DNA methylation and AFLP marker distribution in the soybean genome

Amplified fragment length polymorphisms (AFLPs) have become important markers for genetic mapping because of their ability to reliably detect variation at a large number of loci. We report here the dissimilar distribution of two types of AFLP markers generated using restriction enzymes with varying sensitivities to cytosine methylation in the soybean genome. Initially, AFLP markers were placed on a scaffold map of 165 RFLP markers mapped in 42 recombinant inbred (F_6:7) lines. These markers were selected from a map of over 500 RFLPs analyzed in 300 recombinant inbred (F_6:7) lines generated by crossing BSR101×PI437.654. The randomness of AFLP marker map position was tested using a Poisson-model distribution. We found that AFLP markers generated using EcoRI/MseI deviated significantly from a random distribution, with 34% of the markers displaying dense clustering. In contrast to the EcoRI/MseI AFLP markers, PstI/MseI-generated AFLP markers did not cluster and were under represented in the EcoRI/MseI marker clusters. The restriction enzyme PstI is notably sensitive to cytosine methylation, and these results suggest that this sensitivity affected the distribution of the AFLP markers generated using this enzyme in the soybean genome. The common presence of one EcoRI/MseI AFLP cluster per linkage group and the infrequent presence of markers sensitive to methylation in these clusters are consistent with the low recombination frequency and the high level of cytosine methylation observed in the heterochromatic regions surrounding centromeres. Thus, the dense EcoRI/MseI AFLP marker clusters may be revealing structural features of the soybean genome, including the genetic locations of centromeres. Received: 5 November 1998 / Accepted: 20 February 1999     

An integrated high-density RFLP-AFLP map of tomato based on two Lycopersicon esculentum×L. pennellii F2 populations

 Two independent F₂ populations of Lycopersicon esculentum×L. pennellii which have previously been investigated in RFLP mapping studies were used for construction of a highly saturated integrated AFLP map. This map spanned 1482 cM and contained 67 RFLP markers, 1078 AFLP markers obtained with 22 EcoRI+MseI primer combinations and 97 AFLP markers obtained with five PstI+MseI primer combinations, 231 AFLP markers being common to both populations. The EcoRI+MseI AFLP markers were not evenly distributed over the chromosomes. Around the centromeric region, 848 EcoRI+ MseI AFLP markers were clustered and covered a genetic distance of 199 cM, corresponding to one EcoRI+ MseI AFLP marker per 0.23 cM; on the distal parts 1283 cM were covered by 230 EcoRI+MseI AFLP markers, corresponding to one marker per 5.6 cM. The PstI/MseI AFLP markers showed a more even distribution with 16 PstI/MseI AFLP markers covering a genetic distance of 199 cM around the centromeric regions and 81 PstI/MseI AFLP markers covering a genetic distance of 1283 cM on the more distal parts, corresponding to one marker per 12 and 16 cM respectively. In both populations a large number of loci showed a significant skewed segregation, but only chromosome 10 loci showed skewness that was similar for both populations. This ultra-dense molecular-marker map provides good perspectives for genetic and breeding purposes and map-based cloning. Received: 3 September 1998 / Accepted: 27 October 1998     

AFLP markers in a molecular linkage map of maize: codominant scoring and linkage group ditsribution

We exploited the AFLP technique to saturate a RFLP linkage map derived from a maize mapping population. By using two restriction enzyme, EcoRI and PstI, differing in methylation sensitivity, both in combination with MseI, we detected 1568 bands of which 340 where polymorphic. These were added to the exitsing RFLP marker data to study the effects of incorporation of AFLPs produced by different restriction-enzyme combinations upon genetic maps. Addition of the AFLP data resulted in greater genome coverage, both through linking previously separate groups and the extension of other groups. The increase of the total map length was mainly caused by the addition of markers to telomeric regions, where RFLP markers were poorly represented. The percentage of informative loci was significantly different between the EcoRI and PstI assays. There was also evidence that PstI AFLP markers were more randomly distributed across chromosomes and chromosome regions, while EcoRI AFLP markers clustered mainly at centomeric regions. The more-random ditsribution of PstI AFLP markers on the genetic map reported here may reflect a preferential localisation of the markers in the hypomethylated telomeric regions of the chromosomes. Received: 22 December 1998 / Accepted: 25 March 1999     

Accumulation of astaxanthin and lutein in<Emphasis Type="Italic"> Chlorella zofingiensis</Emphasis> (Chlorophyta)

