Comparison of four molecular markers in measuring relationships among the wild potato relatives Solanum section Etuberosum (subgenus Potatoe)

We evaluated chloroplast DNA (cpDNA), isozymes, single to low-copy nuclear DNA (RFLPs), and random amplified polymorphic DNAs (RAPDs) in terms of concordance for genetic distance of 15 accessions each of Solanum etuberosum and S. palustre, and 4 accessions of S. fernandezianum. These self-compatible, diploid (2n=24), and morphologically very similar taxa constitute all species in Solanum sect. Etuberosum, a group of non-tuber-bearing species closely related to Solanum sect. Petota (the potato and its wild relatives). Genetic distance and multidimentional scaling results show general concordance of isozymes, RFLPs and RAPDs between all three taxa; cpDNA shows S. etuberosum and S. palustre to be more similar to each other than to S. fernandezianum. Interspecific sampling variance shows a gradation of resolution from allozyme (low) to RAPD to RFLP (high); while intraspecific comparisons graded from RFLPs (low) to RAPDs (high; lack of sufficient allozyme variability within species precluded comparisons for allozymes). Experimental error was low in RFLPs and RAPDs.Names are necessary to report factually and available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable     

Comparison of RAPD and RFLP genetic markers in determining genetic similarity among Brassica oleracea L. genotypes

Genetic similarity among 45 Brassica Oleracea genotypes was compared using two molecular markers, random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphisms (RFLPs). The genotypes included 37 broccolis (var. italica), five cauliflowers (var. botrytis) and three cabbages (var. capitata) which represented a wide range of commercially-available germplasm, and included open-pollinated cultivars, commercial hybrids, and inbred parents of hybrid cultivars. Fifty-six polymorphic RFLP bands and 181 polymorphic RAPD bands were generated using 15 random cDNA probes and 62 10-mer primers, respectively. The objectives were to compare RFLP and RAPD markers with regard to their (1) sampling variance, (2) rank correlations of genetic distance among sub-samples, and (3) inheritance. A bootstrap procedure was used to generate 200 random samples of size n (n=2,3,5,... 55) independently from the RAPD and RFLP data sets. The coefficient of variance (CV) was estimated for each sample. Pooled regressions of the coefficient of variance on bootstrap sample size indicated that the rate of decrease in CV with increasing sample size was the same for RFLPs and RAPDs. The rank correlation between the Nei-Li genetic similarity values for all pairs of genotypes (990) based on RFLP and RAPD data was 0.745. Differences were observed between the RFLP and RAPD dendrograms of the 45 genotypes. Overlap in the distributions of rank correlations between independent sub-samples from the RAPD data set, compared to correlations between RFLP and RAPD sub-samples, suggest that observed differences in estimation of genetic similarity between RAPDs and RFLPs is largely due to sampling error rather than due to DNA-based differences in how RAPDs and RFLPs reveal polymorphisms. A crossing algorithm was used to generate hypothetical banding patterns of hybrids based on the genotypes of the parents. The results of this study indicate that RAPDs provide a level of resolution equivalent to RFLPs for detemination of the genetic relationships among genotypes.     

Characterization of replication-competent retroviruses from nonhuman primates with virus-induced T-cell lymphomas and observations regarding the mechanism of oncogenesis.

