Thesis (Ph. D.)--University of Chicago, Dept. of Ecology and Evolution, June 2000. / Includes bibliographical references. Also available on the Internet.

Thesis (PhD)--Montana State University--Bozeman, 2010. / Typescript. Chairperson, Graduate Committee: David M. Ward. Includes bibliographical references.

Thesis (Ph. D.)--Illinois State University, 1998. / Title from title page screen, viewed July 5, 2006. Dissertation Committee: David F. Weber (chair), Marjorie A. Jones, Anthony Otsuka, Derek McCracken, Radheshyam Jayaswal. Includes bibliographical references (leaves 85-91) and abstract. Also available in print.

Thesis (Ph. D.)--University of California, San Diego and San Diego State University, 2006. / Vita. Includes bibliographical references (leaves 162-174).

No description available.

Thesis (MSc (Genetics))--University of Stellenbosch, 200 5. / The Lr19 translocation is associated with deleterious agronomic effects and as a result modified forms of the translocation have been derived by different researchers in an attempt to remove the genes responsible.

Meiotic recombination is a fundamental genetic process in all sexually reproducing eukaryotes, ultimately responsible for the generation of new combinations of alleles upon which natural selection can act. It begins with the formation of programmed double stranded breaks along the genome, and ends with their repair as non-crossover or crossover recombination events. The localization of such events along the genome has important evolutionary consequences for genome structure, base composition, patterns of genetic diversity, linkage disequilibrium and introgression, along the genome, as well as in the evolution of post-zygotic hybrid sterility and speciation. Understanding how meiotic recombination events are localized is thus crucial to the proper interpretation of observed genetic variation, and to the field of population genetics as a whole. However, little is known about how most species localize recombination events. While some species localize meiotic recombination events fairly evenly along the genome (e.g., Caenorhabditis elegans or Drosophila), most species studied to date, including all yeasts, plants and vertebrates, localize the vast majority of meiotic recombination events to narrow intervals of the genome known as recombination hotspots. Within such species, there appear to be at least two general mechanisms underlying the localization of hotspots. First, in many species, including baker’s yeast, canids, birds, and plants, the vast majority of hotspots are found in close proximity with promoter-like features of the genome, such as transcriptional start sites and CpG-islands. Recombination landscapes in these species tend to be highly conserved between closely related species. Second, in mice, primates and cattle, the vast majority of hotspots are found away from promoter-like features of the genome, and at sites bound by the PRDM9 protein, which has a rapidly evolving DNA-binding specificity. Concordantly, the recombination landscapes in these species tends to be rapidly evolving. The aim of Chapter 2 of this dissertation is to characterize the distribution of mechanisms across vertebrates indirectly, by leveraging what is known about their genetic and molecular underpinnings. In particular, I consider what is known about the molecular mechanisms and evolutionary consequences of using PRDM9 to localize recombination events, and attempt to infer which vertebrate species are or are not likely to be using PRDM9 in an analogous manner. I find that PRDM9 has been lost repeatedly within vertebrates, and, moreover, that many species carry partial PRDM9 orthologs lacking one or more feature believed to be important for its role in recombination. In Chapter 3, I demonstrate that swordtail fish, which have such a partial PRDM9 ortholog, do not use PRDM9 to localize recombination events. Instead, they use promoter-like features of the genome, similar to species lacking PRDM9 altogether. This work suggests that only species carrying complete PRDM9 orthologs are likely to use them to localize recombination events, and that upon the partial or complete loss of PRDM9, species typically default to the use of promoter-like features. Beyond more immediately practical insight, understanding the phylogenetic distribution of mechanisms by which meiotic recombination events are localized along the genome will shed light on why different species employ different mechanisms. The repeated losses of PRDM9-directed recombination across vertebrates suggests that selective pressures are not always strong enough to justify the evolutionary maintenance of PRDM9. Notably, theory suggests that PRDM9’s DNA-binding specificity has to be continually evolving in order for it to localize recombination events to hotspots. This is a consequence of gene conversion acting to remove PRDM9 binding sites from the population over time. Models have been proposed in which selection favors younger PRDM9 alleles because their binding sites have experienced less erosion due to gene conversion. Nonetheless, it has remained unclear how the loss of PRDM9 binding sites might cause a reduction in fitness, principally because it has remained unclear what the evolutionary benefit of having hotspots is more generally. Recently, however, a number of studies investigating the role of PRDM9 in mediating hybrid sterility in certain crosses of musculus subspecies have implicated the erosion of its binding sites in this process. In particular, the lineage specific erosion of PRDM9 binding sites causes, in the F1 generation, the PRDM9 alleles from each parental lineage to bind primarily to the non-parental genetic background, where its binding sites have not yet been eroded. These studies suggest that there is a benefit to the symmetric binding of PRDM9 across homologous chromosomes, and that fitness is reduced as a consequence of asymmetry in PRDM9 binding. In Chapter 4 of this dissertation I develop a population genetics based model of the co-evolution of PRDM9 and its binding sites taking into consideration these recent findings. In particular, I model competition between PRDM9 binding sites and define fitness as a function of PRDM9 binding symmetry. This model demonstrates that PRDM9 binding symmetry will decrease over time in randomly mating populations, and that selection for symmetric binding is sufficient to drive the rapid turnover of PRDM9 alleles. Importantly, the requirement for symmetry in this model shapes the recombination landscape by favoring highly skewed binding distributions. This model thus provides theoretical support for the hypothesis that a requirement for symmetry might underlie the evolutionary advantage of recombination hotspots.

