at different clinical settings in the hospital and 4 from environmental sites in an intensive-care unit. Pulsed-field gel electrophoresis analysis and random amplified polymorphic DNA (RAPD) generated by arbitrarily primed polymerase chain reaction of these 203 isolates showed 10 closely related genotypes (10 clones). One (clone 5), belonging to pulsotype E and RAPD pattern 5, predominated (64 isolates, mostly from patients in intensive care). Increasing use of carbapenems and ciprofloxacin (selective pressure) as well as clonal dissemination might have contributed to the wide spread of PDRAB in this hospital.
262 citations
TL;DR: The development and applications of SNP genetic markers in corn and other crop plants are discussed, and the contribution of these studies towards the understanding of the organization of genetic diversity in plants is discussed.
256 citations
TL;DR: Cluster analysis for cultivated chickpea differentiated Kabuli and Desi types but the authors did not detect a clear relationship between groups and the geographical origin of the accessions, suggesting the possibility of gene flow between species.
Abstract: Seventy five accessions belonging to 14 species of the genus Cicer were analysed with PCR-based molecular markers to determine their phylogenetic relationships. Eight of the species were annuals and included the Section Monocicer which contains cultivated chickpea (Cicer arietinum L.). The remaining six species were perennials (five from Section Polycicer and one from Section Acanthocicer). More than one accession per species was analysed in most of the wild species; within C. arietinum, 26 accessions including Kabuli and Desi types, were studied. RAPD analyses using 12 primers gave 234 polymorphic fragments. Variability within species was detected. A dendrogram based on the Jaccard similarity index showed that the distribution pattern of variability between species was related to both growth habit and geographical origin. An accession of Cicer reticulatum was closer to accessions of Cicer echinospermum than to the four remaining of C. reticulatum, suggesting the possibility of gene flow between species. Cluster analysis for cultivated chickpea differentiated Kabuli and Desi types but we did not detect a clear relationship between groups and the geographical origin of the accessions.
202 citations
TL;DR: It is concluded that when the tissue culture technique is used, the analysis of somaclonal variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as the results showed for SSR and RAPD markers.
Abstract: Two different DNA-based techniques, random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers, were used for fingerprinting kiwifruit genotypes and for detecting undesirable genetic variation in micropropagated plants. The fragments were scored as present (1) or absent (0), and those readings were entered in a computer file as a binary matrix (one for each marker). Two cluster analyses were performed to express – in the form of dendrograms – the relationships among the genotypes and the genetic variability detected. Both DNA-based techniques were able to amplify all of the genotypes, but only SSR markers could detect genetic variation induced in micropropagated plants of cv. Tomuri. Two hypotheses were formulated to explain these results, both of them are in agreement with the results obtained using these two types of molecular markers. We conclude that when the tissue culture technique is used, the analysis of somaclonal variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as our results showed for SSR and RAPD markers.
192 citations
TL;DR: The rigorous screening of nuclear and two organellar genomes has demonstrated, for the first time, subtle genetic variation at the DNA sequence level in organized meristem-derived micropropagated plants of tea.
Abstract: An efficient in vitro propagation method using enhanced axillary branching cultures produced plants from nodal explants of three mature, elite tea clones: diploid UPASI 26 and UPASI 27 (2n=2x=30) representing Camellia sinensis (China type) and triploid UPASI 3 (2n=3x=45) representing C. assamica ssp. assamica (Assam-India type). The genetic fidelity of the micropropagated plants of these three tea clones was assessed by analysing their nuclear, mitochondrial (mt), and chloroplast (cp) genomes using multiple molecular DNA markers. A total of 465, 446 and 462 genetic loci were produced with RFLP, RAPD and ISSR fingerprinting in the micropropagated plants and the corresponding mother plant of C. sinensis clone U (UPASI) 26, and C. assamica ssp. assamica clones U3 and U27, respectively. RFLP fingerprinting was performed using six restriction endonuclease digests and 14 mt and cp gene probes in 84 enzyme-probe combinations. For PCR fingerprinting, 50 RAPD and SSR primers were used for amplifications. The micropropagated plants of both the U3 and U27 clones revealed complete stability in the 462 and 446 genetic loci analysed. In comparison, 36 (7.7%) of the 465 loci were polymorphic among micropropagated plants of the U26 clone. The observed polymorphic loci were not restricted to a particular genome (nuclear or organellar), although a relatively low (7.43%) level of polymorphism was observed in the nuclear as compared to the mt genome (16.3%). ISSR fingerprinting (12.8%) detected more polymorphic loci than RAPD fingerprinting (4.28%). No polymorphism was observed in the cp genome of the micropropagated plants of the three tea clones. The rigorous screening of nuclear and two organellar genomes has demonstrated, for the first time, subtle genetic variation at the DNA sequence level in organized meristem-derived micropropagated plants of tea. Clearly, this is another example demonstrating that organized meristem cultures are not always genetically true-to-type. The genomic changes in tea clones are genotype dependent rather than culture condition dependent.