When grown photoautotrophically, Chlorella zofingiensis strain CCAP 211/14 accumulates a significant amount of valuable carotenoids, namely astaxanthin and lutein, of increasing demand for use as feed additives in fish and poultry farming, as colorants in food, and in health care products. Under standard batch-culture conditions, this microalgal strain exhibits high values of both growth rate (about 0.04 h^–1) and standing cell population (over 10¹¹ cells l^–1, or 7 g dry weight l^–1). Lutein, in a free (unesterified) form, was the prevalent carotenoid during early stages of cultivation (over 0.3 pg cell^–1, equal to 4 mg g^–1 dry weight, or 20 mg l^–1 culture), whereas esterified astaxanthin accumulated progressively, to reach a maximum (over 0.1 pg cell^–1, equal to 1.5 mg g^–1 dry weight, or 15 mg l^–1 culture) in the late stationary phase. A differential response of lutein and astaxanthin accumulation was also recorded with regard to the action of some environmental and nutritional factors. C. zofingiensis CCAP 211/14 represents a unique model system for analyzing the differential regulation of the levels of primary (lutein) and secondary (astaxanthin) carotenoids. Relevant also from the biotechnological viewpoint, this photosynthetic organism, with outstanding attributes for fast photosynthetic growth and carotenoid accumulation, might prove most valuable for its application to the mass production of either or both lutein and astaxanthin.     

Genomic Fingerprinting of Virulent and Avirulent Strains of Clavibacter michiganensis subspecies sepedonicus

Genomic fingerprints of C. michiganensis subsp. sepedonicus were generated by CHEF gel electrophoresis of restriction digested high-molecular weight DNA. Low levels of intra-subspecific variation were detected by cluster analysis of the fingerprints. Four haplotypes were identified by genomic fingerprinting with HindIII, and eight were identified with EcoRI. Haplotypes generated with HindIII were less similar than those generated by EcoRI. Haplotypes generated with HindIII formed groups that corresponded well with plant reactions of the strains, but similar types of groupings were less apparent with haplotypes generated with EcoRI. When disease severity in eggplant and potato, population size in potato, and ability to induce a hypersensitive response (HR) in tobacco were overlaid onto dendograms of genetic similarity, avirulent HR-negative strains clustered separately from virulent HR-positive strains in both EcoRI and HindIII profiles. Avirulent HR-positive strains that lack pCS1 clustered with avirulent HR-negative strains in a EcoRI dendogram, but clustered with virulent HR-positive strains in a HindIII dendogram. Genomic fingerprinting of high-molecular weight DNA fragments provided a means for detecting genomic variability associated with virulence in C. michiganensis subsp. sepedonicus. Received: 1 March 2001 / Accepted: 7 June 2001     

An interspecific (Capsicum annuum ×C. chinese) F2 linkage map in pepper using RFLP and AFLP markers

We have constructed a molecular linkage map of pepper (Capsicum spp.) in an interspecific F₂ population of 107 plants with 150 RFLP and 430 AFLP markers. The resulting linkage map consists of 11 large (206–60.3 cM) and 5 small (32.6–10.3 cM) linkage groups covering 1,320 cM with an average map distance between framework markers of 7.5 cM. Most (80%) of the RFLP markers were pepper-derived clones, and these markers were evenly distributed across the genome. By using 30 primer combinations, we were able to generate 444 AFLP markers in the F₂ population. The majority of the AFLP markers clustered in each linkage group, although PstI/MseI markers were more evenly distributed than EcoRI/MseI markers within the linkage groups. Genes for the biosynthesis of carotenoids and capsaicinoids were mapped on our linkage map. This map will provide the basis of studying secondary metabolites in pepper. Received: 20 October 1999 / Accepted: 3 July 2000     

Difference Between Xanthomonas campestris pv. phlei and X.c pv. graminis Revealed by Genomic Fingerprinting and Restriction Fragment Length Polymorphism Patterns

Genomic DNA was prepared from 16 strains of Xanthomonas campestris pv. graminis and Xanthomonas campestris pv. phlei isolated from six species of forage grasses in four countries. The two pathovars could be distinguished clearly by genomic fingerprints generated by EcoRI, BamHI or HindIII digestion. DNA profiles produced by HindIII digestion could differentiate not only between the two pathoars but also among strains within the same pahtovar from different countries. A 1.6 kb EcoRI fragment was cloned from genomic DNA of strain LMG726 and used to detect restriction fragment-length polymorphism among the same strains. EcoRI and BamHI polymorphisms were seen between the two pathovars probed with this 1.6 kb EcoRI fragment (p726EI probe). These polymorphisms appeared to be highly conserved and unique for each pathovar, consistent with previous grouping of the strains based on other criteria.     

AFLP analysis of genetic diversity within and between Arabidopsis thaliana ecotypes.

