Identification of a set of RFLP probes for subspecies differentiation in Oryza sativa L.

Sixty-eight indica-japonica tester-differentiating RFLP probes were tested in seven indica and seven japonica varieties of rice (Oryza sativa L.) with four enzyme digestions (EcoRI, EcoRV, HindIII and DraI). Twenty-one DNA clones were isolated as indica-japonica subspecies-differentiating probes. A set of 13 probes was established as core probes for subspecies differentiation and a pooled blotting analysis was carried out to facilitate the application of RFLP in rice genetics and breeding practice. A dendrogram of 12 wide-compatibility varieties was constructed based on RFLPs detected by 13 core probes with single enzyme digestions. It was speculated that most RFLPs of indica-japonica differentiating probes were generated by insertions/deletions, which may be of great significance for the origin and differentiation of subspecies in Oryza sativa L.     

Seasonal development of apothecia of the cereal eyespot pathogen Tapesia yallundae on straw stubble in the UK

Five field sites growing winter wheat were inoculated with isolates of the W-and R-types of Tapesia yallundae in 1990 and 1991. After harvest, plots of uncultivated stubble were monitored for the production of apothecia during 1992 and 1993. Apothecia were found on the stem bases of straw stubble over a 9-month period from mid-October to July, but with a peak in numbers present during late January to March, 5 to 7 months after harvest. This was associated with mean monthly temperatures between 3°C and 8°C. Rainfall appeared to be less important than temperature in apothecial development. Single ascospore isolates obtained from apothecia collected from areas inoculated with W-, R-, or mixed W- and R-type isolates all produced colonies with morphologies and growth rates characteristic of the W-type. Thus there was no indication that the W- and R-types are sexually compatible.     

Multiple restriction fragment length polymorphisms associated with the Vc determinant of the MN blood group-related chimpanzee V-A-B-D system

Twelve restriction fragment length polymorphisms (RFLPs) were detected in common chimpanzee using two restriction enzymes (HindIII andMspI) and four DNA probes to the coding regions of the human glycophorin A (GPA) and glycophorin B (GPB) genes and their 3-untranslated regions. Seven RFLPs correlated with red cell expression of the V^c determinant of the MN blood group-related V-A-B-D system and five RFLPs correlated with nonexpression of this antigen. Animals heterozygous for theV allele that encodes the V^c determinant had all 12 polymorphic restriction fragments and appeared to show reduced intensity of probe hybridization to these fragments, consistent with the presence of aV and a non-V allele. No RFLPs were detected withEcoRI,SstI, orBamHI, in spite of the relatively large segment of DNA (at least 20 kb) involved in the polymorphisms. The RFLPs were chimpanzee specific and were not found in man, gorilla, orangutan, or gibbon. Multiple RFLPs distinguishing primate species are rare and may be useful markers for molecular evolution.This work was supported in part by National Institutes of Health Grants AM 33463 and CA 33000.     

The Development of Eyespot on Seedling Leaf Sheaths in Winter Wheat and Winter Barley Crops Inoculated with W-type or R-type Isolates of Pseudocercosporella herpotrichoides

In 1986–88 the development of eyespot lesions in winter wheat or winter barley differed plots inoculated with W-type isolates of Pseudocercosporella herpotrichoides and plots inoculated with R-type isolates. In the spring of 1986, after a cold winter, the incidence (%shoots infected) and severity (number of leaf sheaths penetrated) of eyespot lesions in wheat before GS 30/31 were greater in plots inoculated with R-type isolates than in those inoculated with W-type isolates. In 1987, after amild winter, eyespot incidence and severity in both wheat and barley were initially greater in W-type plots than in R-type plots. However, by GS 30/31 or 1987. In 1988, when the crop was October-sown, eyespot incidence and severity were greater in W-type than in R-type plots at GS 30/31. Differences in eyespot incidence and severity between W-type and R-type plots were smaller in barley than in wheat. Both the incidence and severity of eyespot were greater in early-sown than in late-sown plots. Seed rate, had little effect on the rate of lesion development in 1987, but in 1988 the rate of penetration was less at the low seed rate for both wheat and barley.     

