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Insect movement in the landscape remains often poorly known and in some cases does not make it possible to understand the role of the different cultivated and wild habitats in the dynamics of useful and pest insects. Insects are among the greatest pests of agriculture, horticulture and forestry worldwide, inflicting damage and economic costs both directly and by transmitting plant viruses. There is a need for tracking the migrant insects in agroecosystems through space and time to establish their migration. Furthermore, tracing the origin of pest insects allows to design more rapid, efficient and environment-friendly control systems (less use of insecticides). Tracking insects can also help us better understanding their biology (e.g. insect population dynamics, geo-traceability, feeding behavior and other ecological interactions). However, tracking insects presents a considerable challenge as they are often small, cryptic and highly mobile organisms. The most common methods of analysis currently proposed (microsatellite markers, stable isotopes) do not allow for the moment to determine their geographical origin. The ecological niche occupied by the insects highly influences the bacterial communities associated with the insects. Hence understanding the diversity of bacterial communities could be an option to trace the orgins of the pest. This paper presents two new protocols used to extract bacterial DNA from the Cotton Bollworm, Helicoverpa armigera and the analysis of this DNA by PCR-DGGE. This promising method is proposed as a new traceability tool which provides insects with a unique biological barcode and makes it possible to trace back the insects to their original location.

Mutator-like transposase is the most represented transposon transcript in the sugarcane transcriptome. Phylogenetic reconstructions derived from sequenced transcripts provided evidence that at least four distinct classes exist (I-IV) and that diversification among these classes occurred early in Angiosperms, prior to the divergence of Monocots/Eudicots. The four previously described classes served as probes to select and further sequence six BAC clones from a genomic library of cultivar R570. A total of 579,352 sugarcane base pairs were produced from these "Mutator system" BAC containing regions for further characterization. The analyzed genomic regions confirmed that the predicted structure and organization of the Mutator system in sugarcane is composed of two true transposon lineages, each containing a specific terminal inverted repeat and two transposase lineages considered to be domesticated. Each Mutator transposase class displayed a particular molecular structure supporting lineage specific evolution. MUSTANG, previously described domesticated genes, are located in syntenic regions across Sacharineae and, as expected for a host functional gene, posses the same gene structure as in other Poaceae. Two sequenced BACs correspond to hom(eo)logous locus with specific retrotransposon insertions that discriminate sugarcane haplotypes. The comparative studies presented, add information to the Mutator systems previously identified in the maize and rice genomes by describing lineage specific molecular structure and genomic distribution pattern in the sugarcane genome. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12042-012-9104-y) contains supplementary material, which is available to authorized users.

The pepper (Capsicum annuum) Bs3 gene confers resistance to avrBs3-expressing strains of the bacterial spot pathogen Xanthomonas campestris pv. vesicatoria. To physically delimit Bs3, a pepper YAC library was screened with two flanking DNA markers that are separated from Bs3 by 1.0 and 1.2 cM, respectively resulting in the identification of three YAC clones. Genetic mapping of the corresponding YACends revealed however, that these YACs do not cover Bs3 and subsequent screens with newly developed YACend markers failed to identify new YAC clones. Marker saturation at the Bs3 locus was carried out by amplified fragment length polymorphism (AFLP). The analysis of 1,024 primer combinations resulted in the identification of 47 new Bs3-linked AFLPs. High-resolution linkage mapping of Bs3 was accomplished by inspecting more than 4,000 F(2) segregants resulting in a genetic resolution of 0.01 cM. Using tightly Bs3-linked YACend- and AFLP-derived markers we established a Bs3-spanning BAC contig and physically delimited the target gene within one BAC clone. The analysis of the Bs3-containing genomic region revealed substantial local variation in the correlation of genetic and physical distances.

Leaf pubescence in cotton have a potential for insect pest management. Varying degrees of leaf trichome density in Gossypium species and cultivars have been associated to a series of five genes, referred to as t(1)-t(5). We used two segregating interspecific G. hirsutum x G. barbadense backcross populations developed in our laboratory to assess qualitatively and quantitatively leaf and stem pubescence. QTL analyses were performed using simple and composite interval mapping. Based on both types of measurements and under both types of QTL analyses, nine QTLs met permutation-based thresholds. The nine QTLs mapped to four different chromosome regions. Highest LOD values corresponded to the QTLs detected on c6 (four colocalized QTLs) and on D03 (two QTLs) for which the higher pubescence in the progeny derived from the pubescent G. hirsutum parent alleles. Conversely, on c17 (one QTL) and A01 (two QTLs), the G. hirsutum parental alleles affected negatively pubescence. These results combined with another published study confirm (1) the location in a center region of chromosome 6 of the t(1) locus as a major locus/gene determining leaf pubescence, and (2) additional genes located on seven additional chromosomes have been shown to impart trichome density either positively or negatively. The existence of a high density of PCR-based loci in most of the regions identified as harboring leaf pubescence QTLs, particularly that on chromosome 6, will facilitate future efforts for map-based cloning.

