Genetic diversity and phylogenetic relationships in alder,Alnus firma, revealed by AFLP

Molecular markers for alder,Alnus firma Sieb. et Zucc, have not been studied extensively. Here, we used amplified fragment length polymorphism (AFLP) to investigate genetic relationships among 15 natural populations. EcoRI-ACG + Msel-CTG combinations revealed the highest polymorphism (62.2%). A total of 171 DNA fragments were identified. On average, 58.1% of the AFLP markers that were generated using four primer pairs were polymorphic. Diversity was insignificant among the populations. The combination of a wind-pollinated, outcrossing breeding system along with large population sizes, and the ability to regenerate by stump sprouting may explain the high level of genetic diversity within this species. The majority (98%) of the genetic variance resided within populations. The average number of individuals that were exchanged between populations per generation was very high (N _em = 12.3). Gene dispersal in alder is apparently by seed dispersalvia water and human activity as well as through pollen. Five individuals per population were claded in the same cluster.     

Simplified amplified-fragment length polymorphism method for genotyping Mycobacterium tuberculosis isolates

A simplified amplified-fragment length polymorphism (AFLP) method was developed and applied to genotype 52 Mycobacterium tuberculosis isolates. This method can be carried out using only one restriction enzyme (XhoI), one double strand adapter, and one PCR primer. The amounts of DNA and DNA polymerase, and the concentrations of primer and Mg²⁺ in the PCR step were optimized using the Basic Sequential Simplex method. AFLP analysis of the isolates generated a total of 24 differently sized bands ranging from 1537 to 121 bp, and 52 different band patterns, with a minimum of 2 and a maximum of 13 bands. The results were compared with the well-established IS6110 restriction fragment length polymorphism (IS6110-RFLP) typing method, which rendered a total of 32 differently sized bands from 1 to 12 kbp, and 52 different band patterns, with a minimum of 3 and a maximum of 15 bands. Therefore, both genotyping methods showed a discriminatory power of samples of 100%. Nevertheless, pairwise comparisons of the 1326 similarity indexes calculated for both typing methods showed a total absence of correlation between the similarity indexes of the two methods. The simplified AFLP method is expected to be more useful for genotyping M. tuberculosis isolates compared to the IS6110-RFLP method, since the former evaluates genetic variations throughout the M. tuberculosis genome. Furthermore, the relatively rapid and low-cost simplified AFLP method compares favorably to the IS6110-RFLP or conventional AFLP methods, and shows great promise for genotyping M. tuberculosis isolates, especially in developing countries or for preliminary screening.     

AFLP analysis for examining genetic differences in cultivated strains and their single-spore isolates and for confirming successful crosses in <Emphasis Type="Italic">Agaricus blazei</Emphasis>

Amplified fragment length polymorphism (AFLP) analysis was used to examine genetic differences in Agaricus blazei cultivated strains and their single-spore isolates (SSIs). AFLP analysis with five primer combinations identified a total of 267 AFLP bands from nine cultivated strains (one from Brazil and eight from Japan), of which 165 were polymorphic between the nine strains. An AFLP data dendrogram grouped the eight Japanese strains, with the Brazilian strain acting as an outlier, suggesting that the Brazilian and Japanese strains are genetically quite different. Twelve SSIs derived from each of four cultivated strains were subjected to AFLP analysis. All the AFLP bands detected in the cultivated strains were also found in at least one SSI, but some unique bands were detected in SSIs. The total number of AFLP bands from individual SSIs was clearly less than those from their parental strains, and many of polymorphic AFLP bands from the parental strains segregated in SSIs at a ratio of 1 : 1, suggesting that the SSIs are homokaryotic. Distance values based on presence or absence of individual AFLP bands among SSIs from different strains were clearly higher than those among SSIs from a single strain. In addition, AFLP analysis was shown to be useful in confirming hybrid formation in crosses between SSIs.     

AFLP genotyping of Candida metapsilosis clinical isolates: Evidence for recombination

In a collection of 395 independent clinical isolates classified as Candida parapsilosis on a biochemical profile basis, 20 Candida metapsilosis strains were identified by molecular tests with an isolation frequency of 5%. Isolates were screened for their susceptibility to conventionally used antifungals and for virulence determinants, such as biofilm formation and protease production. Molecular characterization of C. metapsilosis independent isolates by amplified fragment length polymorphism (AFLP) revealed a high percentage of polymorphic bands. Statistical analysis of the pairwise genetic distances and bootstrapping revealed that recombination occurs and significantly contributes to C. metapsilosis genetic population variability. No association between specific AFLP markers and drug resistance or other phenotypes was observed.     

