Assessment of molecular diversity at QTLs for preharvest sprouting resistance in wheat using microsatellite markers.

Breeding for preharvest sprouting (PHS) resistance is of great interest in wheat-growing areas where high rainfall occurs during grain ripening and harvest. We have characterized 32 wheat accessions using 33 microsatellite markers flanking PHS quantitative trait loci (QTLs) previously identified on group 3, 4, 5, and 6 chromosomes of hexaploid wheat. A total of 229 alleles, with an average of 6.94 alleles per marker, were observed among the 32 wheat lines. The polymorphic information content (PIC) was estimated and ranged between 0.25 and 0.90, with an average of 0.67. A cluster analysis revealed 3 main clusters and 3 singlet wheat lines, which is in agreement with pedigree-based relationships, seed coat colour, and origin. Canadian wheat accessions were subdivided into 4 sub-clusters based on pedigree and wheat classes. Grouping of preharvest sprouting germplasm into clusters was consistent with cluster-specific allele diversity observed in the PHS-resistant lines AUS1408, Red-RL4137, White-RL4137, and Kenya321. The implications of these findings in white wheat breeding for PHS tolerance are discussed.     

What is the genetic origin of teak (<Emphasis Type="Italic">Tectona grandis</Emphasis> L.) introduced in Africa and in Indonesia?

The first introduction of Tectona grandis in Indonesia took place between the fourteenth and sixteenth centuries and in Africa in the nineteenth century. A total of 1.1 and 0.3 million ha, respectively were planted in the two areas. The extension of teak plantations often started from these first introductions. Unfortunately, the documentation concerning dates, planting stocks and the sources of origin of the teak imported into the different countries was very inaccurate. In this study, the use of 15 microsatellite molecular markers enabled us to compare 22 exotic teak provenances with 17 provenances of the natural range. Results of the analysis showed that the provenances from South India were not related to the provenances that were first introduced in either Africa or Indonesia. Nearly 95% of teak landraces in Benin, Cameroon, Côte d’Ivoire, Tanzania, Togo and Senegal came from North India, and 96% of Indonesian and Ghanaian teak appeared to be very closely linked to Central Laos. The genetic origin of introduced teak was confirmed by the main traits of interest of provenances observed in international trials. Thus, trees from North India had very bad stem forms compared to Laotian and Thai provenances, which generally had good stem forms but low vigour. This genetic knowledge is essential for programmes to develop varieties and to improve the quality of plantations, particularly in Africa.     

Evaluation of cholesteryl ester transfer in the seminiferous tubule cells of immature rats in vivo and in vitro

Sertoli cells and germ cells are separated from the interstitial blood capillaries by an extracellular matrix and the peritubular cells, which constitute a barrier to the movement of plasma lipoproteins. The present study was undertaken to evaluate in vivo and in vitro the high density lipoprotein (HDL) cholesteryl ester transfer from plasma to seminiferous tubule cells in the testis of 30-day-old rats. Firstly, the transfer of HDL cholesteryl oleate from plasma to testicular compartments was evaluated and, secondly, the role of apolipoproteins A-I and E in the uptake of cholesteryl ester by Sertoli cells was investigated. At 2 h after the administration of HDL reconstituted with [3H]cholesteryl ester, dimyristoyl phosphatidylcholine and apolipoproteins, the tissue space in the interstitial cells (740 +/- 60 microliters g-1 cell protein) was fourfold higher than that in the seminiferous tubule cells (170 +/- 10 microliters g-1). Sertoli cells were isolated and incubated with [3H]cholesteryl ester HDL reconstituted with apolipoprotein A-I or E to evaluate the mechanisms of cholesteryl ester influx. At the same apolipoprotein concentration (50 micrograms apolipoprotein ml-1 medium), the uptake of [3H]cholesteryl oleate from phospholipid-apolipoprotein E vesicles was twofold higher than that with phospholipid-apolipoprotein A-I vesicles. The presence of heparin reduced the uptake of cholesteryl ester from apolipoprotein E vesicles but not with apolipoprotein A-I vesicles, indicating that uptake of apolipoprotein A-I vesicles via a secretion of apolipoprotein E by the cells themselves was not involved. These results demonstrate that plasma lipoprotein cholesterol is able to cross the testis lamina propria and that Sertoli cells take up cholesteryl ester for seminiferous tubule cell metabolism mainly via an apolipoprotein E pathway.     