187 citations
TL;DR: The random amplified polymorphic DNA (RAPD) assay and related techniques like the arbitrarily primed polymerase chain reaction (AP-PCR) have been shown to detect genotoxin-induced DNA damage and mutations but further research is required to better understand the potential and limitations of the RAPD assay.
Abstract: The random amplified polymorphic DNA (RAPD) assay and related techniques like the arbitrarily primed polymerase chain reaction (AP-PCR) have been shown to detect genotoxin-induced DNA damage and mutations. The changes occurring in RAPD profiles following genotoxic treatments include variation in band intensity as well as gain or loss of bands. However, the interpretation of the molecular events responsible for differences in the RAPD patterns is not an easy task since different DNA alterations can induce similar type of changes. In this study, we evaluated the effects of a number of DNA alterations on the RAPD profiles. Genomic DNA from different species was digested with restriction enzymes, ultrasonicated, treated with benzo[a]pyrene (B[a]P) diol epoxide (BPDE) and the resulting RAPD profiles were evaluated. In comparison to the enzymatic DNA digestions, sonication caused greater changes in the RAPD patterns and induced a dose-related disappearance of the high molecular weight amplicons. A DNA sample substantially modified with BPDE caused very similar changes but amplicons of low molecular weight were also affected. Appearance of new bands and increase in band intensity were also evident in the RAPD profiles generated by the BPDE-modified DNA. Random mutations occurring in mismatch repair-deficient strains did not cause any changes in the banding patterns whereas a single base change in 10-mer primers produced substantial differences. Finally, further research is required to better understand the potential and limitations of the RAPD assay for the detection of DNA damage and mutations.
184 citations
TL;DR: It is concluded that the method developed here has potential for application in routine diagnostic procedures, and multiplex PCR using the three pairs of SCAR primers in a single reaction enabled the unambiguous identification of each species, even in mixtures.
Abstract: RAPD markers were used to characterize the genetic diversity and relationships of root-knot nematodes (RKN) (Meloidogyne spp.) in Brazil. A high level of infraspecific polymorphism was detected in ...
TL;DR: It appears that the clones present in bovine sources are not transmitted to humans in the Calcutta setting although these strains showed evolutionary relatedness, and STEC has still not become a major problem in India.
Abstract: Antibiotic resistance, virulence gene, and molecular profiles of Shiga toxin-producing Escherichia coli (STEC) non-O157 strains isolated from human stool samples, cow stool samples, and beef samples over a period of 2 years in Calcutta, India, were determined. Resistance to one or more antibiotics was observed in 49.2% of the STEC strains, with some of the strains exhibiting multidrug resistance. The dominant combinations of virulence genes present in the strains studied were stx1 and stx2 (44.5% of strains) and stx1, stx2, and hlyA (enterohemorrhagic E. coli hemolysin gene) (19% of strains). Only 6.4% of the STEC strains harbored eae. The diversity of STEC strains from various sources was assessed by random amplification of polymorphic DNA (RAPD). STEC strains that gave identical or nearly similar DNA fingerprints in RAPD-PCR and had similar virulence genotypes were further characterized by pulsed-field gel electrophoresis (PFGE). Identical RAPD and PFGE profiles were observed in four sets of strains, with each set comprising two strains. There was no match in the RAPD and PFGE profiles between strains of STEC isolated from cows and those isolated from humans. It appears that the clones present in bovine sources are not transmitted to humans in the Calcutta setting although these strains showed evolutionary relatedness. Maybe for this reason, STEC has still not become a major problem in India.