Modified AFLP analysis method for species with small genomes

A modified method for detecting amplified fragment length polymorphism (AFLP) has been developed for species with small genomes. We successfully used a combination of primers with a reduced number of selective bases to differentiate and fingerprint isolates ofColletotrichum acutatum, the causative agent of strawberry black spot, an important strawberry disease.     

Detection of genetic variation among single-spore isolates and identification of genets ofArmillaria ostoyae by AFLP analysis with Texas RedTM-labeled selective primer

AFLP (amplified fragment length polymorphism) analysis was applied toArmillaria ostoyae isolates (single-spore isolates and field isolates from the same forest). For detection of AFLP, we have developed a modified method using DNA sequencer with Texas Red-labeled selective primer. In analysis of single-spore isolates, this technique provided large numbers of highly polymorphic DNA markers, which can be used to identify genets. The results suggested that outbreeding might be common inA. ostoyae.     

Genetic mapping of the novel <Emphasis Type="Italic">Turnip mosaic virus</Emphasis> resistance gene <Emphasis Type="Italic">TuRB03</Emphasis> in <Emphasis Type="Italic">Brassica napus</Emphasis>

A new source of resistance to the pathotype 4 isolate of Turnip mosaic virus (TuMV) CDN 1 has been identified in Brassica napus (oilseed rape). Analysis of segregation of resistance to TuMV isolate CDN 1 in a backcross generation following a cross between a resistant and a susceptible B. napus line showed that the resistance was dominant and monogenic. Molecular markers linked to this dominant resistance were identified using amplified fragment length polymorphism (AFLP) and microsatellite bulk segregant analysis. Bulks consisted of individuals from a BC₁ population with the resistant or the susceptible phenotype following challenge with CDN 1. One AFLP and six microsatellite markers were associated with the resistance locus, named TuRB03, and these mapped to the same region on chromosome N6 as a previously mapped TuMV resistance gene TuRB01. Further testing of TuRB03 with other TuMV isolates showed that it was not effective against all pathotype 4 isolates. It was effective against some, but not all pathotype 3 isolates tested. It provided further resolution of TuMV pathotypes by sub-dividing pathotypes 3 and 4. TuRB03 also provides a new source of resistance for combining with other resistances in our attempts to generate durable resistance to this virus.     

Optimized nonradioisotopic amplified fragment length polymorphism method for European beech (<Emphasis Type="Italic">Fagus sylvatica</Emphasis> L.)

The amplified fragment length polymorphism (AFLP) technique has increasingly been used for the study of forest tree species. A nonradioisotopic AFLP method was optimized for European beech (Fagus sylvatica L.) and found reproducible. However, type ofTaq DNA polymerase and choice of primers must be considered for a consistent AFLP pattern.     

‘Good-genes’ and ‘compatible-genes’ effects in an Alpine whitefish and the information content of breeding tubercles over the course of the spawning season

Abies ziyuanensis is a highly endangered fir species endemic to South China. Unlike other Abies species that are distributed in areas with cold climates, A. ziyuanensis is restricted to several isolated island-like localities at subtropical mountains. In this study, we used dominant amplified fragment length polymorphism (AFLP) and co-dominant simple sequence repeats (SSR) markers to infer the genetic structure of A. ziyuanensis. Seven populations consisting of 139 individuals were sampled across their whole distribution. A. ziyuanenesis has a relatively low level of genetic variation, with a mean genetic diversity per population (He) of 0.136 (AFLP) and 0.337 (SSR), which is lower than that of other reported endemic species based on the same kind of marker. We observed high population differentiation, with Gst = 0.482 (AFLP) and Fst = 0.250 (SSR), among the seven populations. AMOVA also detected significant differentiation among populations (Φst (AFLP) = 0.550 and Φst (SSR) = 0.289) and among regions (Φct (AFLP) = 0.139 and Φct (SSR) = 0.135) in both marker types. Both ongoing evolutionary forces (e.g., genetic drift resulting from small population size) and historical events (e.g., population contraction and fragmentation during and after the Quaternary glacial cycles) may have contributed to the genetic structure in A. ziyuanensis.     

