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Round scad mackerel sampled in 1995–1998 were analysed for genetic variation using mitochondrial-DNA and nuclear-DNA markers. Sequence variation for a fragment of the cytochromeb gene (mitochondrial), amplified by polymerase chain reaction, was screened across individuals using single strand conformation polymorphism (SSCP). Sequence analysis of all SSCP haplotypes indicated two mitochondrial clades separated by, on average, 2.3% nucleotide divergence. The geographic distribution of haplotypes was homogeneous (Weir and Cockerham's \( \hat \theta \) =–0.002). Also, no geographic heterogeneity was detected for length polymorphism of Intron 1 of the gene encoding aldolase B (\( \hat \theta \) =0.005). Although homogeneity in allele frequencies throughout the Indo-Malay archipelago conformed to the expectations for a widely distributed pelagic fish in a highly connected habitat, this was at variance with the sharp geographic structure previously uncovered in Indian scad mackerel, Decapterus russelli, a fish with life-history characteristics similar to D. macrosoma. A remarkable similarity, however, was the occurrence of two similarly distinct clades within each species, suggesting a common history of geographic isolation. Low sea levels in the Pleistocene might have caused the separation and vicariance of populations within both D. macrosoma and D. russelli. Subsequent genetic exchange between populations would then have erased allele-frequency differences at the cytochrome b and aldolase B loci in D. macrosoma while some barrier to gene flow was maintained in D. russelli.

Loubna Tazi a, Barry Kreiswirth b, Christian Carriere c, Michel Tibayrenc a,∗ a Genetics of Infectious Diseases, Unite mixte de Recherche Centre National de la Recherch Scientifique/Institut de Recherche pour le Developpement no. 9926, IRD, BP 64501, 34394 Montpellier Cedex 5, France b Public Health Research Institute Tuberculosis Center, International Center for Public Health, 225 Warren Street, Newark, NJ 07103, USA c Laboratoire de Bacteriologie, Hopital Arnaud de Villeneuve, 371 Avenue du Doyen Giraud, 34295 Montpellier Cedex 5, France

We evaluated cassava bacterial blight (CBB) infection in a pair-cross population of 150 individuals derived from an intra-specific cross between two non-inbred cassava (#Manihot esculenta$ Crantz) lines. The replicated trials were carried out in the field under high disease pressure over two consecutive crop cycles. Evaluations were conducted at 4 and 7 months after planting for the two cycles. Simple regression analysis and the nonparametric Kruskal-Wallis rank-sum test revealed that eight quantitative trait loci (QTLs) were invovled in resistance. We detected changes in QTLs from crop cycle to crop cycle. The pathogen population (#Xanthomonas axonopodis$ pv. #manihotis$) was also monitored over the period, using a restriction fragment length polymorphism probe and pathogenic tests. Changes in QTL detection over the 2 years could be correlated with changes in pathogen population structure. One QTL, located in linkage group D, was conserved over the two crop cycles, and in field to greenhouse evaluations. This study thus identified molecular markers useful for marker assisted-selection, a technique that can accelerate the long, multiple-season process of breeding for CBB resistance. (Résumé d'auteur)

Fifty-eight new isolates were obtained from root nodules of common bean (#Phaseolus vulgaris$) cultivated in soils originating from different agroecological areas in Senegal and Gambia (West Africa). A polyphasic approach including both phenotypic and genotypic techniques was used to study the diversity of the 58 #Rhizobium$ isolates and to determine their taxonomic relationships with reference strains. All the techniques performed, analysis of multilocus enzyme electrophoretic patterns, SDS-PAGE profiles of total cell proteins, PCR-RFLP analysis of the genes encoding 16S rRNA and of the 16S-23S RNA intergenic spacer region (ITS-PCR-RFLP), auxanographic tests using API galleries and nodulation tests lead to the consensus conclusion that the new rhizobial isolates formed two main distinct groups, I and II, belonging to #Rhizobium tropici$ type B and #Rhizobium etli$, respectively. By MLEE #R. etli$ and group II strains showed several related electrophoretic types, evidencing some extent of internal heterogeneity among them. This heterogeneity was confirmed by other techniques (ITS-PCR-RFLP, SDS-PAGE and host-plant-specificity) with the same nine distinct strains of group II showing some differences from the core of group II (54 strains). (Résumé d'auteur)