TL;DR: The approach demonstrates the usefulness and feasibility of marker discovery in one population followed by accurate mapping of that marker onto a core, community-wide map and the probable existence of multiple genes controlling growth habit in common bean.
Abstract: Common bean (Phaseolus vulgaris L.) exhibits a wide variety of seed coat patterns and colors. From a historical perspective, extensive genetic analyses have identified specific genes that control seed coat pattern (T, Z, L, J, Bip, and Ana) and color (P, C, R, J, D, G, B, V, and Rk). Many of these genes exhibit epistatic interactions with other genes, interactions that define the many seed coat patterns and colors observed within the species. To better understand these complex interactions, we began a molecular marker discovery program that previously identified random amplified polymorphic DNA (RAPD) markers linked to many of these genes. We report here the discovery of RAPD markers linked to three additional genes-C, G, and V. These markers, and five RAPD markers we previously discovered linked to other seed coat pattern and color genes, were converted into easily scorable sequence tagged site (STS) markers. We next placed these markers onto a common molecular map shared by the Phaseolus research community and demonstrated a generally wide distribution of the genes throughout the common bean genome. A few previously unrecognized linkages were discovered. The probable existence of multiple genes controlling growth habit in common bean is discussed. Our approach demonstrates the usefulness and feasibility of marker discovery in one population followed by accurate mapping of that marker onto a core, community-wide map.
TL;DR: The importance of the study of the amount and distribution of genetic diversity for a better exploration of olive genetic resources and the design of plant breeding programmes is indicated.
Abstract: Genetic diversity studies using the RAPD technique were carried out in a set of 103 olive cultivars from the World Germplasm Bank of the Centro de Investigacion y Formacion Agraria (CIFA) "Alameda del Obispo" in Cordoba (Spain). A total of 126 polymorphisms (6.0 polymorphic markers per primer) out of 135 reproducible products (6.4 fragments per primer) were obtained from the 21 primers used. The number of bands per primer ranged from 4 to 11, whereas the number of polymorphic bands ranged from 3 to 10, corresponding to 83% of the amplification products. The dendrogram based on unweighted pair-group cluster analysis using Jaccard's index includes three major groups according to their origin: (1) cultivars from the Eastern and Central Mediterranean areas, (2) some Italian and Spanish cultivars, and (3) cultivars from the Western Mediterranean zone. The pattern of genetic variation among olive cultivars from three different Mediterranean zones (West, Centre and East) was analysed by means of the analysis of molecular variance (AMOVA). Although most of the genetic diversity was attributable to differences of cultivars within Mediterranean zones (96.86%) significant φ-values among zones (φst = 0.031; p < 0.001) suggested the existence of phenotypic differentiation. Furthermore, the AMOVA analysis was used to partition the phenotypic variation of Spain, Italy (Western region), Greece and Turkey (Eastern region) into four categories: among regions, among countries (within regions), within countries, and among and within countries of each region. Most of the genetic diversity was attributable to differences among genotypes within a country. These results are consistent with the predominantly allogamous nature of Olea europaea L. species. This paper indicates the importance of the study of the amount and distribution of genetic diversity for a better exploration of olive genetic resources and the design of plant breeding programmes.
TL;DR: Southern hybridization, using PSDM as a probe, showed that PSDM exists in the male and hermaphrodite genomes, but not in the female genome, suggesting that SCARps is a suitable marker for the precise and rapid diagnosis of sex in papaya.
Abstract: The random amplified polymorphic DNA (RAPD) technique was used to determine the sex of a dioecious species, Carica papaya L., with three sex types, male, female and hermaphrodite. A 450 bp marker fragment, named PSDM(Papaya Sex Determination Marker), exists in all male and hermaphrodite plants but not in the female plants so far analyzed. The DNA sequence of PSDM exhibited no significant similarity to previously reported sequences. A sequence-characterized amplified region (SCAR) marker, SCARps, was developed from PSDM to determine the sex of papaya. Southern hybridization, using PSDM as a probe, showed that PSDM exists in the male and hermaphrodite genomes, but not in the female genome. This result strongly suggests that PSDM is located on the chromosome region that is specific to the male and the hermaphrodite. SCARps is a suitable marker for the precise and rapid diagnosis of sex in papaya.