Almost all the nuclear genes of four Gramineae (maize, wheat, barley, rice) and pea are located in DNA fractions covering only a 1–2% GC range and representing between 10 and 25% of the different genomes. These DNA fractions comprise large gene-rich regions (collectively called the ‘gene space’) separated by vast gene-empty, repeated sequences. In contrast, in Arabidopsis thaliana , genes are distributed in DNA fractions covering an 8% GC range and representing 85% of the genome. Here, we investigated the integration of a transferred DNA (T-DNA) in the genomes of Arabidopsis and rice and found different patterns of integration, which are correlated with the different gene distributions. While T-DNA integrates essentially everywhere in the Arabidopsis genome, integration was detected only in the gene space, namely in the gene-rich, transcriptionally active, regions of the rice genome. The implications of these results for the integration of foreign DNA are discussed.

In Bacillus subtilis , the products of the pta and ackA genes, phosphotransacetylase and acetate kinase, play a crucial role in the production of acetate, one of the most abundant by-products of carbon metabolism in this gram-positive bacterium. Although these two enzymes are part of the same pathway, only mutants with inactivated ackA did not grow in the presence of glucose. Inactivation of pta had only a weak inhibitory effect on growth. In contrast to pta and ackA in Escherichia coli , the corresponding B. subtilis genes are not cotranscribed. Expression of the pta gene was increased in the presence of glucose, as has been reported for ackA . The effects of the predicted cis -acting catabolite response element (CRE) located upstream from the promoter and of the trans -acting proteins CcpA, HPr, Crh, and HPr kinase on the catabolite regulation of pta were investigated. As for ackA , glucose activation was abolished in ccpA and hprK mutants and in the ptsH1 crh double mutant. Footprinting experiments demonstrated an interaction between CcpA and the pta CRE sequence, which is almost identical to the proposed CRE consensus sequence. This interaction occurs only in the presence of Ser-46-phosphorylated HPr (HPrSer-P) or Ser-46-phosphorylated Crh (CrhSer-P) and fructose-1,6-bisphosphate (FBP). In addition to CcpA, carbon catabolite activation of the pta gene therefore requires at least two other cofactors, FBP and either HPr or Crh, phosphorylated at Ser-46 by the ATP-dependent Hpr kinase.

Genetic studies of Saccharomyces cerevisiae have identified many components acting to deliver specific proteins to their cellular locations. Genome analysis, however, has indicated that additional genes may also participate in such protein trafficking. The product of the yeast Yarrowia lipolytica TSR1 gene promotes the signal recognition particle-dependent translocation of secretory proteins through the endoplasmic reticulum. Here we describe the identification of a new gene family of proteins that is well conserved among different yeast species. The TSR1 genes encode polypeptides that share the same protein domain distribution and, like Tsr1p, may play an important role in the early steps of the signal recognition particle-dependent translocation pathway. We have identified five homologues of the TSR1 gene, four of them from the yeast Saccharomyces cerevisiae and the other from Hansenula polymorpha. We generated a null mutation in the S. cerevisiae YHC8 gene, the closest homologue to Y. lipolytica TSR1, and used different soluble (carboxypeptidase Y, alpha-factor, invertase) and membrane (dipeptidyl-aminopeptidase) secretory proteins to study its phenotype. A large accumulation of soluble protein precursors was detected in the mutant strain. Immunofluorescence experiments show that Yhc8p is localized in the endoplasmic reticulum. We propose that the YHC8 gene is a new and important component of the S. cerevisiae endoplasmic reticulum membrane and that it functions in protein translocation/insertion of secretory proteins through or into this compartment.

