Showing papers by "Institut national de la recherche agronomique published in 1996"

High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco.

Abstract: Genetic diversity at nine isozyme loci was surveyed in an endangered tree species, the argan tree, endemic to south-western Morocco. The species is highly diverse (3.6 alleles/locus) with populations strongly differentiated from each other (FST=0.25). This example is used to illustrate a method for standardizing measures of allelic richness in samples of unequal sample sizes, which was developed for the estimation of the number of species and relies on the technique of rarefaction. In addition, it is shown that the measure of subdivision, θST, obtained when allelic richness is used in place ofh (Nei's index of diversity), is much larger than the FST [e.g. θST(40)=0.52, where (40) indicates the specified sample used to estimate the allelic richness]. This suggests that rare alleles (which strongly influence measures of allelic richness) have a more scattered distribution than more frequent ones, a result which raises special conservation issues for the argan tree.

Aggregate stability and assessment of soil crustability and erodibility: I. Theory and methodology

Abstract: Summary Crusting and erosion of cultivated soils result from aggregate breakdown and the detachment of soil fragments by rain, and the susceptibility of soil to these processes is often inferred from measurements of aggregate stability. Here, theories of aggregate breakdown are reviewed and four main mechanisms (i.e. slaking, breakdown by differential swelling, mechanical breakdown by raindrop impact and physico–chemical dispersion) are defined. Their relative importance depends on the nature of the rain, as well as on the soil's physical and chemical properties. The relations between aggregate breakdown, crusting and water erosion are analysed, and existing methods for the assessment of aggregate stability are reviewed. A unified framework for the measurement of aggregate stability is proposed to assess a soil's susceptibility to crusting and erosion. It combines three treatments having various wetting conditions and energies (fast wetting, slow wetting, and stirring after pre-wetting) and measures the resulting fragment size distribution after each treatment. It is designed to compare different soils, or different climatic conditions for a given soil, not to compare time-dependent changes in that soil.

GOR method for predicting protein secondary structure from amino acid sequence.

Abstract: Publisher Summary This chapter discusses the Garnier–Osguthorpe–Robson (GOR) method for predicting protein secondary structure from amino acid sequence. The chapter presents the major principles used by the GOR method and some results obtained with an updated version of this method. The GOR method is one of the most popular of the secondary structure prediction schemes. Through the successive incorporation of observed frequencies of single, then pairs of residues on a local sequence of 17 residues, the accuracy of the GOR method has improved from about 55% up to 64.4%. The GOR method has the advantage over neural network-based methods or nearest-neighbor methods in that it clearly identifies what is taken into account for the prediction and what is neglected. The method provides estimates of probabilities for the three secondary structures at each residue position that can be useful for further application of the method.

Measuring and testing genetic differentiation with ordered versus unordered alleles.

Abstract: Estimates and variances of diversity and differentiation measures in subdivided populations are proposed that can be applied to haplotypes (ordered alleles such as DNA sequences, which may contain a record of their own histories). Hence, two measures of differentiation can be compared for a single data set: one (GST) that makes use only of the allelic frequencies and the other (NST) for which similarities between the haplotypes are taken into account in addition. Tests are proposed to compare NST and GST with zero and with each other. The difference between NST and GST can be caused by several factors, including sampling artefacts, unequal effect of mutation rates and phylogeographic structure. The method presented is applied to a published data set where a nuclear DNA sequence had been determined from individuals of a grasshopper distributed in 24 regions of Europe. Additional insights into the genetic subdivision of these populations are obtained by progressively combining related haplotypes and reanalyzing the data each time.

Bootstrap confidence levels for phylogenetic trees.

