Au cours du vieillissement, les caractéristiques organoleptiques du vin se modifient au contact du bois de chêne. Le composé aromatique le plus important, la whisky-lactone, aux notes noix de coco et boisé, est facilement détectable et apprécié par les consommateurs.Quercus petraea et Q. robur, les deux principales espèces européennes de chêne utilisées pour le vieillissement des vins, ont des profils aromatiques très contrastés, particulièrement pour la whisky-lactone. Parvenir à identifier l’espèce de chêne permettrait de fournir aux tonnelleries des lots de bois plus homogènes. L’objectif de cette étude est d’identifier l’espèce de chêne à partir de bois sec, à l’aide de marqueurs moléculaires utilisables dans un contexte industriel. Le bois sec est un tissu mort dans lequel l’ADN est très dégradé et donc difficilement accessible. Pour optimiser l’extraction d’ADN à partir de ce tissu, nous avons développé une méthode de PCR en temps-réel ciblant l’ADN chloroplastique, permettant ainsi d’évaluer l’efficacité des différents protocoles d’extraction. Nous avons également développé des marqueurs moléculaires (SSRs et SNPs) fortement différenciés entre espèces et particulièrement bien adaptés au bois. Grâce à des protocoles d’extraction d’ADN optimisés et ces marqueurs performants, nous avons pu identifier l’espèce sur des lots de bois séchés pendant deux ans. De plus, par l’étude de 262 SNPs dont la moitié est fortement différenciée entre espèces, nous avons démontré que les gènes sélectionnés (loci « outlier ») sont très performants pour délimiter ces deux espèces proches. Ils permettent également de détecter des processus démographiques fins (flux de gènes intra- et interspécifiques), alors que les gènes a priori non-sélectionnés (loci neutres) se révèlent peu informatifs. / Most of aromatic compounds in wine are directly induced during maturation by the contactwith oak wood. For example, whisky-lactone, the most important aromatic compound,which gives a coconut and woody taste, is easily detected and appreciated by consumers.Quercus petraea and Q. robur, the two major European oak species used for wine maturation,have very contrasted aromatic patterns, especially for whisky-lactone. Identifying the speciesused for cooperage will facilitate the maturation process, for instance by providing winerieswith more homogenous batches of barrels. The objective of our study is to characterize theoak species directly from dry wood, using molecular markers that will be applicable in anindustrial context. Unfortunately, dry wood is a dead tissue in which DNA is highlydegraded and difficult to access. To optimize DNA recovery from dry wood, we developed aquantitative PCR protocol based on chloroplast DNA to evaluate the efficiency of DNAisolation protocols. We identified and developed molecular markers (SSRs and SNPs)adapted to dry wood that are particularly diagnostic. Using an optimized DNA isolationprotocol and these powerful markers, the species identity from wood samples dried duringtwo years could be successfully characterized. Using 262 SNPs highly differentiated betweenthe two species, we also demonstrate that genes under selection (outlier loci) haveoutstanding power to delimitate the two oak species and provide unique insights on intraandinterspecific gene flow, whereas genes lacking such a signature (putatively neutral loci)provide little or no resolution.

Magister Scientiae - MSc / The objective of this study was to develop and validate a six Non-CODIS miniSTR genotyping system and to determine its suitability for forensic casework in South Africa. In Non-CODIS miniSTR genotyping systems, smaller PCR products are amplified and the primers are positioned as close as possible to the repeat region. For this reason, these systems can be valuable in a variety of scenarios including complex paternity cases, missing persons work, and mass fatality disasters. / South Africa

<p>In many forensic cases, such as mass disasters reconstruction cases, the recovered DNA is highly degraded. In such incidences, typing of STR loci has become one of the most powerful tools for retrieving information from the degraded DNA. However, as DNA degradation proceeds, three phenomena occur consecutively: loci imbalance, allele dropout and no amplification. To solve the problem of degraded DNA, redesigned primer sets have been developed in which the primers were positioned as close as possible to the STR repeat region. These reduced primer sets were called Miniplexes. Unfortunately, a few of the CODIS STR loci cannot be made into smaller amplicons. For this reason non-CODIS miniSTRs have been developed. The present study was undertaken for the population genetic analysis of microsatellite variation in four South African populations / Afrikaner, Xhosa, Mixed Ancestry and Asian Indian using eight non-CODIS miniSTR loci. These miniSTRs loci were characterized within the populations by estimating the levels of diversity of the markers, estimating the population genetic parameters, and studying the inter-population relationships. All of the miniSTRs were amplified successfully and the genetic variability parameters across all loci in Afrikaner, Mixed Ancestry, Asian Indian and Xhosa were estimated to be in the range of 3 (D4S2364) to 12 (D9S2157) alleles, the total number of alleles over all loci ranged from 100 to 204, the allelic richness ranged from 3.612 to 10.307 and the heterozygosity ranged from 0.4360 to 0.8073. Genetic distance was least between Afrikaner and Asian Indian and highest between Xhosa and Mixed Ancestry. Deviations from Hardy-Weinberg equilibrium were not observed for most of the loci. The low mean FIS (-0.027) and FIT (-0.010) and FST (0.017) values across the populations indicated low level of inbreeding within (FIS) and among (FST) the populations. The Asian Indian population showed higher levels of the inbreeding coefficient, indicating less gene exchange between it and other populations. These 8 markers can be used for genetic investigations and assessing population structure. The study contributed to the knowledge and genetic characterization of four South African populations. In addition, these MiniSTRs prove to be useful in cases where more genetic information is needed.</p>