The gene corresponding to the lactococcal oligopeptidase PepF1 (formerly PepF [V. Monnet, M. Nardi, A. Chopin, M.-C. Chopin, and J.-C. Gripon, J. Biol. Chem. 269:32070-32076, 1994]) is located on the lactose-proteinase plasmid of Lactococcus lactis subsp. cremoris NCDO763. Use of the pepF1 gene as a probe with different strains showed that pepF1 is present on the chromosome of Lactococcus lactis subsp. lactis IL1403, whereas there is a second, homologous gene, pepF2, on the chromosome of strain NCDO763. From hybridization, PCR amplification, and sequencing experiments, we deduced that (i) pepF1 and pepF2 exhibit 80% identity and encode two proteins which are 84% identical and (ii) pepF2 is included in an operon composed of three open reading frames and is transcribed from two promoters. The protein, encoded by the gene located downstream of pepF2, shows significant homology with methyltransferases. Analysis of the sequences flanking pepF1 and pepF2 indicates that only a part of the pepF2 operon is present on the plasmid of strain NCDO763, while the operon is intact on the chromosome of strain IL1403. Traces of several recombination events are visible on the lactose-proteinase plasmid. This suggests that the duplication of pepF occurred by recombination from the chromosome of an L. lactis subsp. lactis strain followed by gene transfer. We discuss the possible functions of PepF and the role of its amplification.

Segregations of rice isozymes made it possible to ascertain the genetic control of 13 enzymes by 30 loci. In addition to numerous cases of independence, several linkages were observed. Got-2 and Enp-1 were localized on chromosome 3 and a linkage group composed of Pox-3, Pox-4, and Est-1 was identified. Inconsistencies of recombination rates between linked loci among different crosses were noted. Several cases of distorted segregations and pseudolinkages were recorded. The relationships between these results and the study of genome organization in cultivated rice are discussed.Key words: Oryza, isozyme, genetic analysis, segregation distortion, linkage.

Fluorescence in situ hybridization (FISH) was used to study the presence of alien chromatin in interspecific hy- brids and one introgressed line (S.288) derived from crosses between the cultivated species Coffea arabica and the diploid relatives C. canephora and C. liberica. In situ hybridization using genomic DNA from C. canephora and C. arabica as probes showed elevated cross hybridization along the hybrid genome, confirming the weak differentiation between parental genomes. According to our genomic in situ hybridization (GISH) data, the observed genomic resemblance between the modern C. canephora genome (C) and the C. canephora-derived subgenome of C. arabica (C a ) appears rather consider- able. Poor discrimination between C and C a chromosomes supports the idea of low structural modifications of both ge- nomes since the C. arabica speciation, at least in the frequency and distribution of repetitive sequences. GISH was also used to identify alien chromatin segments on chromosome spreads of a C. liberica-introgressed line of C. arabica. Further, use of GISH together with BAC-FISH analysis gave us additional valuable information about the physical localization of the C. liberica fragments carrying the SH3 factor involved in resistance to the coffee leaf rust. Overall, our results illustrate that FISH analysis is a complementary tool for molecular cytogenetic studies in coffee, providing rapid localization of ei- ther specific chromosomes or alien chromatin in introgressed genotypes derived from diploid species displaying substantial genomic differentiation from C. arabica. Resume´ : L'hybridation in situ fluorescente (« FISH ») a eteutilisee pour etudier la presence de chromatine introgressee chez des hybrides interspecifiques mais aussi chez une lignee cultivee, issues du croissement entre l'espece cultivee Coffea arabica et ses proches diploo¨des C. canephora et C. liberica, respectivement. L'hybridation in situ en utilisant l'ADN ge ´- nomique des especes C. canephora et C. arabica comme sondes, a montreune hybridation croisee importante chez les ge ´- nomes hybrides, ce qui confirme une etroite differentiation genomique entre les parents. Cette ressemblance entre le genome actuel de C. canephora et le sous-genome de C. arabica derivant de l'espece C. canephora (C a ), semble tresele- vee. De plus, la faible discrimination entre les chromosomes du type C et ceux du type C a , suggere des modifications structurales mineures des l'origine meme de l'espece C. arabica, au moins dans ce qui concerne la frequence et distribu- tion des sequences repetees. L'hybridation genomique in situ (« GISH ») a permis aussi l'identification de differents frag- ments d'introgression chez une ligneed eC. arabica introgressee par C. liberica, ce qui a conduit al'identification de quatre fragments d'introgression. De plus, l'analyse combineGISH plus BAC-FISH a donnedes informations importantes sur la localisation physique du fragment issu de C. liberica porteur du facteur SH 3d e resistance a la rouille des cafeiers. L'ensemble des resultats montre que la technique FISH represente un outil puissant pour l'etude cytogenetique des cafeiers permettant l'identification rapide de chromosomes mais aussi de l'ADN introgressechez les genotypes issus de croissements concernant des especes diploo¨des caracterisees par une differentiation genomique importante par rapport a C. arabica. Mots-cles: cafeier, BAC-FISH, GISH, hybridation interspecifique, introgression, evolution du genome. (Traduit par la Redaction)

