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Sylvain Santoni

Publications and source records attributed to Sylvain Santoni.

9 recordsLinked to original sources
PubMed2006

Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula.

BACKGROUND: Exploiting genetic diversity requires previous knowledge of the extent and structure of the variation occurring in a species. Such knowledge can in turn be used to build a core-collection, i.e. a subset of accessions that aim at representing the genetic diversity of this species with a minimum of repetitiveness. We investigate the patterns of genetic diversity and population structure in a collection of 346 inbred lines representing the breadth of naturally occurring diversity in the Legume plant model Medicago truncatula using 13 microsatellite loci distributed throughout the genome. RESULTS: We confirm the uniqueness of all these genotypes and reveal a large amount of genetic diversity and allelic variation within this autogamous species. Spatial genetic correlation was found only for individuals originating from the same population and between neighbouring populations. Using a model-based clustering algorithm, we identified four main genetic clusters in the set of individuals analyzed. This stratification matches broad geographic regions. We also identified a set of "admixed" individuals that do not fit with this population structure scheme. CONCLUSION: The stratification inferred is discussed considering potential historical events like expansion, refuge history and admixture between neighbouring groups. Information on the allelic richness and the inferred population structure are used to build a nested core-collection. The set of inbred lines and the core collections are publicly available and will help coordinating efforts for the study of naturally occurring variation in the growing Medicago truncatula community.

DNA, Plant↗
PubMed2006

Microsatellite segregation analysis and cytogenetic evidence for tetrasomic inheritance in the American yam Dioscorea trifida and a new basic chromosome number in the Dioscoreae.

Despite the economic and cultural importance of the indigenous "Amerindian" yam Dioscorea trifida, very little is known about their origin, phylogeny, diversity and genetics. Consequently, conventional breeding efforts for the selection of D. trifida genotypes resistant to potyviruses which are directly involved in the regression of this species have been seriously limited. Our objective of this paper is to contribute to the clarification of the cytogenetic status, i.e., inheritance and chromosome number. Our results provide genetic evidence supporting tetrasomic behaviour of the genome of D. trifida based on chromosomal segregation pattern analysis using eight SSRs markers in three different crosses. This is the first reliable evidence of an autopolyploid species in the genus Dioscorea. The second major result in this study is the revealing of a new base chromosome number in the botanical section Macrogynodium to which D. trifida belongs. To date, our assumptions about the ploidy level of yams are based on the observations that the basic chromosome number is 10 or 9, and D. trifida was described as octoploid. The chromosome number of D. trifida accessions was also assessed using somatic chromosomic count techniques. Flow cytometry did not show significant variation of 2C DNA content among 80 accessions indicating homogeneity of the ploidy level of the cultivated D. trifida. This suggests that autotetraploidy is well established as well as the rule for the cultivated pool of D. trifida, even if the direct diploid ancestor remains to be identified. The data presented in this paper are significant and important for the effective breeding and conservation of the species and for elucidating the phylogeny and the origins of the yam and the evolution of the genus Dioscorea.

Chromosome Segregation↗
PubMed2006

Molecular evolution and positive selection of the symbiotic gene NORK in Medicago truncatula.

Understanding the selective constraints of partner specificity in mutually beneficial symbiosis is a significant, yet largely unexplored, prospect of evolutionary biology. These selective constraints can be explored through the study of nucleotide polymorphism at loci controlling specificity. The membrane-anchored receptor NORK (nodulation receptor kinase) of the legume Medicago truncatula controls early steps of root infection by two symbiotic microorganisms: nitrogen-fixing bacteria (rhizobia) and endomycorrhizal fungi (Glomales). We analyzed the diversity of the gene NORK by sequencing 4 kilobases in 28 inbred lines sampled from natural populations. We detected 33 polymorphic sites with only one nonsynonymous change. Analysis based on Tajima's D and Fay and Wu's H summary statistics revealed no departure from the neutral model. We analyzed divergence using sequences from the closely related species M. coerulea. The McDonald-Kreitman test indicated a significant excess of nonsynonymous changes contributing to this divergence. Furthermore, maximum-likelihood analysis of a molecular phylogeny of a few legume species indicated that a number of amino acid sites, likely located in the receptor domain of the protein, evolved under the regime of positive selection. Further research should focus on the rate and direction of molecular coevolution between microorganisms' signaling molecules and legumes' receptors.

Amino Acid Sequence↗
PubMed2006

Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium.

The existence of a large-scale population structure was investigated in Arabidopsis thaliana by studying patterns of polymorphism in a set of 71 European accessions. We used sequence polymorphism surveyed in 10 fragments of approximately 600 nucleotides and a set of nine microsatellite markers. Population structure was investigated using a model-based inference framework. Among the accessions studied, the presence of four groups was inferred using genetic data, without using prior information on the geographical origin of the accessions. Significant genetic isolation by geographical distance was detected at the group level, together with a geographical gradient in allelic richness across groups. These results are discussed with respect to the previously proposed scenario of postglacial colonization of Europe from putative glacial refugia. Finally, the contribution of the inferred structure to linkage disequilibrium among 171 pairs of essentially unlinked markers was also investigated. Linkage disequilibrium analysis revealed that significant associations detected in the whole sample were mainly due to genetic differentiation among the inferred groups. We discuss the implication of this finding for future association studies in A. thaliana.