Cleavase Fragment Length Polymorphism (CFLP): A Methodology to Further Exploit Polymorphisms from PCR Products of Plastid DNA (ptDNA) in Phaseolus

The CFLP methodology was applied for Cleavase I site detection within ptDNA intergenic regions (atpB-rbcL and rps14-psaB) at both interspecific and intraspecific levels in the genus Phaseolus. Optimal Cleavase I reaction temperature was 55°C and the semi-dry electrophoretic transfer was more efficient than the original capillary one. Cleavase reactions yield a high number of fragments as compared to PCR-RFLP and allowed differentiation within and between landraces and wild forms of the Lima bean (Phaseolus lunatus L.) originating from Andean and Mesoamerican regions of Latin America. From sequencing data and using stemloop program (GCG, Madison), congruent numbers of hairpins/fragments were identified within the sequences, highlighting the robustness of the Cleavase I. Our results pointed out the ubiquity of short conserved motifs amongst a geographically localized group of species. In the vicinity of these motifs, synapomorphic-like substitutions were frequently observed. A phylogenetic tree based on these sequences is congruent with the CFLP pattern as well as with the widely accepted phylogeny of the genus. The usefulness of this new tool as alternative and/or complementary to PCR-RFLP technology on ptDNA is suggested and discussed.     

Molecular evidence for an Andean origin and a secondary gene pool for the Lima bean (Phaseolus lunatus L.) using chloroplast DNA

 Chloroplast DNA (cpDNA) diversity has been examined using PCR-RFLP and RFLP strategies for phylogenetic studies in the genus Phaseolus. Twenty-two species, including 4 of the 5 cultivated species (P. lunatus L., the Lima bean; P. vulgaris L., the common bean; P. coccineus L., the runner bean and P. polyanthus Greenman, the year-bean), represented by 86 accessions were included in the study. Six PCR primers designed from cpDNA and a total cpDNA probe were used for generating markers. Phylogenetic reconstruction using both Wagner parsimony and the neighbor-joining method was applied to the restriction fragment data obtained from each of the molecular approaches. P. vulgaris L. was shown to separate with several species of largely Mesoamerican distribution, including P. coccineus L. and P. polyanthus Greenman, whereas P. lunatus L. forms a complex with 3 Andean species (P. pachyrrhizoides Harms, P. augusti Harms and P. bolivianus Piper) co-evolving with a set of companion species with a Mesoamerican distribution. Andean forms of the Lima bean are found to be more closely related to the 3 Andean wild species than its Mesoamerican forms. An Andean origin of the Lima bean and a double derivative process during the evolution of P. lunatus are suggested. The 3 Andean species are proposed to constitute the secondary gene pool of P. lunatus, while its companion allies of Mesoamerican distribution can be considered as members of its tertiary gene pool. On the basis of these data, an overview on the evolution of the genus Phaseolus is also discussed. Received: 1 May 1998 / Accepted: 13 July 1998     

Genetic analyses using GGE model and a mixed linear model approach,and stability analyses using AMMI bi-plot for late-maturity alpha-amylase activity in bread wheat genotypes

Low falling number and discounting grain when it is downgraded in class are the consequences of excessive late-maturity α-amylase activity (LMAA) in bread wheat (Triticum aestivum L.). Grain expressing high LMAA produces poorer quality bread products. To effectively breed for low LMAA, it is necessary to understand what genes control it and how they are expressed, particularly when genotypes are grown in different environments. In this study, an International Collection (IC) of 18 spring wheat genotypes and another set of 15 spring wheat cultivars adapted to South Dakota (SD), USA were assessed to characterize the genetic component of LMAA over 5 and 13 environments, respectively. The data were analysed using a GGE model with a mixed linear model approach and stability analysis was presented using an AMMI bi-plot on R software. All estimated variance components and their proportions to the total phenotypic variance were highly significant for both sets of genotypes, which were validated by the AMMI model analysis. Broad-sense heritability for LMAA was higher in SD adapted cultivars (53%) compared to that in IC (49%). Significant genetic effects and stability analyses showed some genotypes, e.g. ‘Lancer’, ‘Chester’ and ‘LoSprout’ from IC, and ‘Alsen’, ‘Traverse’ and ‘Forefront’ from SD cultivars could be used as parents to develop new cultivars expressing low levels of LMAA. Stability analysis using an AMMI bi-plot revealed that ‘Chester’, ‘Lancer’ and ‘Advance’ were the most stable across environments, while in contrast, ‘Kinsman’, ‘Lerma52’ and ‘Traverse’ exhibited the lowest stability for LMAA across environments.     

Population-Level Impact of Shorter-Course Regimens for Tuberculosis: A Model-Based Analysis

Despite current control efforts, global tuberculosis (TB) incidence is decreasing slowly. New regimens that can shorten treatment hold promise for improving treatment completion and success, but their impact on population-level transmission remains unclear. Earlier models projected that a four-month regimen could reduce TB incidence by 10% but assumed that an entire course of therapy must be completed to derive any benefit. We constructed a dynamic transmission model of TB disease calibrated to global estimates of incidence, prevalence, mortality, and treatment success. To account for the efficacy of partial treatment, we used data from clinical trials of early short-course regimens to estimate relapse rates among TB patients who completed one-third, one-half, two-thirds, and all of their first-line treatment regimens. We projected population-level incidence and mortality over 10 years, comparing standard six-month therapy to hypothetical shorter-course regimens with equivalent treatment success but fewer defaults. The impact of hypothetical four-month regimens on TB incidence after 10 years was smaller than estimated in previous modeling analyses (1.9% [95% uncertainty range 0.6–3.1%] vs. 10%). Impact on TB mortality was larger (3.5% at 10 years) but still modest. Transmission impact was most sensitive to the proportion of patients completing therapy: four-month therapy led to greater incidence reductions in settings where 25% of patients leave care (“default”) over six months. Our findings remained robust under one-way variation of model parameters. These findings suggest that novel regimens that shorten treatment duration may have only a modest effect on TB transmission except in settings of very low treatment completion.     