Rapidly progressive T-cell lymphomas were observed in 3 of 10 rhesus monkeys several months after autologous transplantation of enriched bone marrow stem cells that had been transduced with a retroviral vector preparation containing replication-competent virus (R. E. Donahue, S. W. Kessler, D. Bodice, K. McDonagh, C. Dunbar, S. Goodman, B. Agricola, E. Byrne, M. Raffeld, R. Moen, J. Bacher, K. M. Zsebo, and A. W. Nienhuis, J. Exp. Med. 176:1124-1135, 1992). The animals with lymphoma appeared to be tolerant to retroviral antigens in that their sera lacked antibodies reactive with viral proteins and contained 10(4) to 10(5) infectious virus particles per ml. By molecular cloning and DNA sequencing, we have now demonstrated that the serum from one of the monkeys contained a replication-competent retrovirus that arose by recombination between vector and packaging encoding sequences (vector/helper [V/H] recombinant) in the producer clone used for transduction of bone marrow stem cells. Southern blot analysis demonstrated 14 or 25 copies of this genome per cell where present in two animals. The genome of a second replication-competent virus was also recovered by molecular cloning; it arose by recombination involving the genome of the V/H recombinant and endogenous murine retroviral genomes in the producer clone. Twelve copies of this amphotropic virus/mink cell focus-forming virus genome were present in tumor DNA of one animal, but it was not found in tumor DNA of the other two animals with lymphoma. Southern blot analysis of DNA from various tissues demonstrated common insertion site bands in several samples of tumor DNA from one animal, suggesting clonal origin of the lymphoma. Our data are most consistent with a pathogenic mechanism in which chronic productive retroviral infection allowed insertional mutagenesis of critical growth control genes, leading to cell transformation and clonal tumor evolution.     

Dynamics of benthic algal vegetation and environment in Dutch estuarine salt marshes studied by means of permanent quadrats

Summary Knowledge of the spatial structure of benthic algal vegetations in salt marshes, consisting of about 100 species of blue-green, green, brown and red algae, formed the basis of a detailed study into the dynamics of the algal mat.The temporal changes in algal vegetations and concomitant processes in their environment were studied in 27 permanent quadrats (PQs), plotted in tidal salt marshes and along brackish inland waters in the SW Netherlands. Once a month vegetation and environment of the PQs were examined over the period March 1968-February 1971. From the Spearman rank-correlation between vegetational and environmental parameters it appeared that in semiterrestrial and terrestrial environments the average number of algal species in a relevé and the average similarity between the species composition of successive relevés obtained from one PQ have a significant positive correlation with the stability of the substrate, and hardly any correlation with fluetuations in soil-moisture content and salinity of the soil moisture and with the maximum cover percentage of the phanerogams.Stable substrates tend to bear stable algal mats, as appeared from quantitative data. Small and moderate fluctuations in soil-moisture content and salinity of the soil moisture have no limiting influence on the algal cover degree. During periods of extremely high salinity and concomitant extremely low soil-moisture contents that coincide with evaporation surpluses, the green algal mat bleaches and decreases in cover in semi-terrestrial and terrestrial environments. Below 20% the soil-moisture content is limiting for the expansion of a mat of green algae (Rhizoclonium riparium, Percursaria percursa, Enteromorpha torta, E. prolifera) and Vaucheria species. The mat desiceates and bleaches but recovers after increase of the soil-moisture content above 20% within one month. Two weeks of severe frost (temperature down to – 10°C) do not influence the cover degree of the algal mat in aquatic branckish PQs, but the cover degree in semi-terrestrial PQs decreases. Short lasting soil-moisture salinities of 130–190 Cl^– have no limiting effect on the expansion of the algal mat.Nomenclature authorities are given in Table 3.Contribution to the Symposium of the Working Group for Succession Research on Permanent Plots, held at Yerseke, The Netherlands, October 1975.Communication No. 163 of the Delta Institute for Hydrobiological Research, Yerseke.     

Hemoglobin switching in sheep. Synthesis, cloning, and characterization of DNA sequences coding for the beta B, beta C, and gamma-globin mRNAs.