Abstract: Evolutionary trees are often estimated from DNA or RNA sequence data. How much confidence should we have in the estimated trees? In 1985, Felsenstein [Felsenstein, J. (1985) Evolution 39, 783-791] suggested the use of the bootstrap to answer this question. Felsenstein's method, which in concept is a straightforward application of the bootstrap, is widely used, but has been criticized as biased in the genetics literature. This paper concerns the use of the bootstrap in the tree problem. We show that Felsenstein's method is not biased, but that it can be corrected to better agree with standard ideas of confidence levels and hypothesis testing. These corrections can be made by using the more elaborate bootstrap method presented here, at the expense of considerably more computation.

Molecular identification of zeaxanthin epoxidase of Nicotiana plumbaginifolia, a gene involved in abscisic acid biosynthesis and corresponding to the ABA locus of Arabidopsis thaliana.

Abstract: Abscisic acid (ABA) is a plant hormone which plays an important role in seed development and dormancy and in plant response to environmental stresses. An ABA-deficient mutant of Nicotiana plumbaginifolia, aba2, was isolated by transposon tagging using the maize Activator transposon. The aba2 mutant exhibits precocious seed germination and a severe wilty phenotype. The mutant is impaired in the first step of the ABA biosynthesis pathway, the zeaxanthin epoxidation reaction. ABA2 cDNA is able to complement N.plumbaginifolia aba2 and Arabidopsis thaliana aba mutations indicating that these mutants are homologous. ABA2 cDNA encodes a chloroplast-imported protein of 72.5 kDa, sharing similarities with different mono-oxigenases and oxidases of bacterial origin and having an ADP-binding fold and an FAD-binding domain. ABA2 protein, produced in Escherichia coli, exhibits in vitro zeaxanthin epoxidase activity. This is the first report of the isolation of a gene of the ABA biosynthetic pathway. The molecular identification of ABA2 opens the possibility to study the regulation of ABA biosynthesis and its cellular location.

Efficient insertional mutagenesis in lactococci and other gram-positive bacteria.

Abstract: In lactococci, the study of chromosomal genes and their regulation is limited by the lack of an efficient transposon mutagenesis system. We associated the insertion sequence ISS1 with the thermosensitive replicon pG+ host to generate a mutagenic tool that can be used even in poorly transformable strains. ISS1 transposition is random in different lactococcal strains as well as in Enterococcus faecalis and Streptococcus thermophilus. High-frequency random insertion (of about 1%) obtained with this system in Lactococcus lactis allows efficient mutagenesis, with typically one insertion per cell. After ISS1 replicative transposition, the chromosome contains duplicated ISS1 sequences flanking pG+ host. This structure allows cloning of the interrupted gene. In addition, efficient excision of the plasmid leaves a single ISS1 copy at the mutated site, thus generating a stable mutant strain with no foreign markers. Mutants obtained by this transposition system are food grade and can thus be used in fermentation processes.

Local Adaptation and Gene-For-Gene Coevolution in a Metapopulation Model

Abstract: In several reciprocal cross-infection experiments parasites were found to be significantly more adapted to their local host populations than to hosts from distant populations. We developed a metapopulation model, taking explicit account of both population densities and gene frequencies, to determine the influence of ecological and genetical parameters on the local adaptation of the parasites and on the spatial distribution of resistance and virulence genes. Our results point to the predominant effect of ecological parameters such as parasite growth rate and host and parasite migration rates on coevolutionary outcomes. In particular, the parasites are more likely to be adapted to their local host population than to allopatric hosts when the parasite migration rate is larger than the host migration rate. The opposite should be observed whenever hosts migrate more than parasites.