The Use of DNA Fingerprinting in Ecological Studies of Phragmites australis (Cav.) Trin. ex Steudel

A number of reed populations (Phragmites australis) from natural locations on the shore of Lake Ammersee in the south of Bavaria as well as artificially grown reed plants were analyzed for restriction fragment length polymorphisms (RFLPs) in order to evaluate for further ecological studies the dynamics of the restriction pattern within the genome of plants which propagate themselves asexually. The artificially grown reed plants were raised in four ponds supplemented with different phosphate concentrations (8 μg, 16 μg, 50 μg, and 200 μg/l) from rhizomes taken from a neighbouring fish pond. The genomic DNA of 25 of these plants and the DNA from 37 plants out of 18 stands from the lakeshore was isolated and restricted with the enzyme EcoRI, EcoRV, XbaI and HindIII and hybridized to three probes from a shot-gun cloned reed plasmid library. The probes gave between 15 and 26 bands (DNA fingerprints) of high polymorphic frequency (68% ? 100%) after hybridization with repetitive sequences of restricted DNA. A cluster analysis based on the banding pattern as a measure of genetic similarity (GS) was performed with the two sets of reed plants. The plants from the lakeshore exhibited a clear formation of clusters with GS up to 100%; the 20 plants grown from rhizomes, in contrast, did not show any clear correlation among themselves, neither to the phosphate concentration they grew in, nor to the five plants tested from the pond their rhizomes came from. The value of genetical investigations of the plant genome in context with environmental impact on plants is being discussed.     

Restriction fragment length polymorphism of DQB and DRB class II genes of the ovine major histocompatibility complex

The ovine major histocompatibility complex (MhcOvar) class II region was investigated by Southern blot hybridizations using ovine probes specific for the second exons of Ovar-DRB and Ovar-DQB genes. Multiple bands were revealed when genomic DNA was digested with each of five restriction enzymes (Bam HI, Eco RI, Hin dIII, PvuII and TaqI), and successively hybridized with the two radiolabeled ovine probes. Restriction fragment length polymorphisms (RFLPs) were analysed in 89 sheep originating from six inbred families and the inheritance of the fragment patterns was determined. Forty-one fragments were recorded with the DQB probe; 32 were detected with the DRB probe. They constituted 9 DQB and 10 DRB allelic patterns. Twelve DQB-DRB haplotypes were resolved in this study.     

Localization of the coagulation factor XIII B subunit gene (F13B) to chromosome bands 1q31–32.1 and restriction fragment length polymorphism at the locus

Summary In situ hybridization of tritiated cDNA probes for the gene for the B subunit of coagulation factor XIII localized the F13B locus to bands q31–q32.1 on human chromosome 1 and perhaps more precisely to sub-bands 1q31.2 or 1q31.3. Restriction fragment length polymorphisms (RFLPs) were detected with BglII, EcoRI and XbaI. Because the RFLPs detected with each of the three enzymes were concordant in every individual studied and since each showed a similar size difference, it was concluded that the RFLPs probably result from an insertion or deletion of length approximately 0.37–0.4 kb.     

High rate of restriction fragment length polymorphisms between two population of the nematode Pristionchus pacificus (Diplogastridae)

Pristionchus pacificus (Diplogastridae, Nematoda) has recently been described as a ‘satelite’ organism for a functinal comparative approach, becuase genetic, molecular and cell-biological tools can be used in way similar to the genetic model organism Caenorhabditis elegans. This tudy describes the analysis of two previously isolated strains of P. pacificus for the occurrence of restriction fragment length polymorphisms (RFLPs). In all, 14 of 17 randomly chosen cDNA clones give polymorphisms after hybridization to EcoRI digested genomic DNA of the populations from California and Washington. This polymorphism is much higher than polymorphism found among different strains in C. elegans. Therefore this study compares most of the nucleotide sequence of the Ppa-let-60/ras gene between the two strains. No base-pair substitutions were found between these two sequences within the coding regions. However, within the untranslated region, four base-pair substitutions in introns and the deletion of three base-pairs in the 5′ sequence and in intron 4 have been observed. Since the two strains interbreed, RFLPs can be used as molecular markers for future chromosomal walking and gene cloning.     

Restriction Fragment Length Polymorphism Analysis of the Mitochondrial DNA of Fusarium oxysporum f. sp. ciceris

Seven isolates of Fusarium oxysporum f. sp. ciceris, representing pathogenic races 1 , 2, 3, and 4 from India and 0, 5, and 6 from Spain, were assayed for restriction fragment length polymorphisms (RFLPs) in the mitochondrial DNA,(mt DNA). The mt DNA fraction of total fungal DNA was purified and digested with the restriction endonucleases Bam HI, Bgl II, Eco RI. Kpn I, Sac I, Sal I, Sma I, and Xho I. The mt DNA is a circular molecule of 40.5 kb. No RFLP in the mt DNA was detected among the seven races of F. o. ciceris. The identical restriction patterns of mt DNA indicates an extensive conservation in the gene composition of mt DNA without sequence variation, and suggests that mt DNA of F. o. ciceris may not be responsible for pathogenic diversity. The restriction map of mt DNA from the race 6 isolate Fo 8272 was constructed by digestion of the mt DNA with five restriction enzymes: Eco RI, Kpn I, Sac I, Sal I, and Xho I, either singly or in selected pairs.     