SDS-PAGE of total bacterial proteins was applied to the classification of 25 Sudanese and five Kenyan strains isolated from the root nodules of #Acacia senegal$ and #Prosopis chilensis$. Twenty strains were also studied by multilocus enzyme electrophoresis (MLEE) and the whole 16S rRNA gene was sequenced from two strains representing the two major clusters. These results, together with the previuously reported numerical taxonomy analysis, pulsed-field gel electrophoresis studies, DNA-DNA dot-blot hybridisation, genomic fingerprinting using repetitive sequence-basec PCR, DNA base composition analysis, DNA-DNA reassociation analysis, partial sequencing of the 16S rRNA gene and RFLP analysis of the amplified 16S rRNA gene, showed that all 30 strains belong to the genus #Sinorhizobium$. Two of the strains grouped with #Sinorhizobium saheli$ and seven with #Sinorhizobium terangae$, while the rest did not cluster with any of the established species. The majority of the strains formed two phenotypically and genotypically distinct groups and we therefore propose that these strains should be classified as two new species, #Sinorhizobium arboris$ sp. nov. and #Sinorhizobium kostiense$ sp. nov. (Résumé d'auteur)

Eight Frankia-Gymnostoma nitrogen-fixing symbioses endemic to New Caledonia were studied using a range of techniques including molecular typing of Frankia , infectivity/effectivity and host spectrum of the isolates. The study was conducted on 128 Frankia isolates from the eight Gymnostoma species. The RFLP analysis of the rRNA 16S-23S ITS allowed us to cluster the strains in four groups. Symbiotic characterization of the four groups failed to reveal any host specificity both in term of infectivity or effectivity. The characteristics of the strains were those of Eleagnaceae -infective Frankia strains. Co-inoculation of two Gymnostoma species with mixtures of strains evidenced 11 % of mixed RFLP profiles. In such controlled conditions, this was interpreted as co-infections. This work evidenced original features of these Gymnostoma isolates: (i) they were closer to Eleagnaceae -infective Frankia than Casuarina -infective Frankia ; (ii) closer to atypical Frankia from Casuarina ; (iii) poorly host-specific; and (iv) they had a tendency of co-infection. They could represent a primitive group of Frankia able to survive in a wide range of habitats.

Polyploids in Tripsacum, a wild relative of maize, reproduce through the diplosporous type of apomixis, an asexual mode of reproduction through seeds. Diplosporous apomixis involves both the failure of meiosis and the parthenogenetic development of the unreduced gametes, resulting in progenies that are exact genetic copies of the mother plant. Apomixis is believed to be controlled by one single dominant allele, responsible for the whole developmental process. Construction of a linkage map for the chromosome controlling diplosporous apomixis in Tripsacum was carried out in both tetraploid-apomictic and diploid-sexual Tripsacum species using maize restriction fragment length polymorphism (RFLP) probes. A high level of collinearity was observed between the Tripsacum chromosome carrying the control of apomixis and a duplicated segment in the maize genome. In the apomictic tetraploid, there was a strong restriction to recombination, as compared to the corresponding genomic segment in sexual plants and maize. This suggests that apomixis, although inherited as a single Mendelian allele, might really be controlled by a cluster of linked loci. The analysis also revealed the tetrasomic nature of the inheritance of the chromosomal segment controlling apomixis, which contradicts the usually accepted hypothesis of an allopolyploid origin of apomictic species. The implications of these data for the transfer of apomixis into cultivated crops are discussed, and a new approach to studying the genetics of apomixis, based on comparative mapping, is proposed.

The risk of serious infections caused by Staphylococcus aureus is well-known. However, most studies regarding the distribution of (clinically relevant) S. aureus among humans and animals took place in the western hemisphere and only limited data are available from (Central) Africa. In this context, recent studies focused on S. aureus strains in humans and primates, but the question of whether humans and monkeys share related S. aureus strains or may interchange strains remained largely unsolved. In this study we aimed to evaluate the distribution and spread of human-like S. aureus strains among great apes living in captivity. Therefore, a primate facility at the International Centre for Medical Research of Franceville (Gabon) was screened. We detected among the primates a common human S. aureus strain, belonging to the spa -type t148. It was isolated from three different individuals of the western lowland gorilla ( Gorilla gorilla gorilla ), of which one individual showed a large necrotizing wound. This animal died, most probably of a staphylococcal sepsis. Additionally, we discovered the t148 type among chimpanzees ( Pan troglodytes ) that were settled in the immediate neighbourhood of the infected gorillas. A detailed analysis by pulsed field gel electrophoresis showed that the gorilla and chimpanzee isolates represented two closely related strains. To our knowledge, this is the first report of a human-associated S. aureus strain causing disease in great apes. The simultaneous detection in gorillas and chimpanzees indicated an interspecies transmission of this S. aureus strain. Our results recommend that protection of wild animals must not only be based on habitat conservation, but also on the assessment of the risk of contact with human pathogens.