Le charbon est une maladie présente dans toutes les zones de culture de la canne à sucre, à l'exception de la Papouasie-Nouvelle-Guinée, qui est pourtant le berceau de l'espèce ancestrale domestiquée, Saccharum officinarum. Des études permettent désormais de mieux cerner la diversité génétique de ce champignon et le déterminisme génétique de la résistance de la canne.

International audience; A three-generation outbred pedigree of 186 individuals was used to identify the genomic regions involved in the variability of chemical and physical wood properties of Pinus pinaster. A total of 54 quantitative trait loci (QTLs) was detected, with an average of 2.4 QTLs per trait. Clusters of wood properties QTLs were found at several points in the genome, suggesting the existence of pleiotropic effects of a limited number of genes. The colocalizations observed in this study are in accordance with the genetic correlations previously reported in the literature. In addition, in an attempt to identify the genes underlying the QTLs, nine wood quality candidate genes involved in cell wall structure were localized on the genetic map. Only one of them, Korrigan, a gene encoding for a β 1-4 endo-glucanase known in Arabidopis thaliana to be involved in polysaccharide biosynthesis, co-localized with a wood quality QTL cluster involved in hemicellulose content and fibre characteristics. This finding is in accordance with results previously reported for this gene regarding its expression variability (transcriptome and proteome levels) and patterns of molecular evolution. The pertinence of this result will be tested in more rigorous designs in order to identify early selection predictors for wood quality.

International audience; Nucleotide diversity in eight genes related to wood formation was investigated in two pine species, Pinus pinaster and P. radiata. The nucleotide diversity patterns observed and their properties were compared between the two species according to the specific characteristics of the samples analysed. A lower diversity was observed in P. radiata compared with P. pinaster. In particular, for two genes (Pp1, a glycin-rich protein homolog and CesA3, a cellulose synthase) the magnitude of the reduction of diversity potentially indicates the action of nonneutral factors. For both, particular patterns of nucleotide diversity were observed in P. pinaster (high genetic differentiation for Pp1 and close to zero differentiation associated with positive Tajima's D-value for CesA3). In addition, KORRIGAN, a gene involved in cellulose-hemicellulose assembly, demonstrated a negative Tajima's D-value in P. radiata accompanied by a high genetic differentiation in P. pinaster. The consistency of the results obtained at the nucleotide level, together with the physiological roles of the genes analysed, indicate their potential susceptibility to artificial and/or natural selection

Within the Musa Genomics Consortium three BAC libraries were constructed from the genomes of Musa acuminata (cvs 'Calcutta 4' and 'Grande naine') and Musa balbisiana (PKW). The three BAC libraries have been anchored to the existing Musa consensus genetic map using a set of single-copy RFLP markers. The three BAC libraries are a publicly available resource and represent a critical tool to achieve the goals of the recently created Global Musa Genomics Consortium. To study the structure and evolution of Musa genomes in relation to those of rice and sorghum, 50 Sorghum bicolor cDNA clones, previously mapped in sorghum and rice with large-hybridization spectrum (EGRAM genes), were used as probes to screen the M. acuminata 'Calcutta-4' BAC library. Banana BACs that hybridized to 9 EGRAM probes of known function were further analysed by BAC end sequencing and RFLP fingerprinting, and individual BAC clones were selected and subcloned for complete sequencing. In addition, BAC clones believed to arise from the homoeologous region on the A and B Musa genomes were identified using M. acuminata RFLP genetically mapped probes encoding for genes of agronomic interest and involved in plant defense (1-3 glucanase) and control of plant height (GA 20-oxidase). Altogether, 13 Musa BACs have been sequenced, totalling over one Mb. A preliminary analysis showed that the gene density in the sampled Musa genomic regions was approximately one per 5 kb and that coding regions are 65-75% similar to those from both rice and Arabidopsis. The relationship between rice and Arabidopsis genomes and the gene content and organization of the sequenced banana regions the will be reported. The first insights provided by the international Musa sequencing project cover: 1. the relationship between duplicated regions within the M. acuminata genome, 2. the comparison of orthologous genomic regions in rice and banana, 3. the conservation of homoeologous regions in M. acuminata and M. balbisiana. These data will shed some light on the relationships, at the microsynteny level, between chromosomal regions of agronomic interest for banana breeding in distantly related monocot species. (Texte intégral)