Prediction of Eyespot Severity on Winter Wheat or Winter Barley Inoculated with W-type or R-type Isolates of Pseudocercosporella herpotrichoides

In crops of winter wheat (1986—88) or winter barley (1987—88) inoculated with W-type or R-type isolates of Pseudocercosporella herpotrichoides and sown on different dates (1986) or at different seed rates (1987,1988) eyespot epidemics developed in different ways. Methods of measuring eyespot incidence/severity during crop growth were compared for their ability to predict eyespot severity at grain filling. Regressions were calculated for eyespot severity score at GS 71 on earlier measurements, either at GS 30/31 (11 methods) or from GS 22 to GS 65 (3 methods). Based on measurements at GS 30/31, all the methods predicted eyespot severity at GS 71 well in plots of winter barley inoculated with W-type isolates (r, 0.83—0.97) but the accuracy of predictions in plots inoculated with R-type isolates was very variable (r, 0.09—0.71). Predictions for 1987 and 1988 were less accurate in wheat than in W-type plots of barley, but did not differ between W-type and R-type plots (r, 0.70—0.89). When the wheat data for 1986 were also included predictions were less accurate, especially in R-type plots (r, 0—0.59). Generally, it was easier to predict eyespot severity at GS 71 in W-type than in R-type plots, especially in barley and in wheat before GS 37/39. Predictions of eyespot severity at GS 71 based on measurements before GS 25 were inaccurate for both wheat and barley. After GS 25 the accuracy of the prediction was generally good in W-type plots and did not improve greatly except in wheat after GS 59. However, there was a steady improvement in the accuracy of the prediction in R-type plots of barley from GS 24 to GS 53. Assessments of eyespot incidence on stems predicted eyespot severity at GS 71 more accurately than assessments on leaf sheaths on wheat after GS 37/39, but were not as good on barley until GS 53.     

RFLP analysis of the wild potato species,Solanum acaule Bitter (Solanum sect. Petota)

Summary Intraspecific variation of a wild potato species, Solanum acaule Bitt., was analyzed by RFLPs of genomic DNA. One hundred and five accessions were selected throughout the distribution area, including all subspecies, i.e., ssp. albicans (hexaploid), ssp. punae (tetraploid), ssp. acaule (tetraploid) and ssp. aemulans (tetraploid). Twenty-seven low-copy DNA clones (probes) were Southern hybridized with EcoRI, EcoRV, HindIII, and XbaI digests of total DNA of all accessions. In total, 238 RFLPs were detected from 94 enzyme x probe combinations. Among them, 49 RFLPs were specific to ssp. albicans, suggesting that the additional third genome is distinct from its two other genomes. RFLPs between and within subspecies were analyzed by principal component analysis. DNA similarities between subspecies coincided with a former taxonomic treatment in the sense that ssp. albicans is the most distantly related to ssp. acaule and ssp. aemulans is distantly related. Subspecies acaule and ssp. punae were indistinguishable. In addition, RFLPs could be used to distinguish groups within subspecies. Subspecies aemulans, confined to Argentina, was divided into two populations, one from the province of La Rioja and the other from the province of Jujuy. In ssp. acaule, some accessions from the southernmost distribution area were clearly distinguishable, while the others varied continuously, showing a geographical cline from Peru to Argentina.Reference to a specific brand or firm name does not constitute endorsement by the US Department of Agriculture over others of similar nature not mentioned     

Restriction fragment length polymorphisms distinguish ectomycorrhizal fungi

Basidiomycetous fungi, two saprophytes and three mycorrhizal, were used to assess the specificity of DNA hybridization for distinguishing genera from one another. Interspecific comparisons were done with several isolates of mycorrhizal fungi,Laccaria bicolor andL. laccata, collected from diverse geographical sites. The DNAs were digested with four restriction nucleases and separated by gel electrophoresis into patterns of DNA fragments called restriction fragment length polymorphisms (RFLPs). The RFLPs were hybridized with a radioactively-labeled DNA probe encoding Basidiomycetous ribosomal RNA genes. The five genera were discernable using both unprobed and probed RFLPs. Hybridization of probe DNA with RFLPs was isolate-specific for all nine Laccaria isolates examined. The reclassification of aL. bicolor isolate is supported, demonstrating that hybridization of RFLPs offers an additional tool for taxonomy of ectomycorrhizal fungi. The method may have field application for distinguishing known isolates if their DNA fingerprints are previously ascertained and are distinct from RFLPs of indigenous organisms.     