Genetic diversity in recent elite faba bean lines using AFLP markers

Amplified fragment length polymorphism (AFLP) markers were used to study the genetic diversity among a large set (n = 79) of inbred lines of recent elite faba bean (Vicia faba L.) cultivars with Asian, European (Northern and Southern) and North African origin. The inbred lines were analyzed using eight selected AFLP primer combinations that produced 477 polymorphic fragments. Errors when scoring repeated lanes of one pre-amplification reaction on one gel were negligible, whereas errors when scoring lanes of two individuals of the same inbred line run on different gels were markedly higher. Scoring across gels should be backed by replicates and several appropriate check entries. Based on clustering with Jaccard's similarity coefficient and Principal Coordinate Analysis, only the Asian lines were distinct as a group, the other lines showed no marked further grouping. Nevertheless, several known pedigree relationships were verified. A priori grouping of inbred lines (geographic origin and seed size) and AFLP data corroborate available information on the history of spread and cultivation of faba bean in the studied regions. Based on the diversity observed, studies especially concerning the relationship between genetic similarity based on AFLP markers and hybrid performance within the European elite germplasm have been launched.Communicated by H.F. Linskens     

Comparative Analysis of Phylogenetic Relationships of Grain Amaranths and Their Wild Relatives (Amaranthus; Amaranthaceae) Using Internal Transcribed Spacer, Amplified Fragment Length Polymorphism, and Double-Primer Fluorescent Intersimple Sequence Repeat Markers

The most economically important group of species in the genus Amaranthus is the A. hybridus species complex, including three cultivated grain amaranths, A. cruentus, A. caudatus, and A. hypochondriacus, and their putative wild progenitors, A. hybridus, A. quitensis, and A. powellii. Taxonomic confusion exists among these closely related taxa. Internal transcribed spacer (ITS) of nuclear ribosomal DNA, amplified fragment length polymorphism (AFLP), and double-primer fluorescent intersimple sequence repeat (ISSR) were employed to reexamine the taxonomic status and phylogenetic relationships of grain amaranths and their wild relatives. Low ITS divergence in these taxa resulted in poorly resolved phylogeny. However, extensive polymorphisms exist at AFLP and ISSR loci both within and among species. In phylogenetic trees based on either AFLP or ISSR or the combined data sets, nearly all intraspecific accessions can be placed in their corresponding species clades, indicating that these taxa are well-separated species. The AFLP trees share many features in common with the ISSR trees, both showing a close relationship between A. caudatus and A. quitensis, placing A. hybridus in the same clade as all grain amaranths, and indicating that A. powellii is the most divergent taxon in the A. hybridus species complex. This study has demonstrated that both AFLP and double-primer fluorescent ISSR have a great potential for generating a large number of informative characters for phylogenetic analysis of closely related species, especially when ITS diversity is insufficient.     

The comparison of RFLP,RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis

The utility of RFLP (restriction fragment length polymorphism), RAPD (random-amplified polymorphic DNA), AFLP (amplified fragment length polymorphism) and SSR (simple sequence repeat, microsatellite) markers in soybean germplasm analysis was determined by evaluating information content (expected heterozygosity), number of loci simultaneously analyzed per experiment (multiplex ratio) and effectiveness in assessing relationships between accessions. SSR markers have the highest expected heterozygosity (0.60), while AFLP markers have the highest effective multiplex ratio (19). A single parameter, defined as the marker index, which is the product of expected heterozygosity and multiplex ratio, may be used to evaluate overall utility of a marker system. A comparison of genetic similarity matrices revealed that, if the comparison involved both cultivated (Glycine max) and wild soybean (Glycine soja) accessions, estimates based on RFLPs, AFLPs and SSRs are highly correlated, indicating congruence between these assays. However, correlations of RAPD marker data with those obtained using other marker systems were lower. This is because RAPDs produce higher estimates of interspecific similarities. If the comparisons involvedG. max only, then overall correlations between marker systems are significantly lower. WithinG. max, RAPD and AFLP similarity estimates are more closely correlated than those involving other marker systems.Abbreviations RFLP restriction fragment length plymorphism - RAPD random-amplified polymorphic DNA - AFLP amplified fragment length polymorphism - SSR simple sequence repeat - PCR polymerase chain reaction - TBE Tris-borate-EDTA buffer - MI marker index - SENA sum of effective numbers of alleles     