Chloroplast dna phylogeography of the common beech (fagus sylvatica l.) in europe

Abstract: expression III an andromonoecious plant. Ecology 66: 13211332. STERK, A. A. 1969a. Biosystematic studies of Spergularia media and S. marina in the Netherlands 1. The morphological variability of S. media. Acta Bot. Neer. 18:325-338. ---. 1969b. Reduction of the androecium in Spergularia marina (Caryophyllaceae). Acta Bot. Neer. 19:488-494. STERK, A. A., AND L. DIJKHUIZEN. 1972. The relation between the genetic determination and the ecological significance of the seed wing in Spergularia media and S. marina. Acta Bot. Neerl. 21: 481-490. THOMPSON, J. N., AND O. PELLMYR. 1989. Origins of variance in seed number and mass: Interaction of sex expression and herbivory in Lomatium salmoniflorum Oecologia 79:395-402. THOMSON, J. D. 1985. Pollination and seed set in Diervilla lonicera (Caprifoliaceae): Temporal patterns of flower and ovule development. Am. J. Bot. 72:737-740. ---. 1989. Deployment of ovules and pollen among flowers within inflorescences. Evo!. Trends Plants 3:65-68. THOMSON, J. D., AND S. C. H. BARRETT. 1981. Temporal variation of gender in Aralia hispida Vent. (Araliaceae). Evolution 35: 1094-1107. THOMSON, J. D., M. A., McKENNA, AND M. B. CRUZAN. 1989. Temporal patterns of nectar and pollen production in Aralia his-

Plant Cell Responses to Arbuscular Mycorrhizal Fungi: Getting to the Roots of the Symbiosis.

Abstract: Since their colonization of terrestrial ecosystems, plants have developed numerous strategies to cope with the diverse bi? otic and abiotic challenges that are a consequence of their sedentary life cycle. One of the most successful strategies is the ability of root systems to establish mutualistic and reciprocally beneficial symbiotic relationships with microorganisms. Mycorrhizas, the intricate associations roots form with specific fungal groups, are by far the most frequent of these and rep? resent the underground absorbing organs of most plants in nature (Gianinazzi-Pearson, 1984). Through their function in the efficient exploitation of soil mineral resources and their bioprotective role against a number of common soilborne pathogens, mycorrhizas are instrumental in the survival and fitness of many plant taxa in diverse ecosystems, including many crop species (reviewed in Allen, 1991; Bethlenfalvay and Linderman, 1992). Several kinds of mycorrhizal associations can be distin? guished according to their morphology and the plant and fungal taxa concerned. They fail almost exclusively into two broad groups: (1) the ectomycorrhizas of woody Angiosperms and Gymnosperms, in which Basidiomycetes, Ascomycetes, or Zygomycetes develop intercellular hyphae from a mycelial sheath covering the surface of short lateral roots; and (2) the endomycorrhizas, characterized by intraradical mycelium growth and intracellular fungal proliferation, which are formed by Basidiomycetes in the Orchidaceae (orchidoid mycorrhiza), Ascomycetes in the Ericales (ericoid mycorrhiza), and Zygomy? cetes in most other terrestrial plant taxa (arbuscular mycorrhiza; reviewed in Harley and Smith, 1983). Plant compatibility with mycorrhizal fungi is a generalized and ancient phenomenon. Species in >80?/o of extant plant families are capable of establishing arbuscular mycorrhiza (AM), and fossil evidence suggests that symbioses of this kind existed >400 million years ago in the tissues of the first land plants (Pirozynski and Dalpe, 1989; Remy et al., 1994). As such, the ability of plants to form AM must be under the control of mechanisms that have been conserved in new plant taxa as they appeared during evolution. This compatibility also implies that selective recognition processes in plants discriminate be? tween beneficial and harmful microorganisms and that the essential genetic determinants for AM establishment are com? mon to an extensive part of the plant kingdom. In contrast to their extremely wide host range and despite their ancient origins, only six genera of fungi belonging to the order Glomales of the Zygomycetes have evolved the ability to form AM (Morton and Benny, 1990). Interactions between an AM fungus and a plant begin when a hypha from a ger? minating soilborne spore comes into contact with a host root. Thi step is followed by induction of an appressorium, from which an infection hypha penetrates deep into the parenchyma cortex (Figure 1A), where interand intracellular proliferation of mycelium is intense. Here, fungal development culminates in the differentiation of intracellular haustoria, known as arb scules (Figure 1B). These fungal structures, which establish large surface of contact with the plant protopiast, are attrib? uted a key role in reciprocal nutrient exchange between the plant cells and the AM fungal symbionts (Smith and Smith, 1990). However, arbuscules are ephemeral structures, and an individual arbuscule reaches full development within several days, after which it begins to senesce (Alexander et al., 1988). AM development continues within a root system as the fungus spre ds to newly emerging roots. In this way, fungal coloniza? tion occurs concomitantly in different roots in an unsynchronized manner.