Ninety-three accessions representing 21 species from the genus Oryza were examined for restriction fragment length polymorphism. The majority (78%) of the accessions, for which five individuals were tested, were found to be monomorphic. Most of the polymorphic accessions segregated for only one or two probes and appeared to be mixed pure lines. For most of the Oryza species tested, the majority of the genetic variation (83%) was found between accessions from different species with only 17% between accessions within species. Tetraploid species were found to have, on average, nearly 50% more alleles (unique fragments) per individual than diploid species reflecting the allopolyploid nature of their genomes.Classification of Oryza species based on RFLPs matches remarkably well previous classifications based on morphology, hybridization and isozymes. In the current study, four species complexes could be identified corresponding to those proposed by Vaughan (1989): the O. ridleyi complex, the O. meyeriana complex, the O. officinalis complex and the O. sativa complex. Within the O. sativa complex, accessions of O. rufipogon from Asia (including O. nivara) and perennial forms of O. rufipogon from Australia clustered together with accessions of cultivated rice O. sativa. Surprisingly, indica and japonica (the two major subspecies of cultivated rice) showed closer affinity with different accessions of wild O. Rufipogon than to each other, supporting a hypothesis of independent domestication events for these two types of rice. Australian annual wild rice O. meridionalis (previously classified as O. rufipogon) was clearly distinct from all other O. rufipogon accessions supporting its recent reclassification as O. meridionalis (Ng et al. 1981). Using genetic relatedness as a criterion, it was possible to identify the closest living diploid relatives of the currently known tetraploid rice species. Results from these analyses suggest that BBCC tetraploids (O. malampuzhaensis, O. punctata and O. minuta) are either of independent origins or have experienced introgression from sympatric C-genome diploid rice species. CCDD tetraploid species from America (O. latifolia, O. alta and O. grandiglumis) may be of ancient origin since they show a closer affinity to each other than to any known diploid species. Their closest living diploid relatives belong to C genome (O. eichingeri) and E genome (O. Australiensis) species. Comparisons among African, Australian and Asian rice species suggest that Oryza species in Africa and Australia are of polyphyletic origin and probably migrated to these regions at different times in the past.Finally, on a practical note, the majority of probes used in this study detected polymorphism between cultivated rice and its wild relatives. Hence, RFLP markers and maps based on such markers are likely to be very useful in monitoring and aiding introgression of genes from wild rice into modern cultivars.

A thermophilic terephthalate-degrading methanogenic consortium was successfully enriched for 272 days in an anaerobic hybrid reactor, and the microbial structure was characterized using terminal RFLPs, clone libraries and fluorescence in-situ hybridization with rRNA-targeted oligonucleotide probes. All the results suggested that Methanothrix thermophila-related methanogens, Desulfotomaculum-related bacterial populations in the Gram-positive low-G + C group, and OP5-related populations were the key members responsible for terephthalate degradation under thermophilic methanogenic conditions except during periods when the reactor experienced heat shock and pump failure. These perturbations caused a significant shift in bacterial population structure in sludge samples taken from the sludge bed but not from the surface of the packing materials. After system recovery, many other bacterial populations emerged, which belonged mainly to the Gram-positive low-G + C group and Cytophaga-Flexibacter-Bacteroides, as well as beta-Proteobacteria, Planctomycetes and Nitrospira. These newly emerged populations were probably also capable of degrading terephthalate in the hybrid system, but were out-competed by those bacterial populations before perturbations.