Using the tert-Butanol RNA extraction protocol, we succeeded, for the first time, in isolating RNA from cocoa organs infected by C. perniciosa. These results have led to new perspectives regarding the understanding, through genomic studies, of the cellular mechanisms of the infection of the cocoa tree by destructive pathogens such as Crinipellis or Phytophthora spp. The collection of ESTs we obtained will provide new data about the physiology of the interaction between Theobroma cacao and C. perniciosa. In the short term, we plan to do a functional analysis of some candidate genes, which can also be used for mapping, to facilitate introgression strategies and to create new varieties resistant to C. perniciosa. These data may also be related to research on gene expression of cocoa challenged with other pathogens, such as Phytophthora spp.

Chromosome pairing studies at meiosis have revealed that translocations are frequent in banana genomes. In Musa acuminata, seven groups of translocation have been identified (Standard, North Malaysia, Malaysia Mountains, North A, North B, Indonesia, and East Africa). Each group comprises accessions having the same chromosome structure. Translocations increase the difficulty of constructing a genetic map, studying the inheritance of agronomical characters and breeding in general. The objectives of our study were to develop a tool to characterize translocations on chromosomes based on fluorescent in situ hybridization of BAC clones (BAC-FISH) and to use this tool to characterize the translocations in the accessions 'Calcutta 4' (2n=2x=22, translocation group North A) and 'Madang' (2n=2x=22, translocation group Standard). To achieve this, a genetic map and a 'Calcutta 4' BAC library were built, the BAC-FISH technology was adapted to bananas and a banana cytogenetic map was initiated. The genetic map was based on a F2 population from a 'Calcutta 4' x 'Madang' cross. It encompasses 120 markers (20 RFLPs, 81 AFLPs and 19 SSR markers) distributed over 14 linkage groups and covering 597 cM. The 'Calcutta 4' BAC library comprises 55 152 clones with an average insert size of 100 Kb. About 1.5% of these clones present chloroplast and mitochondrial DNA inserts. This library covers 9 to 10 times the banana genome. Linkage group Il (LGII) was chosen to search for translocations since some of its characteristic (such as a high number of distorted markers) suggested that this group contained chromosomes with translocations. Four BAC clones corresponding to 3 RFLPs and 1 SSR loci distributed on LG II were localized on the 'Calcutta 4' and 'Madang' chromosomes. The results showed that the markers involved in the LG II were localized on three chromosomes, whose structure was different in 'Calcutta 4' and 'Madang', with two linked translocations observed in 'Calcutta 4'. In 'Madang', the markers mMaCIR161-rMaCIR 560, rMaCIR 1125 and rMaCIR 36 were localized on three chromosomes (A, B and C). In 'Calcutta 4' these markers were localized on only two chromosomes (A and B). The marker rMaCIR 1125 localized on the 'Madang' C chromosome, was localized in the proximal position of the 'Calcutta 4' B chromosome. We also initiated a global cytogenetic map of 'Calcutta 4' that comprises 16 loci (14 BAC clones selected by RFLP and SSR markers and the ribosome probes 45S and 5S). The 14 linkage groups of the 'Calcutta 4' x 'Madang' genetic map are anchored to this cytogenetic map. (Texte intégral)

We have constructed and validated the first cocoa ( Theobroma cacao L.) BAC library, with the aim of developing molecular resources to study the structure and evolution of the genome of this perennial crop. This library contains 36,864 clones with an average insert size of 120 kb, representing approximately ten haploid genome equivalents. It was constructed from the genotype Scavina-6 (Sca-6), a Forastero clone highly resistant to cocoa pathogens and a parent of existing mapping populations. Validation of the BAC library was carried out with a set of 13 genetically-anchored single copy and one duplicated markers. An average of nine BAC clones per probe was identified, giving an initial experimental estimation of the genome coverage represented in the library. Screening of the library with a set of resistance gene analogues (RGAs), previously mapped in cocoa and co-localizing with QTL for resistance to Phytophthora traits, confirmed at the physical level the tight clustering of RGAs in the cocoa genome and provided the first insights into the relationships between genetic and physical distances in the cocoa genome. This library represents an available BAC resource for structural genomic studies or map-based cloning of genes corresponding to important QTLs for agronomic traits such as resistance genes to major cocoa pathogens like Phytophthora spp ( palmivora and megakarya), Crinipellis perniciosa and Moniliophthora roreri.