TL;DR: Production of amicoumacin antibiotics by B. subtilis is a common characteristic of individual strains that presented genetic and physiological homogeneity, and no association was detected between RAPD profiles and the geographic origin or habitat of the strains tested.
TL;DR: Twenty two RAPD and 22 ISSR markers were evaluated for their potential use in determination of genetic relationships in chickpea cultivars and breeding lines and were able to identify six cultivar-specific markers.
Abstract: Twenty two RAPD and 22 ISSR markers were evaluated for their potential use in determination of genetic relationships in chickpea (Cicer arietinum L.) cultivars and breeding lines. We were able to identify six chickpea cultivars/breeding lines by cultivar-specific markers. All of the cultivars tested displayed a different phenotype generated either by the RAPD or ISSR primers. Though ISSR primers generated less markers than RAPD primers, the ISSR primers produced higher levels of polymorphism (% of polymorphic markers per primer) than RAPD primers. A high level of within cultivar homogeneity was observed in chickpea. Cultivars/breeding lines originating from a common genetic background showed closer genetic relationship. Chickpea lines with similar seed type(kabuli or desi) had a tendency to cluster together.
TL;DR: The authors' data indicate that different genomic-based methods can be used to type B. cepacia genomovar III isolates depending on the situation and the epidemiologic question being addressed, and BOX-PCR fingerprints can be considered a rapid and easy alternative to MLRT.
Abstract: We analyzed a collection of 97 well-characterized Burkholderia cepacia genomovar III isolates to evaluate multiple genomic typing systems, including pulsed-field gel electrophoresis (PFGE), BOX-PCR fingerprinting and random amplified polymorphic DNA (RAPD) typing. The typeability, reproducibility, and discriminatory power of these techniques were evaluated, and the results were compared to each other and to data obtained in previous studies by using multilocus restriction typing (MLRT). All methods showed excellent typeability. PFGE with SpeI was more reproducible than RAPD and BOX-PCR fingerprinting. The discriminatory power of the methods was variable, with PFGE and RAPD typing having a higher index of discrimination than BOX-PCR fingerprinting. In general, the results obtained by PFGE, BOX-PCR fingerprinting, and MLRT were in good agreement. Our data indicate that different genomic-based methods can be used to type B. cepacia genomovar III isolates depending on the situation and the epidemiologic question being addressed. PFGE and RAPD fingerprinting are best suited to addressing small-scale studies (i.e., local epidemiology), whereas BOX-PCR fingerprinting is more appropriate for large-scale studies (i.e., global epidemiology). In this regard, BOX-PCR fingerprinting can be considered a rapid and easy alternative to MLRT.
TL;DR: The study suggests the need to breed for high genetic diversity to serve as a buffer against potential epidemics and demonstrates that only cultivar VH-137 possesses a diverse genetic background.
Abstract: Epidemics of cotton leaf curl virus disease (CLCD) was the compelling factor in the decision to devise new strategies for cotton breeding programs of Pakistan. The genetic similarity among the elite cotton (Gossypium spp.) cultivars released before the advent of CLCD epidemics was in the range of 81.5 to 93.41%. New cultivars were developed by crossing the exotic resistant germplasm (LRA-5166, CP-15/2, and Cedix) with adapted varieties highly susceptible to CLCD. A study was designed to assess the genetic relatedness or diversity among the newly released, extremely resistant and resistant cultivars. After screening 27 cotton genotypes by different diagnostic methods such as field evaluation, whitefly-transmission studies, grafting, dot-blot hybridization, and multiplex PCR using conserved primers sequences, 20 extremely resistant and resistant cultivars were selected for a random amplified polymorphic DNA (RAPD) analysis. The genetic similarity of the exotic germplasm with the elite cultivars was in the range of 81.45 to 90.59%. Similarly, the genetic relatedness among the elite cultivars was in the range of 81.58 to 94.90%. The average genetic similarity among all studied genotypes was 89.55%. We have demonstrated that only cultivar VH-137 possesses a diverse genetic background. Our study suggests the need to breed for high genetic diversity to serve as a buffer against potential epidemics.