Sensitivity to prochloraz in populations of the eyespot fungus, Pseudocercosporella herpotrichoides, in relation to fungicide treatments and their efficacy in continuous winter wheat

Eyespot was assessed and grain yields determined in the eighth and ninth years (1992 and 1993) of a field experiment in which the fungicides carbendazim and prochloraz were applied, separately or in mixtures, to plots of successive crops of winter wheat. Populations of the eyespot fungus, Pseudocercosporella herpotrichoides, were characterised by the proportions of cultures grown on agar from infected stems that were W-type or R-type, or were carbendazim-resistant or carbendazim-sensitive. Sensitivity to prochloraz in agar was determined for isolates from populations sampled in 1992 using restricted maximum likelihood analysis of EC50s (concentrations needed to decrease colony growth by 50%), to deal with the unbalanced data, and comparisons were made by Wald statistics. Control by prochloraz was maintained but in 1992, as in some previous years, its application with carbendazim was more effective than its application alone. Selection by prochloraz for strains sensitive to carbendazim continued to occur and may have contributed to its sometimes relatively poorer performance in the absence of carbendazim. R-type isolates taken from prochloraz-treated plots, with or without carbendazim, in 1992 were less sensitive to prochloraz than were isolates from plots untreated with prochloraz. There was evidence of a greater range of sensitivities to prochloraz in R-type than in W-type isolates (although some uncertainty results from the small numbers of W-type isolates obtained from some treatments), which would explain the selection of the R-type by prochloraz. The significance of these findings to modern wheat growing practices is considered.     

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.     

Restriction Fragment Length Polymorphism Analyses of the Plasmid DNAs in Strains of Xanthomonas campestris pv. vesicatoria from Different Geographic Areas

Restriction fragment length polymorphisms (RFLPs) of plasmid DNAs in Xanthomonas campestris pv. vesicatoria were analysed using 77 strains from the United states, Argentina, Australia, Taiwan, and Korea. One or more plasmids were detected in all tested strains, irrespective of geographic origin, host plant from which isolated, or chemical resistance. All Korean strains contained a few plasmids of similar high molecular weight, whereas some small plasmids occured only in strains from the United States, Argentina, and Taiwan. After digesting total plasmid DNAs with each of four restriction endonucleases, 18 fragments with sizes from about 1 to 23 kb were visualized. Seventy-seven strains of diverse geographic origins, with different levels of resistance to streptomycin and copper, were classified into the 14 RFLP groups based on the restriction endonuclease digestion patterns of their plasmid DNAs. Strains belonging to each group shared DNA fragments of identical size, suggesting the possible presence of similar plasmids in these strains. A 5.8-kb EcoRI plasmid DNA probe prepared from the United States strain 81-23 hybridized to EcoRI plasmid digests from all tested strains. Other plasmid DNA fragments of the strain81-2,3 used as probes had no homology to plasmid DNA fragments from several strains around the world. The variation in hybridization profiles of plasmid DNA was very similar to the results obtained by RFLP analysis of plasmid DNA digested by four restriction enzymes. Most of the Korean strains tested were highly sensitive to streptomycin and copper, whereas most strains from other geographic areas showed a high level of resistance to one or two of the chemicals. Cluster analysis of genetic distance between the strains based on the data obtained generated the dendrograms that separated all Korean strains from the other strains, suggesting that plasmid DNA of the Korean strains may be genetically very different from those of the others.     

Restriction Fragment Length Polymorphisms of Mitochondrial and Nuclear DNAs among Korean Races of Magnaporthe grisea

Three KJ-races of Magnaporthe grisea (virulent to only japonica type rice cultivars) and seven KI-races (virulent to either indica or japonica type cultivars) isolated from various rice-growing areas of Korea were assayed for restriction fragment length polymorphisms (RFLPs) in mitochondrial and nuclear DNAs of the fungus. The size of mitochondrial DNA of M. grisea was estimated to be approximately 39. 8 kb. No RFLP in the mt DNA was detected among the 10 Korean races, indicating an extensive conservation in the gene composition of mt DNA without sequence variation. The identical restriction patterns of mt DNA also suggest that mt DNA of M. grisea may not be responsible for pathotypic diversity and variability. Southern blot analysis with five single-copy DNA probes showed considerable polymorphisms. Much diversity was detected in the three KI-races predominated during 1978–1985 in Korea. In contrast, no genetic variation was detected between other four KI-races and three KJ-races. RFLPs in nuclear DNA were correlated to some extent with the prevailing races in Korea. However, relationship between RFLPs in nuclear DNA and virulence of M. grisea races was inconclusive.     