<p>In many forensic cases, such as mass disasters reconstruction cases, the recovered DNA is highly degraded. In such incidences, typing of STR loci has become one of the most powerful tools for retrieving information from the degraded DNA. However, as DNA degradation proceeds, three phenomena occur consecutively: loci imbalance, allele dropout and no amplification. To solve the problem of degraded DNA, redesigned primer sets have been developed in which the primers were positioned as close as possible to the STR repeat region. These reduced primer sets were called Miniplexes. Unfortunately, a few of the CODIS STR loci cannot be made into smaller amplicons. For this reason non-CODIS miniSTRs have been developed. The present study was undertaken for the population genetic analysis of microsatellite variation in four South African populations / Afrikaner, Xhosa, Mixed Ancestry and Asian Indian using eight non-CODIS miniSTR loci. These miniSTRs loci were characterized within the populations by estimating the levels of diversity of the markers, estimating the population genetic parameters, and studying the inter-population relationships. All of the miniSTRs were amplified successfully and the genetic variability parameters across all loci in Afrikaner, Mixed Ancestry, Asian Indian and Xhosa were estimated to be in the range of 3 (D4S2364) to 12 (D9S2157) alleles, the total number of alleles over all loci ranged from 100 to 204, the allelic richness ranged from 3.612 to 10.307 and the heterozygosity ranged from 0.4360 to 0.8073. Genetic distance was least between Afrikaner and Asian Indian and highest between Xhosa and Mixed Ancestry. Deviations from Hardy-Weinberg equilibrium were not observed for most of the loci. The low mean FIS (-0.027) and FIT (-0.010) and FST (0.017) values across the populations indicated low level of inbreeding within (FIS) and among (FST) the populations. The Asian Indian population showed higher levels of the inbreeding coefficient, indicating less gene exchange between it and other populations. These 8 markers can be used for genetic investigations and assessing population structure. The study contributed to the knowledge and genetic characterization of four South African populations. In addition, these MiniSTRs prove to be useful in cases where more genetic information is needed.</p>

Magister Scientiae - MSc / In many forensic cases, such as mass disasters reconstruction cases, the recovered DNA is highly degraded. In such incidences, typing of STR loci has become one of the most powerful tools for retrieving information from the degraded DNA. However, as DNA degradation proceeds, three phenomena occur consecutively: loci imbalance, allele dropout and no amplification. To solve the problem of degraded DNA, redesigned primer sets have been developed in which the primers were positioned as close as possible to the STR repeat region. These reduced primer sets were called Miniplexes. Unfortunately, a few of the CODIS STR loci cannot be made into smaller amplicons. For this reason non-CODIS miniSTRs have been developed. The present study was undertaken for the population genetic analysis of microsatellite variation in four South African populations; Afrikaner, Xhosa, Mixed Ancestry and Asian Indian using eight non-CODIS miniSTR loci. These miniSTRs loci were characterized within the populations by estimating the levels of diversity of the markers, estimating the population genetic parameters, and studying the inter-population relationships. All of the miniSTRs were amplified successfully and the genetic variability parameters across all loci in Afrikaner, Mixed Ancestry, Asian Indian and Xhosa were estimated to be in the range of 3 (D4S2364) to 12 (D9S2157) alleles, the total number of alleles over all loci ranged from 100 to 204, the allelic richness ranged from 3.612 to 10.307 and the heterozygosity ranged from 0.4360 to 0.8073. Genetic distance was least between Afrikaner and Asian Indian and highest between Xhosa and Mixed Ancestry. Deviations from Hardy-Weinberg equilibrium were not observed for most of the loci. The low mean FIS (-0.027) and FIT (-0.010) and FST (0.017) values across the populations indicated low level of inbreeding within (FIS) and among (FST) the populations. The Asian Indian population showed higher levels of the inbreeding coefficient, indicating less gene exchange between it and other populations. These 8 markers can be used for genetic investigations and assessing population structure. The study contributed to the knowledge and genetic characterization of four South African populations. In addition, these MiniSTRs prove to be useful in cases where more genetic information is needed. / South Africa