TL;DR: Despite the heterogenous fermentation results for some genotypic profiles, a ranking of RAPD groups is possible and can be useful in the further selection and study of B. subtilis strains.
TL;DR: An improved genetic linkage map has been constructed for cowpea based on the segregation of various molecular markers and biological resistance traits in a population of 94 recombinant inbred lines derived from the cross between 'IT84S-2049' and '524B'.
Abstract: An improved genetic linkage map has been constructed for cowpea (Vigna unguiculata L. Walp.) based on the segregation of various molecular markers and biological resistance traits in a population o...
TL;DR: Randomly amplified polymorphic DNA (RAPD) has emerged as an effective genetic marker for analysis of Trypanosoma cruzi population variability and was used to study the genetic variability of Mexican T. cruzi stocks and to relate these results to previous classifications.
Abstract: Randomly amplified polymorphic DNA (RAPD) has emerged as an effective genetic marker for analysis of Trypanosoma cruzi population variability. This method has been used to study the genetic variability of Mexican T. cruzi stocks and to relate these results to previous classifications. High clonal diversity was observed among the Mexican populations: 24 RAPD types were scored among 56 stocks analyzed. Only two stocks (3.6%) belonged to the T. cruzi II lineage, while all others belonged to T. cruzi I. The robustness of these clusters was statistically highly significant. Mexican T. cruzi I stocks formed a homogeneous group with reduced genetic distances among its members. Parasites from this group were isolated from both domestic and sylvatic cycles over a broad geographic area in Mexico. The two Mexican stocks classified as T. cruzi II (isolated from sylvatic cycles) were of the same RAPD type, although they were not closely related to the three reference T. cruzi II stocks circulating in domestic cycles in Argentina, Brazil, Bolivia, and Chile. These stocks were also unrelated to the formerly named Zymodeme III.
TL;DR: Enterococcus faecium strains from various sources were characterized by random amplified polymorphic DNA (RAPD)-PCR, amplified fragment length polymorphism (AFLP), and pulsed-field gel electrophoresis (PFGE) analysis of SmaI restriction patterns, revealing high genetic strain diversity within the two genomic groups.
Abstract: Seventy-eight Enterococcus faecium strains from various sources were characterized by random amplified polymorphic DNA (RAPD)-PCR, amplified fragment length polymorphism (AFLP), and pulsed-field gel electrophoresis (PFGE) analysis of SmaI restriction patterns. Two main genomic groups (I and II) were obtained in both RAPD-PCR and AFLP analyses. DNA-DNA hybridization values between representative strains of both groups demonstrated a mean DNA-DNA reassociation level of 71%. PFGE analysis revealed high genetic strain diversity within the two genomic groups. Only group I contained strains originating from human clinical samples or strains that were vancomycin-resistant or beta-hemolytic. No differentiating phenotypic features between groups I and II were found using the rapid ID 32 STREP system. The two groups could be further subdivided into, respectively, four and three subclusters in both RAPD-PCR and AFLP analyses, and a high correlation was seen between the subclusters generated by these two methods. Subclusters of group I were to some extent correlated with origin, pathogenicity, and bacteriocinogeny of the strains. Host specificity of E. faecium strains was not confirmed.
TL;DR: This study identified genetic loci associated with 14 quantitative traits responsible for seed yield, yield components, and plant architecture traits in common bean to improve understanding of the genetic factors conditioning these traits and is expected to assist in the selection of superior genotypes.