The degree of genetic diversity within and between 21 Arabidopsis thaliana (L.) Heynh ecotypes was estimated by AFLP analysis. Within seven of the 21 ecotypes, a low but significant level of polymorphism was detected, and for five of these ecotypes two or three distinct subgroups could be distinguished. As these ecotypes represent natural populations, this intra-ecotypic diversity reflects natural genetic variation and diversification within the ecotypes. The source of this diversity remains unclear but is intriguing in view of the predominantly self-fertilizing nature of Arabidopsis. Interrelationships between the different ecotypes were estimated after AFLP fingerprinting using two enzyme combinations (EcoRI/MseI and SacI/MseI) and a number of selective primer pairs. SacI recognition sites are less evenly distributed in the genome than EcoRI sites, and occur more frequently in coding sequences. In most cases, AFLP data from only one enzyme combination are used for genetic diversity analysis. Our results show that the use of two enzyme combinations can result in significantly different classifications of the ecotypes both in cluster and ordination analysis. This difference most probably reflects differences in the genomic distribution of the AFLP fragments generated, depending on the enzymes and selective primers used. For closely related varieties, as in the case of Arabidopsis ecotypes, this can preclude reliable classification. Received: 25 September 1998 / Accepted: 3 March 1999     

Further characterization of AFLP® data as a tool in genetic diversity assessments among maize (Zea mays L.) inbred lines

AFLP® markers generated by CNG methylation sensitive (PstI/MseI) and CNG methylation insensitive (EcoRI/MseI) enzyme combinations and AFLP markers collected from hypomethylated (PstI/MseI) and hypermethylated (^m PstI/MseI) regions were compared for their polymorphism information content, sampling variance and patterns of genetic diversity in a representative sample of 33 inbred lines of maize (Zea mays L.). We demonstrate that the mean polymorphism information content generated by sets of PstI/MseI and ^m PstI/MseI markers (0.38) is significantly higher than by sets ofEcoRI/MseI markers (0.33). Also the sampling variance highlighted the distinctive nature of the ^(m) PstI/MseI markers: to achieve a mean standard deviation of 5% in the estimation of genetic distance among the 33 inbreds, the PstI/MseI and ^m PstI/MseI marker sets (135 and 129 markers, respectively) are clearly smaller than the EcoRI/MseI marker set (173 markers). A further minimizing of the sampling variance of AFLP data in the estimation of genetic similarities was obtained by reducing marker information redundancy by selecting markers evenly distributed over each chromosome: a set of only 106 AFLP markers, sampled conditionally on their genetic map position, was required for a mean standard deviation of 5% in the estimation of genetic distance among the 33 inbreds.     

Optimisation of DNA extraction for AFLP analysis of mycorrhizal fungi of terrestrial orchids caladeniinae and drakaeinae

Published DNA extraction methods present a number of problems when applied to mycorrhizal fungi of native Australian terrestrial orchids. Grinding with liquid nitrogen shears the DNA, and other pulverisation methods yield too little DNA. We found that freezing the fungal sample with liquid nitrogen, with no grinding, followed by the Qiagen DNeasy extraction procedure produced good yields of high-molecular-weight DNA. The DNA was then used for amplified fragment length polymorphism (AFLP) fingerprinting. Good fingerprints were produced by restriction withEcoRI/MseI enzymes, the use of preamplification primer mix II (for small genomes), and a 2-base extensionMseI primer (m-cc) with 3-base extensionEcoRI primers in the selective amplification. This protocol may be of general utility for other fungi with similarly fragile DNA.     

A genetic linkage map of tef [Eragrostis tef (Zucc.) Trotter] based on amplified fragment length polymorphism

A genetic linkage map of tef was constructed with amplified fragment length polymorphism (AFLP) markers using F₅ recombinant inbred lines (RILs) derived by single seed descent from the intraspecific cross of ’Kaye Murri’×’Fesho’. A total of 192 EcoRI/MseI primer combinations were screened for parental polymorphism. Around three polymorphic fragments per primer combination were detected, indicating a low polymorphism level in tef. Fifty primer combinations were selected to assay the mapping population, and 226 loci segregated among 85 F₅ RILs. Most AFLP loci behaved as dominant markers (presence or absence of a band), but about 15% of the loci were codominant. Significant deviations from the expected Mendelian segregation ratio were observed for 26 loci. The genetic linkage map comprised 211 markers assembled into 25 linkage groups and covered 2,149 cM of genome. AFLP is an efficient marker system for mapping plant species with low polymorphism such as tef. This is the first genetic linkage map constructed for tef. It will facilitate the mapping of genes controlling agronomically important traits and cultivar improvement in tef. Received: 27 April 1998 / Accepted: 4 January 1999     