The South American Leaf Blight (SALB), caused by the fungus Microcyclus ulei, is the major rubber tree disease in all Central and South America. A population of 192 progeny individuals derived from a cross between a resistant clone and a susceptible cultivated clone was planted in a field trial in French Guiana in order to evaluate the resistance parameters under real infestation conditions. The resistance type (RT), the presence of stromata (ST) and the level of attack (AT) were observed 20-times on a 22-months period, and semi-quantitative evaluation of stromata was registered only once. The search for QTLs was performed using the Kruskal-Wallis test, Interval Mapping and the Composite Interval Mapping method. One major QTL located on linkage group g13 was detected on the RO 38 map, responsible for 36 to 89% of the phenotypic variance of resistance. This resistance QTL corresponds to one that had previously been detected under controlled conditions of infestation and we called it M13-1bn. Surprisingly, the effect of this QTL was larger under natural conditions of infestation than under controlled inoculation. Other minor QTLs (four on the RO38 map and one on the PB 260 map) were also detected. The type of resistance brought by M13-1bn, as well as its durability, are discussed. Applications for rubber tree breeding programs are considered.

The present invention relates to the isolation of DNA sequences from the Hevea brasiliensis containing the promoter and regulatory region of hevein genes. The promoter sequences of the hevein genes also act as an inducible promoter regulated by wounds and pathogen infection.

La plasticité phénotypique, capacité d'adaptation morphophysiologique au conditions environnementale, est une composante importante de la vigueur au départ des cultures. Ce travail avait pour objet l'étude de la plasticité phénotypique du système racinaire au stade précoce du développement du riz (O. saliva) et de ses bases génétiques. Il s'inscrit dans le cadre d'un projet de recherche pluridisciplinaire cherchant à mieux comprendre le contrôle génétique et physiologique de la vigueur au départ, et à contribuer ultérieurement à l'amélioration des variétés dans ce sens. La carence en phosphore a été utilisée pour évaluer la capacité de deux lignées parentales IR64 (indica) et Azucena (japonica) et de 179 lignées recombinantes, cultivées en hydroponie, de modifier la répartition de leurs biomasses entre la partie aérienne et le système racinaire. Le dispositif expérimental comprend 2 traitements (P+ et P-) et 3 répétitions. Treize QTL sûrs, dont onze QTL impliqués dans l'expression constitutive de la morphologie du système racinaire et deux QTL inductibles liés aux effets relatifs du traitement P-, ont été mis en évidence. Ce sont surtout des QTL à effets mineurs répartis sur de nombreuses régions du génome (chromosome 1, 2, 6, 11 et 12). Ce travail a permis d'identifier des locus intéressants contrôlant la croissance et .la répartition des assimilâts. Après validation des QTL détectés, il sera possible de les utiliser dans des expériences de Sélection Assistée par Marqueurs (SAM) et d'identifier les gènes et fonctions précises associés à ces locus. Des études en génomique fonctionnelle sont en cours au CIRAD et profiteront des résultats de ce travail.

Direct detection of fluorescent in situ hybridization signals on R-banded chromosomes stained with propidium iodide is a rapid and efficient method for constructing cytogenetic maps for species with R-banded standard karyotypes. In this paper, our aim is to establish an R-banded rabbit karyotype nomenclature that is in total agreement with the 1981 G-banded standard nomenclature. For this purpose, we have produced new GTG- and RBG-banded mid-metaphase karyotypes and an updated version of ideograms of R-banded rabbit chromosomes. In addition, to confirm correlations between G- and R-banded chromosomes, we have defined a set of 23 rabbit BAC clones, each containing a specific gene, one marker gene per rabbit chromosome, and we have localized precisely each BAC clone by FISH on both G- and R-banded chromosomes.

A review of the present and future of rice genomics is presented. Rice is a model species for cereals as well as a very important crop. Its genome has been the focus of many mapping experiments associated with QTL localization. These genetic maps now serve as a background for physical mapping, genome sequencing and gene discovery. Recent progress are reviewed. The next step in rice genomics is functional genomics with the determination of the function of the genes. The most straightforward approaches are discussed.