Abstract: SBreeding effort to improve yield and other quantitative traits in common bean (Phaseolus vulgaris L.) has proven to be difficult. The use of molecular markers will improve our understanding of the genetic factors conditioning these traits and is expected to assist in the selection of superior genotypes. This study was conducted to identify genetic loci associated with 14 quantitative traits responsible for seed yield, yield components, and plant architecture traits in common bean. A population of 142 F(2:4) lines that was developed from a cross between OAC Seaforth and OAC 95-4, was evaluated at two locations in Canada in 1998. The lines were assayed for random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), simple sequence repeat (SSR), and amplified fragment length polymorphism (AFLP) markers. One hundred fourteen markers were assigned to 12 linkage groups. Growth habit and resistance to common bacterial blight [CBB, caused by Xanthomonas axonopodis pv. phaseoli (Smith) Vauterin, Hoste, Kosters & Swings = syn. X. campestris pv. phaseoli (Smith) Dye] were each mapped as single major genes on linkage groups G11 and G5, respectively. An alignment of the current map with the previous linkage map developed at the University of Florida and the core linkage map of bean was produced from 30 RFLP loci. Twenty quantitative trait loci (QTL) were identified for the 14 traits that were analyzed. The number of QTL identified per trait ranged from one to three. A multiple QTL model for each trait showed that these genomic regions accounted for 11.3 to 43.1% of the total phenotypic variation for the traits. Five of the twenty QTL were detected at both locations. The strengths of QTL effects for a given trait appeared to be slightly different among locations, but the positions of QTL on the map were stable across locations.
TL;DR: Recombinant inbred lines developed from a cross between 'IR50' and 'IR54745-2-21-12-17-6' were used to identify random amplified polymorphic DNA (RAPD) markers closely linked to a BPH Biotype-4 resistance gene derived from Oryza officinalis Wall, which will be useful for a positional cloning strategy to isolate the resistance gene.
Abstract: Brown plant hopper (BPH), Nilaparvata lugens (Stal.), is a serious insect pest of rice in Asia, causing direct losses and vectoring Rice grassy stunt virus (RGSV) and Rice ragged stunt virus (RRSV). Recombinant inbred lines (RILs) developed from a cross between 'IR50' and 'IR54745-2-21-12-17-6' were used to identify random amplified polymorphic DNA (RAPD) markers closely linked to a BPH Biotype-4 resistance gene [Bphl3 (t)] derived from Oryza officinalis Wall. Bulked segregant analysis (BSA) using RAPD primers identified 11 polymorphic fragments. Six fragments, AJ09 260 a, AL05 220 a, AK10 690 a, AK10 430 c, AK10 380 d, and AJ01 200 a, were linked in coupling phase to the Bphl3 (t) locus. The remaining five fragments, AJ09 230 b, AJ09 180 c, AJ09 100 d, AL05 400 b, and AK10 340 e, were linked in repulsion. The most closely linked RAPD marker, AJ09 230 b, was converted to a codominant linked sequence tagged sites (STS) marker. This marker mapped 1.3 centimorgans (cM) from the resistance gene and was placed on rice chromosome 3 by means of 'IR64' × 'Azucena' doubled haploid (DH) population. The tightly linked STS marker could be used for marker-assisted selection (MAS). In addition, these markers will be useful for a positional cloning strategy to isolate the resistance gene.
TL;DR: In this paper, the authors measured the potential effects of fragmentation and reduced population size on the future viability of populations of Platanthera leucophaea (Nuttall) Lindley (Orchidaceae), a threatened species, and found that small populations are especially vulnerable to loss of variation through stochastic events.
Abstract: Species that have become rare or endangered due to human disturbance are at increased risk of extinction as a result of environmental, demographic, and genetic stochasticity. Smaller populations, which can be typical of endangered species, are especially vulnerable to loss of variation through stochastic events. For 10 populations of Platanthera leucophaea (Nuttall) Lindley (Orchidaceae), a threatened species, genetic variation at allozyme and random amplified polymorphic DNA (RAPD) loci was measured to assess the potential effects of fragmentation and reduced population size on the future viability of populations. Allozymes revealed very low levels of diversity (AP = 1.18; PP = 12%; HO = 0.008) and high levels of population differentiation (FST = 0.75). Additionally, inbreeding coefficients were very high in five of the 10 populations surveyed, due largely to the fixation of alternative alleles at two loci in different populations. In contrast, every individual displayed a unique RAPD fingerprint, yielding higher levels of polymorphism (PP = 45%) and gene diversity (Nei's H = 0.159). Estimates of population differentiation based on RAPD are moderate as measured by amova (ΦST = 0.21), Wright's F-statistics (GST = 0.26), or Shannon's information index (Hamong = 0.30). However, genetic and geographic distances are not significantly correlated, suggesting a lack of interpopulation gene flow and/or genetic drift within populations. Population size is not a good predictor of genetic variation in the present study, and it is hypothesized that plant dormancy patterns and chaotic fluctuations in population size from year to year may buffer against stochastic events, especially in small populations.