Rice progenies used for the construction of genetic maps permit exhaustive identification and characterization of resistance genes present in their parental cultivars. We inoculated a rice progeny derived from the cross IR64 x Azucena with different Magnaporthe grisea isolates that showed differential responses on the parental cultivars. By QTL mapping, nine unlinked loci conferring resistance to each isolate were identified and named Pi-24( t) to Pi-32( t). They could correspond to nine specific resistance genes. Five of these resistance loci (RLs) were mapped at chromosomal locations where no resistance gene was previously reported, defining new resistance genes. Using degenerate primers of the NBS (nucleotide binding site) motif found in many resistance genes, two resistance gene analogues (RGAs) IR86 and IR14 were identified and mapped closely to two blast RLs (resistance identified in this study, i.e. Pi-29(t) and Pi-30(t) respectively). These two RLs may correspond to the Pi-11 and Pi-a blast resistance genes previously identified. Moreover, the ir86 and ir14 genes have been identified "in silico" on the indica rice cultivar 93-11, recently sequenced by Chinese researchers. Both genes encodes NBS-LRR-like proteins that are characteristics of plant-disease resistance genes.

At the present time, the precise taxonomial status of many strains classified as #Bradyrhizobium$ still remains unclear. There is a need to develop a reliable grouping method, specifying the genetic relationships between these strains. Phenotypic methods as auxanography or protein profiling did not prove valuable for classification of bradyrhizobia and were not in good agreement with phylogenetic data. The purpose of this work is to develop a strategy to analyse the diversity of bradyrhizobia and to identify genomic groups among our collection of strains isolated from 9 small legume species in Senegal. #B. japonicum$, #B. elkanii$ and representatives of previously described groups by Moreira et al. (1993) and Dupuy et al. (1994) were included as references. Bacterial diversity was assessed by two different techniques, PCR-RFLP analysis of the IGS region between 16S and 23S rDNA (IGS) and the AFLP technique. Groupings of strains obtained by the two methodologies will be presented and compared. 16S rDNA PCR-RFLP analysis of strains representative of IGS clusters from small legumes was also performed. (Résumé d'auteur)

One of the enduring problems in the epidemiology of sleeping sickness is that there are 3 morphologically indistinguishable subspecies of Trypanosoma brucei involved in a complex transmission cycle between humans, tsetse and reservoir hosts. Two subspecies, T. b. gambiense and T. b. rhodesiense, are infective to man and cause gambian and rhodesian sleeping sickness, respectively. The third subspecies T. b. brucei cannot by definition infect humans, but coexists with the other trypanosomes in reservoir hosts and vectors.

Cultivated varieties of rice are the result of several thousands of years of human selection from the available genetic diversity, in various natural environments and human cultures. The process of gathering varieties from different geographic origins, planting them in the same field, and selecting particular genotypes among the offsprings of natural hybridization can still be observed in traditional societies and has no doubt been going on since early days. Modern breeding in the last century has done little more than to control the process of hybridization and selection in a more efficient way, and the result has been to adapt varieties to better controlled and fertilized environments. The basic approach consists of choosing parents with complementary characters in order to combine them. Unexpected (transgressive) characters are also obtained in the process. Evaluation of germplasm is generally a matter of screening for useful characters although the understanding of the genetic structure of genetic resources can give a clue to obtain transgressive characters (Second and Charrier 1989).

The taxonomy of the #Culex pipiens$ complex remains a controversial issue in mosquito systematics. Based on morphologic characters, 2 allopatric taxa are recognized, namely #Cx. pipiens$ (including the form "#molestus$") in temperate areas and #Cx. quinquefasciatus$ in tropical areas. Here we report on variability at nucleotide level of an acetylcholinesterase gene in several strains and natural populations of this species complex. Few polymorphisms were found in coding regions within a subspecies but many polymorphisms were observed between subspecies in noncoding regions. We describe a method based on a restriction enzyme polymorphism in polmerase chain reaction-amplified DNA, in which the presence or absence of one restriction site discriminates #Cx. pipiens$, #Cx. quinquefasciatus$, and their hybrids. This technique reliably discriminates mosquitoes from more than 30 worldwide strains or populations. Polymerase chain reaction amplification of specific alleles may also be a useful tool for characterizing specific alleles of each sibling taxon. (Résumé d'auteur)