We identified an Arabidopsis thaliana gene, AtMAP3K(epsilon)1, and a Brassica napus cDNA, BnMAP3K(epsilon)1, encoding functional protein serine/threonine kinases closely related to cdc7p and cdc15p from Schizosaccharomyces pombe and Saccharomyces cerevisiae, respectively. This is the first report of cdc7-related genes in non-fungal eukaryotes; no such genes have as yet been identified in Metazoans. The B. napus protein is able to partially complement a cdc7 loss of function mutation in S. pombe. RT-PCR and in situ hybridisation revealed that the A. thaliana and B. napus genes are expressed in both the sporophytic and the gametophytic tissues of the respective plant species and revealed further that expression is highest in dividing cells. Moreover, AtMAP3K(epsilon)1 gene expression is cell cycle-regulated, with higher expression in G2-M phases. Our results strongly suggest that the plant cdc7p-related protein kinases are involved in a signal transduction pathway similar to the SIN pathway, which positively regulates cytokinesis in S. pombe.

To clone the goat Polled Intersex Syndrome (PIS) gene(s), a chromosome walk was performed from six entry points at 1q43. This enabled 91 BACs to be recovered from a recently constructed goat BAC library. Six BAC contigs of goat chromosome 1q43 (ICC1–ICC6) were thus constructed covering altogether 4.5 Mb. A total of 37 microsatellite sequences were isolated from this 4.5-Mb region (16 in this study), of which 33 were genotyped and mapped. ICC3 (1500 kb) was shown by genetic analysis to encompass the PIS locus in a ∼400-kb interval without recombinants detected in the resource families (293 informative meioses). A strong linkage disequilibrium was detected among unrelated animals with the two central markers of the region, suggesting a probable location for PIS in ∼100 kb. High-resolution comparative mapping with human data shows that this DNA segment is the homolog of the human region associated withBlepharophimosis Ptosis Epicanthus inversus Syndrome(BPES) gene located in 3q23. This finding suggests that homologous gene(s) could be responsible for the pathologies observed in humans and goats.[The sequence data, PCR primers and PCR conditions for STS and microsatellites described in this paper have been submitted to the GenBank data library under accession nos.AQ666547–AQ666579, AQ686084–AQ686129, AQ793920–793931,AQ810429–AQ810527, G41201–G41228, and G54270–G54286.]

The purpose of this study was to increase the number of genes assigned by in situ hybridization to equine chromosomes and thus the number of links for comparative mapping with other species. Forty-four new sequences were added to the horse cytogenetic map by FISH mapping of BAC clones containing genes (35) or ESTs (9). Three approaches were developed: use of horse BAC clones screened with (i) horse EST primers, (ii) interspecific consensus intraexonic primers, and (iii) use of goat BAC containing genes previously localized on goat chromosomes. Present data suggest that the second approach is the most promising. A total of 46 segments containing one or several genes could be compared, among which 40 loci could be included in 16 synteny groups between human and horse, displaying one ordered segment and several breaking points along chromosomes. All single BAC localizations confirm the most recent mapping data. Twenty-six out of 31 chromosomes now contain a gene mapped by in situ hybridization, and 14 new arm-to-arm segment homologies were revealed.

International audience

Summary: The XPR2 gene from Yarrowia lipolytica encodes an inducible alkaline extracellular protease. Its complex regulation involves pH, carbon, nitrogen and peptones. Two previously identified upstream activating sequence (UAS) regions were analysed in a reporter system, outside the XPR2 context. Fragments from the UAS regions were inserted upstream of a minimal LEU2 promoter directing the expression of a reporter gene. The activity of the hybrid promoters was assessed following integration into the Y. lipolytica genome. This study confirmed the presence of two UASs composed of several interacting elements. Within the distal UAS (UAS1), a TUF/RAP1 binding site exhibited a UAS activity, which was enhanced by the presence of two adjacent repeats, overlapping sites similar to the CAR1 upstream repressing sequence from Saccharomyces cerevisiae. Within the proximal UAS (UAS2), the UAS activity required the interaction of both an ABF1-like binding site and a decameric repeat, containing Aspergillus nidulans PacC site consensus sequences. This decameric repeat was able to mediate repression due to carbon and/or nitrogen sources as well as pH-dependent activation. A study in the context of trans-regulatory mutations in the Y. lipolytica RIM101 gene showed that the PacC-like sites, potential binding sites for YIRim101p, were implicated in the derepression of UAS2-driven expression at neutral-alkaline pH. The in vivo response of the PacC-like decamers to external pH was dependent on the status of the pH-regulated activator YIRim101p, which is homologous to the A. nidulans PacC regulator. The carbon/nitrogen regulation imposed on the decamers was shown to be independent of YIRim101p and to override its effects.