Arabidopsis↗
PubMed2006

Dental wear study in a 14th century skull of the Sao tribe, Cameroon.

The aim of this work was to study the wear affecting the almost complete dentition of a Sao individual fossil from Cameroon prehistory (XIVth century). Occlusal surfaces of the fossil fragile pieces were plaster replicated with an original technique adapted from usual dental impression methods (silicon elastomer polymerising by addition). Axial macro-photographs of both sectional dental casts and original pieces made it possible to produce drawings of the occlusal areas on transparencies in order to superimpose the lateral hemiarch counterparts in their optimal intercuspal position. The study of interarch contacts was completed by confronting and observing the occluding position of hemiarch replicas. The occlusal analysis revealed that the wear extent was equivalent on left and right molars. Hall's occlusal wear index and Van Reenen and Reinach's classification of proximal wear allow assessment of the degree of wear extent on premolar and molar sections in relation to the side or the arch observed. The even bilateral proximal and occlusal wears observed on the different kinds of homologous teeth appeared as the main contributor to this well-balanced interarch occlusion. The mandibular incisor losses and the particular type of wear affecting lower canines led to the conclusion of the presence of a labret, a great number of which was found in the area. According to Miles' method of age assessment based on tooth wear, the pieces studied belonged to an individual between 30 and 40 years old.

Age Determination by Teeth↗
PubMed2006

Dental contribution to paleo-odontological study of interarch relations in a human fossil.

In paleo-anthropology the fragility of fossil pieces (teeth and supporting bones) reduces their possible manipulation when studying the interarch relations. Two original impression methods of the jaw pieces are proposed, both adapted from those currently practiced in odontology. The plaster replicas of the dental occlusal parts are prepared according to the manufacturing procedures used in prosthetic dental laboratories. This study led to the following observations: 1) the impression techniques used by odontologists are adapted to the moulding of fragile samples. 2) The replicas elaborated from these mouldings made easier the cast manipulation in confrontation. 3) Macrophotography is a complement to direct observation of the pieces and their replicas. 4) For paleoanthropologic purposes, such studies can be easily carried out on almost any animal or human fossils.

Cameroon↗
PubMed2005

Dental arch relations analysed in a 14th century fossil skull of the Sao tribe, Cameroon.

Dental occlusal relations are rarely reported in paleo-anthropology. The manipulation of hemi-arch replicas, as well as the superimposition of drawings on calques traced from photographs, facilitated the description of the intra- and interarch relations. The occlusal interarch confrontation and the intermolar relation were observed and assessed in the horizontal, frontal and sagittal planes. Some measurements were helpful in the functional study. On the basis of knowledge in mandible kinematics a movement envelope of the first molar displacement during mastication was proposed. The dentition studied here was highly regular. It was a fine example of balanced wear for post-canine sectors. In spite of the lower canine extrusion, due to tribal mutilation of anterior teeth and to subsequent labret wearing, the interarch relations seemed not to have been altered.

Cameroon↗
PubMed2003

Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers.

BACKGROUND: Alfalfa (Medicago sativa) is a major forage crop. The genetic progress is slow in this legume species because of its autotetraploidy and allogamy. The genetic structure of this species makes the construction of genetic maps difficult. To reach this objective, and to be able to detect QTLs in segregating populations, we used the available codominant microsatellite markers (SSRs), most of them identified in the model legume Medicago truncatula from EST database. A genetic map was constructed with AFLP and SSR markers using specific mapping procedures for autotetraploids. The tetrasomic inheritance was analysed in an alfalfa mapping population. RESULTS: We have demonstrated that 80% of primer pairs defined on each side of SSR motifs in M. truncatula EST database amplify with the alfalfa DNA. Using a F1 mapping population of 168 individuals produced from the cross of 2 heterozygous parental plants from Magali and Mercedes cultivars, we obtained 599 AFLP markers and 107 SSR loci. All but 3 SSR loci showed a clear tetrasomic inheritance. For most of the SSR loci, the double-reduction was not significant. For the other loci no specific genotypes were produced, so the significant double-reduction could arise from segregation distortion. For each parent, the genetic map contained 8 groups of four homologous chromosomes. The lengths of the maps were 2649 and 3045 cM, with an average distance of 7.6 and 9.0 cM between markers, for Magali and Mercedes parents, respectively. Using only the SSR markers, we built a composite map covering 709 cM. CONCLUSIONS: Compared to diploid alfalfa genetic maps, our maps cover about 88-100% of the genome and are close to saturation. The inheritance of the codominant markers (SSR) and the pattern of linkage repulsions between markers within each homology group are consistent with the hypothesis of a tetrasomic meiosis in alfalfa. Except for 2 out of 107 SSR markers, we found a similar order of markers on the chromosomes between the tetraploid alfalfa and M. truncatula genomes indicating a high level of colinearity between these two species. These maps will be a valuable tool for alfalfa breeding and are being used to locate QTLs.

Alleles↗