Synthetic double-stranded DNAs (sDNAs) were prepared from sheep globin mRNA templates isolated from reticulocytes producing either hemoglobin B (HbB) (alpha 2 beta B2), HbC (alpha 2 beta C2), or HbF (alpha 2 gamma 2). These DNAs were inserted into the Eco RI site of plasmid pMB9 by the homopolymer tailing method and used to transform Escherichia coli X1776 to tetracycline resistance. Recombinant clones were identified by colony hybridization and further characterized by molecular hybridization and restriction endonuclease analysis. All plasmids analyzed thus far contained either beta- or gamma-globin DNA sequences. Moreover, sDNAs used for cloning yielded restriction endonuclease fragments consistent with the presence of predominantly beta- or gamma-sDNA, indicating that formation of double-stranded alpha-sDNA proceeds much less efficiently under our conditions than the formation of non-alpha-sDNAs. Three recombinant plasmids, pS beta B2, pS beta C69, and pS gamma 56, were selected for detailed study. These were shown to contain, respectively, beta B-, beta C-, and gamma-DNA sequences by molecular hybridization and by protection of the appropriate cDNAs from S1 nuclease digestion. Each contained all of the restriction endonuclease sites defined for the synthetic sDNAs and protected at least 90% of the sequence length of homologous cDNA. Restriction endonuclease maps of the beta B- and beta C-globin genes were identical at all 12 sites that were mapped, whereas four differences were identified in the gamma gene compared to the two others; three of these corresponded to differences in amino acid sequence of the globins. A method was developed to isolate the anti-mRNA strand of the insert for use as a specific molecular hybridization probe analogous to complementary DNA.     

Collapse of morphological species in the wild potato Solanum brevicaule complex (Solanaceae: sect. Petota)

The major cultivated potato, Solanum tuberosum, and six other related cultivated species, are hypothesized to have arisen from a group of weedy relatives indigenous to the central Andes of central Peru, Bolivia, and northern Argentina. A major problem hindering investigations of the origins of the cultivated species has been a continuing debate over the species boundaries of their putative progenitors. This study investigated the morphological phenetic species boundaries of these putative progenitors and five cultivated taxa, here collectively referred to as the Solanum brevicaule complex. Two hundred fifteen accessions of 30 taxa in the S. brevicaule complex and 42 accessions of six taxa outside of the complex were assessed for 53 morphological traits in replicate plots in a common garden, resulting in a total of over 81;t3000 data points. Phenetic analyses of these data are unable to support 30 taxa, suggesting instead a single variable complex at best only weakly divided into three widely intergrading sets of populations: (1) Peruvian and geographically adjacent Bolivian accessions (including wild species and all the cultigens), (2) Bolivian and Argentinian accessions and S. verrucosum from Mexico (including only wild species), and (3) the Bolivian and Argentinian wild species S. oplocense. These and other data suggest that Hawkes's 1990 treatment (The Potato: Evolution, Biodiversity, and Genetic Resources, Smithsonian Institute Press, Washington, DC.) of 232 morphological species is an overestimate for sect. Petota.     

Changing Estuaries, Changing Views

During the design and the execution of the Delta project, carried out after the storm flood of 1953 in the SW Netherlands, the importance of the long-term effects of morphological and ecological developments driven by tides and currents, have been underestimated. Due to these processes the height of the dams will have to be increased for centuries to come, because the land behind the levees cannot grow in elevation anymore with the rising of the sea. Maintenance of the civil-engineering structures, and mitigating their unpredictable impacts on ecosystems, involve very high recurrent costs. The chance of flooding is reduced, but the potential damage after a storm flood is enlarged: seawalls and dykes provide a false sense of safety against flooding. Changes in the role of agricultural use in the European context, offer an opportunity to abandon arable fields and to retrocede them to the sea in order to absorb tidal energy and to allow the land to rise concomitant with the sea. A cost-benefit analysis of this approach should assess the direct and indirect economic values, as well as the non-use (intrinsic) values, whereby public engagement in management questions, facilitates decision-making processes. Reversible and resilient economic measures within the limits of the natural processes are preferable. A future, speculative perspective is an urbanised landscape, where people and investments are located in safe places, e.g. on floating, or sea-encircled artificial dwelling-mounds, surrounded by a landscape that is ruled by the forces of nature. New approaches such as developed in the Westerschelde offer flexible solutions to flooding problems, and are worth a broader evaluation. A worldwide platform of experts should be organised to study the future management of estuaries and deltas, and to develop and exchange new ideas and techniques.