TL;DR: Genetic linkage maps for two apricot cultivars have been constructed using AFLP, RAPD, RFLP and SSR markers in 81 F1 individuals from the cross 'Goldrich' × 'Valenciano', the most-important virus affecting Prunus species.
Abstract: Genetic linkage maps for two apricot cultivars have been constructed using AFLP, RAPD, RFLP and SSR markers in 81 F1 individuals from the cross 'Goldrich' × 'Valenciano'. This family segregated for resistance to 'plum pox virus' (PPV), the most-important virus affecting Prunus species. Of the 160 RAPD arbitrary primers screened a total of 44 were selected. Sixty one polymorphic RAPD markers were scored on the mapping population: 30 heterozygous in 'Goldrich', 19 heterozygous in 'Valenciano', segregating 1:1, and 12 markers heterozygous in both parents, segregating 3:1. A total of 33 and 19 RAPD markers were mapped on the 'Goldrich' and 'Valenciano' maps respectively. Forteen primer combinations were used for AFLPs and all of them detected polymorphism. Ninety five markers segregating 1:1 were identified, of which 62 were heterozygous in the female parent 'Goldrich' and 33 in the male parent 'Valenciano'. Forty five markers were present in both parents and segregated 3:1. A total of 82 and 48 AFLP markers were mapped on the 'Goldrich' and 'Valenciano' maps. Twelve RFLPs probes were screened in the population, resulting in five loci segregating in the family, one locus heterozygous for 'Valenciano' and four heterozygous for both, segregating 1:2:1. Of the 45 SSRs screened 17 segregated in the mapping family, resulting in seven loci heterozygous for the maternal parent and ten heterozygous for both, segregating 1:2:1 or 1:1:1:1. A total of 16 and 13 co-dominant markers were mapped in the female and male parent maps respectively. A total of 132 markers were placed into eight linkage groups on the 'Goldrich' map, defining 511 cM of the total map-length. The average distance between adjacent markers was 3.9 cM. A total of 80 markers were placed into seven linkage groups on the 'Valenciano' map, defining 467.2 cM of the total map-distance, with an average interval of 5.8 cM between adjacent markers. Thirty six marker loci heterozygous in both parents revealed straightforward homologies between five linkage groups in both maps. The sharka resistance trait mapped on linkage group 2. The region containing sharka resistance is flanked by two co-dominant markers that will be used for targeted SSR development employing a recently constructed complete apricot BAC library. SSRs tightly linked to sharka resistance will facilitate MAS in breeding for resistance in apricot.
TL;DR: A novel set of 50 highly polymorphic microsatellite markers developed and mapped on existing RAPD framework maps of Eucalyptus grandis and E. urophylla represents a significant step toward the development of a genus-wide reference linkage map for Eucallyptus.
Abstract: A novel set of 50 highly polymorphic microsatellite markers were developed and mapped on existing RAPD framework maps of Eucalyptus grandis and E urophylla Together with the twenty previously developed microsatellite markers, these were used to align the existing maps for the two most commercially important Eucalyptus species in the tropics Sixty-three microsatellite markers were placed on the E grandis map in 11 linkage groups, and 53 on the E urophylla map distributed in 10 linkage groups Approximately 66% of the microsatellite markers segregated in a fully informative fashion, allowing the establishment of colinear syntenic linkage groups between the two maps The 50 new microsatellite markers were highly informative, with an average of 14 alleles per locus, and average expected heterozygosity between 082 and 087 Furthermore, within the subgenus Symphyomyrtus, to which the vast majority of commercially important Eucalyptus species belong, these markers display on average 90% transportability This set of 70 mapped microsatellite markers represents a significant step toward the development of a genus-wide reference linkage map for Eucalyptus These highly multiallelic and transportable markers constitute a powerful tool for QTL discovery and validation, and can be used in directed searches for QTL allele variation across Eucalyptus pedigrees
TL;DR: UPGMA cluster analysis carried out on these data separately for RAPDs and AFLPs and on the combined data reflected, to some extent, pedigree relationships and cophenetic correlations that indicate a good fit of respective clusters to genetic similarity data.