Methods for multiple-marker mapping of quantitative trait loci in half-sib populations.

Abstract: In this paper we consider the detection of individual loci controlling quantitative traits of interest (quantitative trait loci or QTLs) in the large half-sib family structure found in some species. Two simple approaches using multiple markers are proposed, one using least squares and the other maximum likelihood. These methods are intended to provide a relatively fast screening of the entire genome to pinpoint regions of interest for further investigation. They are compared with a more traditional single-marker least-squares approach. The use of multiple markers is shown to increase power and has the advantage of providing an estimate for the location of the QTL. The maximum-likelihood and the least-squares approaches using multiple markers give similar power and estimates for the QTL location, although the likelihood approach also provides estimates of the QTL effect and sire heterozygote frequency. A number of assumptions have been made in order to make the likelihood calculations feasible, however, and computationally it is still more demanding than the least-squares approach. The least-squares approach using multiple markers provides a fast method that can easily be extended to include additional effects.

Red Xylem and Higher Lignin Extractability by Down-Regulating a Cinnamyl Alcohol Dehydrogenase in Poplar

Abstract: Cinnamyl alcohol dehydrogenase (CAD) catalyzes the last step in the biosynthesis of the lignin precursors, the monolignols. We have down-regulated CAD in transgenic poplar (Populus tremula X Populus alba) by both antisense and co-suppression strategies. Several antisense and sense CAD transgenic poplars had an approximately 70% reduced CAD activity that was associated with a red coloration of the xylem tissue. Neither the lignin amount nor the lignin monomeric composition (syringyl/guaiacyl) were significantly modified. However, phloroglucinol-HCl staining was different in the down-regulated CAD plants, suggesting changes in the number of aldehyde units in the lignin. Furthermore, the reactivity of the cell wall toward alkali treatment was altered: a lower amount of lignin was found in the insoluble, saponified residue and more lignin could be precipitated from the soluble alkali fraction. Moreover, large amounts of phenolic compounds, vanillin and especially syringaldehyde, were detected in the soluble alkali fraction of the CAD down-regulated poplars. Alkaline pulping experiments on 3-month-old trees showed a reduction of the kappa number without affecting the degree of cellulose degradation. These results indicate that reducing the CAD activity in trees might be a valuable strategy to optimize certain processes of the wood industry, especially those of the pulp and paper industry.

Metabolic and endocrine changes induced by chronic heat exposure in broiler chickens: growth performance, body composition and energy retention.

Abstract: The present study was performed in order to investigate the effect of chronic heat exposure (32 degrees, constant) on growth, body composition and energy retention of broiler chickens in relation to age. At 2 and 4 weeks of age, fifty-four male Shaver broiler chickens were allocated to three treatments according to the following design: 22 degrees, ad lib. feeding (22AL); 32 degrees, ad lib. feeding (32AL); and 22 degrees, pair-feeding with the 32 degrees group (22PF). Ambient temperature was kept constant at either 22 or 32 degrees for 2 weeks. Heat exposure decreased feed intake by 14% between 2 and 4 weeks and by 24% between 4 and 6 weeks of age. Even with the same feed intake, chicks gained less weight at 32 degrees than at 22 degrees, 5.5% less in young chickens and 22% less in older ones. Hot environmental conditions thus resulted in decreased feed efficiency; the feed:gain ratio was 2.85 at 32 degrees compared with 2.06 at 22 degrees in 22AL birds for the period 4-6 weeks. Body composition appeared significantly affected by high ambient temperature. Feathering was reduced at 32 degrees in absolute weight but not as a proportion of body weight. Heat-exposed birds showed a decrease in body protein content, protein gain and protein retention. Group 32AL birds were fatter than the pair-fed (22PF) or ad lib.-fed (22AL) groups at 22 degrees. The percentage of energy retained as fat was 79 in heat-exposed chickens compared with 64 in the control groups. The energy retained as protein:energy retained as fat for groups maintained at 22 degrees (0.56) was twice that for those maintained at 32 degrees (0.28). These modifications should be investigated further in relation to metabolic and endocrinological changes.