We report here the cloning and functional analysis of a novel homologue of the mitochondrial carriers predominantly expressed in the central nervous system and referred to as BMCP1 (brain mitochondrialcarrier protein-1). The predicted amino acid sequence of this novel mitochondrial carrier indicates a level of identity of 39, 31, or 30%, toward the mitochondrial oxoglutarate carrier, phosphate carrier, or adenine nucleotide translocator, respectively, and a level of identity of 34, 38, or 39% with the mitochondrial uncoupling proteins UCP1, UCP2, or UCP3, respectively. Northern analysis of mouse, rat, or human tissues demonstrated that mRNA of this novel gene is mainly expressed in brain, although it is 10–30-fold less expressed in other tissues.In situ hybridization analysis of brain showed it is particularly abundant in cortex, hippocampus, thalamus, amygdala, and hypothalamus. Chromosomal mapping indicates that BMCP1 is located on chromosome X of mice and at Xq24 in man. Expression of the protein in yeast strongly impaired growth rate. Analysis of respiration of total recombinant yeast or yeast spheroplasts and in particular of the relationship between respiratory rate and membrane potential of yeast spheroplasts revealed a marked uncoupling activity of respiration, suggesting that although BMCP1 sequence is more distant from the uncoupling proteins (UCPs), this protein could be a fourth member of the UCP family.

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Des cartes saturées en liaisons génétiques ont été établies à l'aide d'isoenzymes et de marqueurs moléculaires (RAPD, RFLP, AFLP et microsatellites) pour différentes descendances de #Theobroma cacao# localisées en Côte d'Ivoire, au Cameroun, à la Trinité-et-Tobago et en France, afin d'identifier les régions du génome impliquées dans la résistance au #Phytophthora#. Les caractères de résistance au #Phytophthora# (#P. palmivora#, #P. capsici# et #P. megakarya#) ont été évalués de différentes façons : en champ par le pourcentage de cabosses infectées, à l'aide de tests d'inoculation artificielle sur feuilles et cabosses, et par l'analyse des pertes de rendement au cours de plusieurs années. Quelques QTL ont pu être identifiés ce qui permet de prévoir une utilisation de ces techniques pour une sélection assistée

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url=http://www.tarweed.com/pgr/PGR98-105.html

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Cet article fait partie du dossier : L’augmentation de la prolificité des truies : acquis, progrès envisageables et conséquences; National audience

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International audience; Proline 40 in Escherichia coli thioredoxin is located close to the redox active site (Cys32-Cys35) within the alpha2 helix. The conservation of this residue among most of the thioredoxins suggests that it could play an important role in the structure and/or function of this protein. We have substituted Pro40 for Ala by using site-directed mutagenesis and expressed the mutant P40A in E.coli. The effects of the mutation on the biophysical and biological properties of thioredoxin have been analyzed and compared with molecular dynamics simulations. Modeling predicted that the replacement of Pro40 by Ala induced a displacement of the active site which exposes Trp31 to the solvent and opens a cleft located between helices alpha2 and alpha3. The solvation free energy (SFE) calculation also indicated that P40A became more hydrophobic as W31 became more accessible. These predictions were totally in agreement with the experimental results. The mutant P40A exhibited chromatographic behavior and fluorescence properties very different from those of the wild-type (WT) protein, in relationship with the displacement of W31. The determination of the free energy of unfolding of P40A showed that the mutant was globally destabilized by 2.9 kcal/mol. However, the effect of the mutation on the transition curve was highly unusual as the midpoint of the unfolding transition increased, indicating that some local structures were actually stabilized by the mutation. Despite these structural modifications, neither the ability of the protein to reduce a chloroplastic enzyme nor its reactivity with the bacterial reductase decreased. The only functional difference was the higher stability of P40A in light activation of NADP-malate dehydrogenase under air, which suggests that the mutant was less rapidly re-oxidized than WT. Therefore, it can be concluded that Pro40 is not essential for maintaining the redox function of thioredoxin but rather is required for the stability of the protein.