Abstract: In order to obtain an overview of the genetic diversity present within the set of pea cultivars released in Germany, 21 cultivars were analysed at the DNA level by random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs), as well as for agronomic traits. Yield of grain cultivars ranged from 2.95 to 3.87 t/ha. Based on the screening of 60 RAPD primers and 32 Eco RI + 3/Mse I+3 AFLP primer combinations, 20 RAPD primers and 11 Eco RI + 3/MseI+ 3 primer combinations generating polymorphic and distinct fragments were chosen for estimation of genetic diversity. Twenty RAPD primers amplified a total of 314 scorable bands ranging from about 262 bp to 1996 bp. Of these, 175 fragments (55.7%) were polymorphic. Based on these data, genetic similarity (GS) was estimated between 0.80 (‘Lisa’ vs.‘Grapis’) and 0.94 (‘Bohatyr’ vs. ‘Sponsor’; mean GS = 0.88). Eleven AFLP primer combinations led to the amplification of 949 scorable fragments ranging from 43 to 805 bp and of these, 462 (48.7%) were polymorphic. Genetic similarity based on AFLPs was calculated between 0.85 (‘Lisa’ vs.‘Laser’) and 0.94 (‘Bohatyr’ vs. ‘Sponsor’, mean GS = 0.90). Correlation of genetic similarity estimated on RAPDs and AFLPs was estimated at r = 0.79** using Spearman's rank correlation coefficient and at r = 0.84 by the Mantel test, respectively. UPGMA cluster analysis carried out on these data separately for RAPDs and AFLPs and on the combined data reflected, to some extent, pedigree relationships and cophenetic correlations (r = 0.89 for RAPDs, r = 0.88 for AFLPs, and r = 0.93 RAPDs + AFLPs) indicate a good fit of respective clusters to genetic similarity data. The correlation of cluster analyses to pedigree information and the impact on parental genotype selection is discussed.
TL;DR: This PCR-based detection procedure is a powerful tool for diagnosis of B. cinerea in symptomless strawberry plants, and should allow infection and latency sites to be localized in order to improve knowledge of the epidemiology of the pathogen under field conditions.
Abstract: Random amplified polymorphic DNA (RAPD) assays were applied on 34 fungal strains isolated from strawberry and other host plants, in order to detect polymorphism to consequently identify and isolate molecular markers specific to Botrytis cinerea. Among the 26 10-mer primers tested, one primer mainly amplified a 750-bp product present in all the B. cinerea strains and absent in the other species and genera examined. This product was cloned and sequenced in order to design a specific 20-mer primer pair, which was tested on the 34 fungal isolates by polymerase chain reaction (PCR). A single 0.7-kb band was amplified in all the 13 strains of B. cinerea isolated from different host plants. Moreover, a 0.6-kb band was amplified in both Botrytis fabae strains. No band was observed for the nine other Botrytis species and 12 fungal genera isolated from strawberry plants. A comparison between the 0.7-kb B. cinerea sequence and the 0.6-kb B. fabae sequence revealed 98% homology and one 122-bp deletion for B. fabae, including an EcoRI site. Hybridization of Southern blots with RAPD and EcoRI-digested DNA confirmed the specificity of the marker. The limit of detection of B. cinerea genomic DNA was approximately 0.2 pg. The PCR procedure was able to amplify the 0.7-kb B. cinerea fragment form mixed samples of DNA as low as 2 pg B. cinerea genomic DNA and 1 μg plant DNA. Thus this PCR-based detection procedure is a powerful tool for diagnosis of B. cinerea in symptomless strawberry plants, and should allow infection and latency sites to be localized in order to improve knowledge of the epidemiology of the pathogen under field conditions.