POLYPHYLETIC ORIGIN OF THE DICTYOSPHAERIUM MORPHOTYPE WITHIN CHLORELLACEAE (TREBOUXIOPHYCEAE)1

The green algal Dictyosphaerium morphotype is characterized by spherical or oval cells connected by gelatinized strands to microscopic colonies, which are covered by prominent mucilaginous envelopes. Combined SSU and ITS rRNA gene sequence analyses revealed that this morphotype evolved independently both in the Chlorella and Parachlorella clades of the Chlorellaceae. It was shown that strains exhibiting the morphology of the type species Dictyosphaerium ehrenbergianum Nägeli established a sister lineage to Parachlorella. The strain D. ehrenbergianum CCAP 222/1A was designated as an authentic strain for establishing the epitype of the genus Dictyosphaerium. The comparison of this strain with the authentic strain of Parachlorella beijerinckii Krienitz, E. Hegewald, Hepperle, V. Huss, T. Rohr et M. Wolf (SAG 2046) showed considerable differences in the secondary structure of the ITS region. Within the whole ITS‐1 and ITS‐2 region, 27 compensatory base changes (CBCs) were recognized. In the conserved Helix III of the ITS‐2, five CBCs/HemiCBCs were detected. This is a conclusive argument for separation of these two species. The clear definition of Dictyosphaerium is intended to be the necessary starting point of taxonomic reevaluation of Dictyosphaerium‐like algae within different evolutionary lineages of the Chlorellaceae.     

MOLECULAR PHYLOGENY AND PHENOTYPIC VARIATION IN THE HETEROTROPHIC GREEN ALGAL GENUS PROTOTHECA (TREBOUXIOPHYCEAE,CHLOROPHYTA)1

Species of the heterotrophic green microalgal genus Prototheca and related taxa were phylogenetically analyzed based on the nuclear small subunit (SSU) and the 5′ end of the large subunit (LSU) rRNA gene (rDNA) sequences. We propose restricting the genus Prototheca to the four species: P. moriformis Krüger, P. stagnora (Cooke) Pore, P. ulmea Pore, and P. zopfii Krüger. The main diagnostic feature of these taxa is the absence of growth on trehalose.Of these, it was suggested that P. moriformis should be merged into P. zopfii; P. moriformis and three varieties of P. zopfii constituted a paraphyletic assemblage with estimated short evolutionary distances. The trehalose‐assimilating strains (Prototheca wickerhamii Tubaki et Soneda strains and Auxenochlorella protothecoides (Krüger) Kalina et Pun?ochá?ová SAG 211‐7a), together with an invertebrate pathogen Helicosporidium sp., diverged before the radiation of the four species of Prototheca in the SSU rDNA and composite (SSU rDNA plus LSU rDNA) analyses. Comparison between the results from physiological data in this work (fermentative pattern) and those described earlier (growth requirements) lead us to propose a hypothesis that the phenotypic variation, which did not represent diagnostic characters for species delimitation, may reflect the history of genetic diversification within the genus Prototheca as inferred from rDNA sequence characters.     

Microalgal biotechnology: Carotenoid production by the green algae<Emphasis Type="Italic">Dunaliella salina</Emphasis>

Unicellular green algae of the genusDunaliella thrive in extreme environmental conditions such as high salinity, low pH, high irradiance and subzero temperatures. Species ofDunaliella are well known in the alga biotechnological industry and are employed widely for the production of valuable biochemicals, such as carotenoids. Some strains ofDunaliella are cultivated commercially in large outdoor ponds and are harvested to produce dry algal meals, such as polyunsaturated fatty acids and oils for the health food industry, and coloring agents for the food and cosmetic industries. During the past decade, the advances in molecular biology and biochemistry of microalgae, along with the advances in biotechnology of microalgal mass cultivation, enabled this microalga to become a staple of commercial exploitation. In particular, the advent of molecular biology and mutagenesis inDunaliella has permitted enhancements in the carotenoids content of this green alga, making it more attractive for biotechnological applications. Accordingly, the present review summarizes the recent developments and advances in biotechnology of carotenoid production inDunaliella.     

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

Four species of the unicellular green alga Chlorella, C. vulgaris, C. luteoviridis, C. minutissima, and C. zofingiensis, were characterized with respect to DNA similarities as determined by quantitative DNA hybridization procedures. In contrast to previous DNA hybridization procedures. In contrast to previous results, C. vulgaris turned out to be a homogeneous species with the exception of strain 211-11c of the Göttingen collection, which was shown to belong to C. kessleri. Similary, C. luteoviridis and C. minutissima represent well defined species in terms of phenotypic and genotypic features. Whitin C. zofingiensis on strain is clearly different with respect to DNA base composition and DNA hybridization data even though it shares phenotypic characteristics with the other strains of C. zofingiensis.     