Somaclonal variation in rye (<Emphasis Type="Italic">Secale cereale</Emphasis> L.) analyzed using polymorphic and sequenced AFLP markers

Amplified fragment length polymorphism (AFLP) analysis of 24 in vitro regenerated rye plants was performed in order to evaluate the somaclonal variation rate in this species and to identify rye genomic regions where mutations are preferentially promoted by in vitro culture processes. Regenerated plants were obtained from cell lines derived from immature embryos and plants were regenerated by somatic embryogenesis. Twenty-three regenerants showed variation when compared against sibling plants obtained from the same cell line. A total number of 887 AFLP markers were scored, and 8.8% identified the same polymorphism in plants obtained independently from different cell lines, revealing putative mutational hot spots. Using controlled crossings and analysis of the corresponding progenies, we were able to verify the genetic stability in the next generation for only five of these polymorphisms. The nucleotide sequence of the AFLP amplicon of four of the polymorphic markers was obtained, but only the sequence of two markers was clearly identified in the databases. The sequence of marker A1-303 was identified as part of a tandemly repeated sequence, the 120-bp family, which is located at telomeric regions and is widely distributed among rye chromosomes. The marker A5-375 showed high similarity with regions of Angela retrotransposons.     

Isolation of a homothallic mutant in <Emphasis Type="Italic">Lentinula edodes</Emphasis>

To obtain a homothallic mutant in Lentinula edodes, basidiospores derived from the common Bmut dikaryon (A1B1mut × A2B1mut) were treated with UV irradiation. Of a total of approximately 5000 monosporous cultures recovered, a single basidiospore isolate was found to produce the hyphae bearing clamp connections without mating. This mutant strain could form fruit bodies, and all its single basidiospore isolates developed into colonies with clamp connections. Such homothallic behaviors were transmitted from the mutant strain to the next generation. During the germination and following hyphal elongation in a single basidiospore of mutant strain, clamp connections were clearly detected in multicellular hyphae, which contained two nuclei in each cell. Their clamp connections were morphologically variable, viz., pseudo, abnormal, and true clamps. Amplified fragment length polymorphism (AFLP) profiles among the basidiospore isolates of mutant strain were identical, indicating that the mutant strain produced isogenic basidiospore progeny. Contribution no. 385 from the Tottori Mycological Institute     

Comparative evaluation of three molecular typing methods in their applicability to differentiate Lactobacillus strains with human origin

We isolated a total of 49 strains of lactic acid bacteria from the faeces of healthy donors. The species in that group were determined as L. plantarum (11 strains), L. casei (11 strains), L. rhamnosus (seven strains), L. fermentum (seven strains), L. gasseri (six strains), L. delbrueckii ssp. lactis (four strains), L. salivarius (two strains), and L. acidophilus (one strain). Genotyping at strain level was performed using random amplification of polymorphic DNA (RAPD), pulsed field gel electrophoresis (PFGE) with endonucleases ApaI and XhoI and amplified fragment length polymorphism (AFLP) with enzymes XhoI and TaqI. The main objective was the comparison of three molecular typing techniques: AFLP, PFGE and RAPD in their applicability to determine the genetic diversity among the isolates. RAPD was the easiest, comparatively rapid and fairly strain discriminative tool. PFGE was the most laborious method but producing the most stable profiles with satisfactory discriminatory power. AFLP proved to be the most discriminative approach for typing of the strains. AFLP could differentiate strains with the same PFGE profiles. Therefore, AFLP successfully could replace the labor consuming PFGE. The specially developed AFLP and PFGE proved very high potential to evaluate the strain diversity of Lactobacillus spp. with human origin.     

Genetic diversity of Ustilago maydis strains

Thirty wild isolates belonging to five different locations in Mexico plus two laboratory strains of Ustilago maydis were characterized by restriction fragment length polymorphism (RFLP) analysis using 23 different clones as probes derived from a PstI library and two restriction enzymes. All loci analysed presented a high level of polymorphism, including one locus with thirty one different alleles. Geographical grouping of the populations was based on Nei's genetic distance and there was no correlation between genetic and geographic distances among these isolates. Our results suggest that DNA fingerprinting is a useful method for detecting genetic variation in populations of U. maydis. This work demonstrated that considerable genetic variation may be present within field populations of U. maydis.     