Subfossil diatoms from Hann Park pond,Dakar, Senegal: floristic inventory and palaeoenvironmental reconstruction

Diatoms in a 100 cm-long core from a pond in Hann Forest Park, western Senegal, were studied with the aim of reconstituting this interdune depression’s history, particularly the human influence, during the last century. Sixty-three species and varieties of diatoms belonging to 32 genera were identified, of which twelve are reported for the first time in Senegambia. The genera most represented were Nitzschia (10 species), Eunotia (9 species) and Pinnularia (6 species). The microflora was characterised by a dominance of epipelic, epiphytic and aerophilic species. Diatom assemblage analyses, combined with lithological core data, showed that the pond has remained very shallow throughout its evolution. The disappearance of acidophilic species and the development of mesosaprobes and mesoeutrophic alkaliphilic species in the upper part of the core can be attributed to organic pollution caused by human activities, which resulted in eutrophication of the pond waters since the beginning of the 20th century.     

Species-Specific Activity of HIV-1 Vpu and Positive Selection of Tetherin Transmembrane Domain Variants

Tetherin/BST-2/CD317 is a recently identified antiviral protein that blocks the release of nascent retrovirus, and other virus, particles from infected cells. An HIV-1 accessory protein, Vpu, acts as an antagonist of tetherin. Here, we show that positive selection is evident in primate tetherin sequences and that HIV-1 Vpu appears to have specifically adapted to antagonize variants of tetherin found in humans and chimpanzees. Tetherin variants found in rhesus macaques (rh), African green monkeys (agm) and mice were able to inhibit HIV-1 particle release, but were resistant to antagonism by HIV-1 Vpu. Notably, reciprocal exchange of transmembrane domains between human and monkey tetherins conferred sensitivity and resistance to Vpu, identifying this protein domain as a critical determinant of Vpu function. Indeed, differences between hu-tetherin and rh-tetherin at several positions in the transmembrane domain affected sensitivity to antagonism by Vpu. Two alterations in the hu-tetherin transmembrane domain, that correspond to differences found in rh- and agm-tetherin proteins, were sufficient to render hu-tetherin completely resistant to HIV-1 Vpu. Interestingly, transmembrane and cytoplasmic domain sequences in primate tetherins exhibit variation at numerous codons that is likely the result of positive selection, and some of these changes coincide with determinants of HIV-1 Vpu sensitivity. Overall, these data indicate that tetherin could impose a barrier to viral zoonosis as a consequence of positive selection that has been driven by ancient viral antagonists, and that the HIV-1 Vpu protein has specialized to target the transmembrane domains found in human/chimpanzee tetherin proteins.     

Species-Specific Activity of SIV Nef and HIV-1 Vpu in Overcoming Restriction by Tetherin/BST2

Tetherin, also known as BST2, CD317 or HM1.24, was recently identified as an interferon-inducible host–cell factor that interferes with the detachment of virus particles from infected cells. HIV-1 overcomes this restriction by expressing an accessory protein, Vpu, which counteracts tetherin. Since lentiviruses of the SIV_smm/mac/HIV-2 lineage do not have a vpu gene, this activity has likely been assumed by other viral gene products. We found that deletion of the SIV_mac239 nef gene significantly impaired virus release in cells expressing rhesus macaque tetherin. Virus release could be restored by expressing Nef in trans. However, Nef was unable to facilitate virus release in the presence of human tetherin. Conversely, Vpu enhanced virus release in the presence of human tetherin, but not in the presence of rhesus tetherin. In accordance with the species-specificity of Nef in mediating virus release, SIV Nef downregulated cell-surface expression of rhesus tetherin, but did not downregulate human tetherin. The specificity of SIV Nef for rhesus tetherin mapped to four amino acids in the cytoplasmic domain of the molecule that are missing from human tetherin, whereas the specificity of Vpu for human tetherin mapped to amino acid differences in the transmembrane domain. Nef alleles of SIV_smm, HIV-2 and HIV-1 were also able to rescue virus release in the presence of both rhesus macaque and sooty mangabey tetherin, but were generally ineffective against human tetherin. Thus, the ability of Nef to antagonize tetherin from these Old World primates appears to be conserved among the primate lentiviruses. These results identify Nef as the viral gene product of SIV that opposes restriction by tetherin in rhesus macaques and sooty mangabeys, and reveal species-specificity in the activities of both Nef and Vpu in overcoming tetherin in their respective hosts.