Alleviation of type I restriction in adenine methylase (dam) mutants of Escherichia coli

Summary The host-controlled EcoK-restriction of unmodified phage .O is alleviated in dam mutants of Escherichia coli by 100- to 300-fold. In addition, the EcoK modification activity is substantially decreased in dam ^- strains. We show that type I restriction (EcoB, EcoD and EcoK) is detectably alleviated in dam mutants. However, no relief of EcoRI restriction (Type II) occurs in dam ^- strains and only a slight effect of dam mutation on EcoP1 restriction (Type III) is observed. We interpret the alleviation of the type I restriction in dam ^- strains to be a consequence of induction of the function which interferes with type I restriction systems.     

Transduction of Plasmid Antibiotic Resistance Determinants with PseudoT-Even Bacteriophages

Transduction of antibiotic resistance determinants of the plasmid pBR322 with pseudoT-even bacteriophages RB42, RB43, and RB49 was studied. It is established that antibiotic resistance determinants of plasmid pBR322 fromEscherichia coli recA ⁺ and recA ^– donor strains do not differ significantly in respect to the efficiency of transduction. Amber mutants RB43-21, RB43-33, and a double amber mutant RB43am21am33 were obtained. These mutants facilitated transduction experiments in some cases. Transduction of antibiotic resistance markers of the vector plasmid pBR325 and recombinant plasmid pVT123, containing a DNA fragment with hoc–segE–uvsW genes of phage T4, was studied. The frequency of appearance of transductants resistant to pseudoT-even bacteriophages used in transduction was determined, and the sensitivity of resistant transductants to 32 RB bacteriophages and also to phages , T2, T4, T5, T6, T7, and BF23 was estimated. The efficiency of plating pseudoT-even bacteriophages RB42 and RB43 on strain E. coli 802 himA hip carrying mutations in genes that encode subunits of the Integration Host Factor (IHF) was shown to be higher than on isogenic strain E. coli 802. The growth of pseudoT-even bacteriophages limitedin vivo by modification–restriction systems of chromosomal (EcoKI, EcoBI), phage (EcoP1I), and plasmid (EcoRI, EcoR124I, and EcoR124II) localization was analyzed. It was shown that these phages were only slightly restricted by the type I modification–restriction systemsEcoBI, EcoR124I, and EcoR124II. Phage RB42 was restricted by systems EcoKI, EcoP1I, and EcoRI; phage RB43, by systems EcoKI and EcoRI; and phage RB49, by the EcoRI modification–restriction system.     

Mapping of the resistance genes of the R plasmid NR1.

Summary The drug resistance genes on the r-determinants component of the composite R plasmid NR1 were mapped on the EcoRI restriction endonuclease fragments of the R plasmid by cloning the fragments using the plasmid RSF2124 as a vector. The sulfonamide (Su) and streptomycin/spectinomycin (Sm/Sp) resistance genes are located on EcoRI fragment G of NR1. The expression of resistance to mercuric ions (Mer) requires both EcoRI fragment H and I of NR1. The expression of chloramphenicol (Cm) and fusidic acid (Fus) resistance requires EcoRI fragments A and J of NR1. The kan fragment of the related R plasmid R6-5 can substitute for EcoRI fragment J of NR1 in the expression of Cm and Fus resistance. The structural genes for Cm and Fus resistance appear to be a part of an operon whose expression is controlled by the same promoter.     

Establishment of AFLP technique and assessment of primer combinations for mei flower

Mei flower is one of the most famous ornamental flowers in eastern Asia for its blossoming in early spring. Amplified fragment length polymorphism (AFLP) is one of the most frequently used techniques for analysis of genetic variation and is used herein for the first time inPrunus mume. This research provides a detailed and modified AFLP protocol for Mei genomic DNA digested withEcoRI/PstI restriction endonuclease combinations. The 10 best primer pairs of high polymorphism were screened from 256 primer combinations that could reliably and repetitively distinguish 14 Mei samples and would be suitable for genetic analysis of more cultivars. Ten primer pairs produced up to a total of 524 AFLP bands and up to 233 polymorphic bands. The ratio of polymorphic bands scoped from 35.71% to 59.67%, and the average ratio was 44.46% in the 10 primers. AFLP is an effective, inexpensive, and timesaving technique for the genetic differentiation of the Mei cultivars, as evidenced in this study.