Poa annua L. in Antarctic: searching for the source of introduction

The level of polymorphism, genetic variability and relatedness of a population of Poa annua L. from South Shetlands Islands was studied and compared with results obtained for populations from two potential sources of introduction (Argentina—Ushuaia and Poland—Dziekanów Leśny) using the amplified fragment length polymorphism (AFLP) approach. Five primer pairs used for AFLP profiling amplified 226 scoreable DNA fragments that were used for Clustral and Factorial analyses. The level of molecular variability among all individuals from all the analysed populations reaches 30%. Clustral and Factorial analyses show that all populations formed clear-cut uniform groups according to their locations. However, population from King George Island show high variability. High genetic diversity may be related with escalated human activity at the area of Arctowski Station, favouring introductions of P. annua from many different sources and by many different vectors.     

DNA-fingerprinting (AFLP and RFLP) for genotypic identification in species of the <Emphasis Type="Italic">Pleurotus eryngii</Emphasis> complex

Wild populations of edible species are important source of genetic variability for cultivated lines that can undergo a drastic loss of diversity resulting from man’s selection. The development of tools aimed at the clear-cut and safe identification and assessment of genetic variability of the wild and cultivated strains is thus a fundamental goal of molecular genetic research. In this study, we used two polymerase chain reaction (PCR)-based fingerprinting methods—amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) of laccase and manganese peroxidase genes—to assess genetic differences among strains and independently evolving lineages belonging to the Pleurotus eryngii complex. Both laccase RFLP and AFLP have been proved to distinguish unambiguously the three taxa studied: Pleurotus ferulae, P. eryngii, and P. eryngii var. nebrodensis. AFLP also showed enough sensitivity to detect polymorphisms among the strains, proving to be an efficient DNA fingerprinting tool in studies of strain assignment. The divergent RFLP laccase and manganese peroxidase patterns are also discussed in relation to the role played by these genes in the interaction between these fungi and their host plants.     

Quantitative trait loci and molecular markers associated with wheat allelopathy

Wheat (Triticum aestivum L.) has been examined for allelopathic potential against annual ryegrass (Lolium rigidum). The bioassay technique, 'equal-compartment-agar-method', was employed to evaluate seedling allelopathy in a doubled-haploid (DH) population derived from cv Sunco (weakly allelopathic) and cv Tasman (strongly allelopathic). A significant difference in allelopathic activity was found among the DH lines, which inhibited the root length of ryegrass across a range from 23.7 to 88.3%. The phenotypic data showed that wheat allelopathic activity was distributed normally within this DH population and a substantial transgressive segregation for seedling allelopathic activity was also found. Analysis of restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP) and microsatellite (SSRs) markers identified two major QTLs on chromosome 2B associated with wheat allelopathy. The linkage analysis of genetic markers and the QTLs may improve genetic gains for the allelopathic activity through marker-assisted selection in wheat breeding. The development of wheat allelopathic cultivars could reduce the over-reliance of weed control on synthetic herbicides.Communicated by J. Dvorak     

Molecular tagging and mapping of the erect panicle gene in rice

Erect panicle (EP) is one of the more important traits of the proposed ideotype of high-yielding rice. Several rice cultivars with the EP phenotype, which has been reported to be controlled by a dominant gene, have been successfully developed and released for commercial production in North China. To analyze the inheritance of the EP trait, we generated segregating F₂ and BC₁F₁ populations by crossing an EP-type variety, Liaojing 5, and a curved-panicle-type variety, Fengjin. Our results confirmed that a dominant gene controls the EP trait. Simple-sequence repeat (SSR) and bulked segregant analyses of the F₂ population revealed that the EP gene is located on chromosome 9, between two newly developed SSR markers, RM5833-11 and RM5686-23, at a genetic distance of 1.5 and 0.9 cM, respectively. Markers closer to the EP gene were developed by amplified fragment length polymorphism (AFLP) analysis with 128 AFLP primer combinations. Three AFLP markers were found to be linked to the EP gene, and the nearest marker, E-TA/M-CTC₂₀₀, was mapped to the same location as SSR marker RM5686-23, 1.5 cM from the EP gene. A local map around the EP gene comprising nine SSR and one AFLP marker was constructed. These markers will be useful for marker-assisted selection (MAS) for the EP trait in rice breeding programs.