Gene silencing mediated by promoter homology occurs at the level of transcription and results in meiotically heritable alterations in methylation and gene activity

Abstract: The promoter homology-dependent inactivation of a 35Spro-hygromycin phosphotransferase (hpt) gene, which is present at the H2 locus, by the multipurpose 271 silencing locus has been studied. The 271 locus can silence any gene under the control of the 35Spro as well as endogenous nitrite reductase (NiR) genes of tobacco because of the presence of a chimeric antisense gene (35Spro-RiN). All F1 progeny of a cross between homozygous H2 and 271 lines were sensitive to hygromycin and were chlorotic (a symptom of nitrogen deficiency). These phenotypes were accompanied by a reduction in the steady-state levels of Hyg and NiR transcripts. Transcriptional run-on experiments indicated, however, that while NiR silencing occurred post-transcriptionally, the hpt gene was inactivated at the transcriptional level; this was associated with increased methylation of the 35Spro of the hpt gene. NiR gene expression recovered uniformly to wild-type levels in first generation backcross (BC1) progeny that did not inherit the 271 locus. In contrast, hygromycin resistance was only partially and non-uniformly regained among adult BC1 plants. Moreover, substantial silencing of the hpt gene could persist into the BC2 generation. Genomic sequencing demonstrated that the meiotic heritability of hpt silencing in the absence of the 271 locus was correlated with cytosine methylation primarily at CpG and CpNpG residues. Despite this residual methylation, H2 loci weakened by an association with 271 did not acquire the ability to silence a 'naive' H2 locus. Fluorescence in situ hybridization revealed that the 271 locus was located at a telomere. The results strengthen the distinction between silencing effects involving homology restricted to coding or promoter regions, respectively. The former is a post-transcriptional process that is meiotically reversible; the latter is due to transcriptional inactivation and is associated with increased promoter methylation, which can lead to meiotically heritable reductions in target gene activity. The relevance of these data for the meiotic heritability of silencing, the non-transferability of silencing activity, and the basis of 271 silencing effects is discussed.

Demand-Driven Control of Root ATP Sulfurylase Activity and SO42- Uptake in Intact Canola (The Role of Phloem-Translocated Glutathione).

Abstract: The activity of ATP sulfurylase extracted from roots of intact canola (Brassica napus L. cv Drakkar) increased after withdrawal of the S source from the nutrient solution and declined after refeeding SO42- to S-starved plants. The rate of SO42- uptake by the roots was similarly influenced. Identical responses were obtained in SO42- -fed roots when one-half of the root system was starved for S. The internal levels of SO42- and glutathione (GSH) declined after S starvation of the whole root system, but only GSH concentration declined in +S roots of plants from split root experiments. The concentration of GSH in phloem exudates decreased upon transfer of plants to S-free solution. Supplying GSH or cysteine to roots, either exogenously or internally via phloem sap, inhibited both ATP sulfurylase activity and SO42- uptake. Buthionine sulfoximine, an inhibitor of GSH synthesis, reversed the inhibitory effect of cysteine on ATP sulfurylase. It is hypothesized that GSH is responsible for mediating the responses to S availability. ATP sulfurylase activity and the SO42- uptake rate are regulated by similar demand-driven processes that involve the translocation of a phloem-transported message (possibly GSH) to the roots that provides information concerning the nutritional status of the leaves.