COMPARISON OF CHLOROPLAST DNA AND ALLOZYME VARIATION IN WINTER STRAINS OF THE MARINE DIATOM SKELETONEMA COSTATUM(BACILLARIOPHYTA)1

Restriction fragment length polymorphisms (RFLPs) were examined in 12 winter strains of the marine diatom Skeletonema costatum (Grev.) Cleve using homologous chloroplast gene probes. The winter strains included eight different allozyme genotypes exhibiting physiological differences. These 12 winter strains were representative of the least diverse genetic group present in Narragansett Bay populations. Five chloroplast DNA probes and four different restriction enzymes were used to analyze the 12 Narragansett Bay strains and a reference strain “Skel.” A total of 46 restriction fragments were identified. All 12 of the winter strains had identical patterns. Strain Skel exhibited two RFLPs in comparison to the Narragansett Bay strains. Calculated diversity within the winter strain group was 0.0 and 0.85 for the chloroplast DNA and allozyme data, respectively. The chloroplast DNA polymorphisms revealed by this study are expected to represent a minimum level of the chloroplast DNA diversity present in Narragansett Bay seasonal populations.     

DNA polymorphisms in commercial and wild strains of the cultivated mushroom,Agaricus bisporus

Summary DNA from the cultivated mushroom, Agaricus bisporus, was cloned into the bacteriophage lambda vector EMBL3 creating a partial genomic library. Ten random clones from the library were used to probe for restriction fragment length polymorphisms (RFLPs). Six of the ten probes detected polymorphisms and were used to demonstrate variation in wild and cultivated strains of the mushroom. These results suggest that RFLPs could form a basis for genetic finger-printing and subsequent strain protection in A. bisporus. In single spore progeny, RFLPs were used to demonstrate normal meiotic segregation and to differentiate between homokaryons and heterokaryons. RFLPs therefore have great potential in the development of the genetics and breeding of this commercially important species.     

Haplotype frequencies of the collagen type-I genes in the Italian population

Summary We have determined the frequencies of six restriction fragment length polymorphisms (RFLPs) of type-I collagen genes in a random sample of 100 subjects. Alpha 1 gene (COL1A1) DNA polymorphisms, FG2/MspI, 2FC6/RsaI, and NST70/RsaI, had polymorphism information content (PIC) values of 0.35, 0.32, and 0.26, respectively. Alpha 2 gene (COL1A2) RFLPs, NJ3/EcoRI, Hf32/RsaI, and Hf32/MspI had PIC values of 0.36, 0.35, and 0.25, respectively. The combined haplotype PIC values were 0.71 at the COL1A1 locus and 0.73 for COL1A2. Two COL1A1 and two COL1A2 RFLPs were more polymorphic than in the English population, making them better markers for the analysis of Italian families affected by osteogenesis imperfecta and some other inherited collagen diseases.     

Restriction Fragment Length Polymorphisms Detected with Novel DNA Probes Differentiate among Diverse Lineages of Serogroup 4 Listeria monocytogenes and Identify Four Distinct Lineages in Serotype 4b

Listeria monocytogenes of serotype 4b has been implicated in numerous outbreaks of food-borne listeriosis and in ca. 40% of sporadic cases. Strains of this serotype appear to be relatively homogeneous genetically, and molecular markers specific for distinct serotype 4b lineages have not been frequently identified. Here we show that DNA fragments derived from the putative mannitol permease locus of Listeria monocytogenes had an unexpectedly high potential to differentiate among different strains of serotype 4b when used as probes in Southern blotting of EcoRI-digested genomic DNA, yielding four distinct restriction fragment length polymorphism (RFLP) patterns. Strains of two epidemic-associated lineages, including the major epidemic clone implicated in several outbreaks in Europe and North America, had distinct RFLPs which differed from those of all other serotype 4b strains that we screened but which were encountered among strains of serotypes 1/2b and 3b. In addition, three serogroup 4 lineages were found to have unique RFLPs that were not encountered among any other L. monocytogenes strains. One was an unusual lineage of serotype 4b, and the other two were members of the serotype 4a and 4c group. The observed polymorphisms may reflect evolutionary relationships among lineages of L. monocytogenes and may facilitate detection and population genetic analysis of specific lineages.