Fifty-one fast growing rhizobial strains isolated from root nodules of #Acacia senegal$ and #Prosopis chilensis$ in Sudan and Kenya were divided into DNA homology groups using non-radioactive DNA-DNA dot-blot hybridisation. #Rhizobium leguminosarum$ , #R. galegae$, #R. tropici$, #Mesorhizobium loti$, #Sinorhizobium fredii$, #S. meliloti$ used in numerical taxonomy were included in the hybridisation experiments as reference strains and, at a later strage #S. saheli$ and #S. terangae$. Scores given to the intensities of dots detected in the hybridisation experiments were used in principal component analysis, which clustered the majority of the tree rhizobia in two separate DNA-homology groups. The 51 strains were also analysed by genomic fingerprinting using the repetitive sequence-based polymerase chain reaction (rep-PCR) method with REP, ERIC, BOX and GTG5 primers. The resulting genomic fingerprints were compared with strains representing 15 rhizobial species. The relationship of 17 Sudanese strains to established sinorhizobial species was examined using the optical renaturation rates method and the G+C content of nine strains was determined. Results from dot-blot hybridisation and rep-PCR experiments were found to be in close agreement with each other and with the results obtained from spectrophotometric reassociation analysis. We suggest that rep-PCR fingerprinting can be used as a first and dot-blot hybridisation as a second rapid and dependable genomic screening method to classify new rhizobial isolates of unknown taxonomic status and to choose the representative strains for the more laborious DNA-DNA reassociation experiments. (Résumé d'auteur)

We obtained nine bacterial isolates from root or collar nodules of the non-stem-nodulated #Aeschynomene$ species #A. elaphroxylon$, #A. uniflora$, or #A. schimperi$ and 69 root or stem nodule isolates from the stem-nodulated #Aeschynomene$ species #A. afraspera$, #A. ciliata$, #A. indica$, #A. nilotica$, #A. sensitiva$, and #A. tambacoundensis$ from various places in Senegal. These isolates, together with 45 previous isolates from various #Aeschynomene$ species, were studied for host-specific nodulation within the genus #Aeschynomene$, also revisiting cross-inoculation groups described previously by D. Alazard (Appl. Environ. Microbiol. 50:732-734, 1985). The whole collection of #Aeschynomene$ nodule isolates was screened for synthesis of photosynthetic pigments by spectrometry, high pressure liquid chromatography, and thin layer chromatography analyses. The presence of puf genes in photosynthetic #Aeschynomene$ isolates was evidenced both by Southern hybridization with a #Rhodobacter capsulatus$ photosynthetic gene probe and by DNA amplificaton with primers defined from photosynthetic genes. In addition, amplified 16S ribosomal DNA restriction analysis was performed on 45 #Aeschynomene$ isolates, including strain BTAi1, and 19 reference strains from #Bradyrhizobium japonicum$, #Bradyrhizobium elkani$, and other #Bradyrhizobium$ sp. strains of uncertain taxonomic positions. The 16S rRNA gene sequence of the photosynthetic strain ORS278 (LMG 12187) was determined and compared to sequences from databases. Our main conclusion is that photosynthetic #Aeschynomene$ nodule isolates share the ability to nodulate particular stem-modulated species and form a separate subbranch on the #Bradyrhizobium$ rRNA, distinct from #B. japonicum$ and #B. elkanii$. (Résumé d'auteur)

The African Anopheles funestus and the Asian An. minimus groups are closely related and are probably considered distinct only because of their geographic separation. This study aimed at improving two identification methods based on polymerase chain reactionrestriction fragment length polymorphism (PCR-RFLP) already devel- oped for either group. Each PCR-RFLP, either on the internal transcribed spacer 2 (ITS2) for the An. minimus group, and domain 3 (D3) for the An. funestus group, was applied to the other group for the standardization of one identifi- cation method applicable on both continents. The ITS2 fragment digested by Bsi ZI showed the highest diagnostic power. This assay allowed the discrimination of at least 13 Anopheles species within the subgenus Cellia from two continents (Africa and Asia), among which are five major malaria vectors. Moreover, digestion of the D3 with Msp I showed intragenomic variations within An. funestus populations. Two types of D3 copies (M and W) occurred in specimens from southern Africa. The populations from West-Central Africa presented only type W and East-Malagasy populations exhibited type M. Since An. funestus shows a great capacity of adaptation, these molecular variations, along with behavioral and ecologic ones, reinforce the hypothesis of a species complex that will need to be further investigated.