No description available.

<p> The phenomenon of genetic recombination is of fundamental importance to the evolution and adaptation of species, and is a valuable laboratory aid to the biological scientist. Probable mechanisms of control of recombination are largely unknown, due partly to the difficulty of obtaining artificial mutants affecting the process. The studies reported here avoid this difficulty by the use of different factors controlling recombination which occur naturally in the species Neurospora crassa and N. sitophila. Studies of hybrid N. crassa strains carrying factors from N. sitophila are described, and some models for the control of genetic recombination are discussed. </p> / Thesis / Master of Science (MSc)

La recombinaison génétique est un processus biologique fondamental, ayant lieu au cours de la méiose et assurant la bonne ségrégation des chromosomes, ainsi que le maintien de la variabilité génétique grâce au brassage intrachromosomique. La recombinaison a été étudiée dans de nombreuses espèces, en particulier chez les Mammifères et les animaux d’élevage, comme les bovins, les porcs ou les ovins. Dans tous les cas, une variation du taux de recombinaison a été observée entre les individus et il a été démontré qu’elle était héritable et sous déterminisme génétique. Dans certaines espèces, des cartes génétiques ont également été construites, ce qui a permis de localiser les crossingovers et de détecter de très petites zones du génome où la recombinaison était importante : les points chauds. En race ovine Lacaune, de nombreuses données de génotypages sont disponibles, notamment grâce à l’existence de deux puces : une de moyenne densité avec 54 000 marqueurs et une de haute densité avec 600 000 marqueurs. Deux jeux de données étaient donc disponibles ; un jeu de données familial avec près de 6 000 individus apparentés et génotypés pour les 54 000 marqueurs et un jeu de données comportant 70 Lacaune non apparentés et génotypés pour les 600 000 marqueurs. Des cartes génétiques ont donc été créées pour ces deux jeux de données. Avec les animaux non apparentés, environ 50 000 points chauds ont été détectés. Le jeu de données familial a permis d’observer des motifs de distribution de la recombinaison communs aux autres Mammifères. Enfin, la combinaison des deux jeux de données a révélé la présence de signatures de sélection et a permis de créer une carte génétique de haute densité. De plus, une variation du taux de recombinaison a été observée entre les individus et a pu être liée à l’existence de 2 QTLs majeurs sur les chromosomes 6 et 7. Des gènes candidats plus ou moins bien connus ont pu être proposés, voire étudiés : RNF212 et HEI10. De plus, une comparaison avec une autre population ovine a permis de montrer que les cartes de recombinaison étaient quasiment identiques, mais que le taux de recombinaison individuel était soumis à un déterminisme génétique différent. Il a également été possible de proposer une application concrète pour l’utilisation des cartes génétiques en sélection génomique, grâce à la création de puces basse densité pouvant être utilisées pour l’imputation des reproducteurs et donc favoriser le génotypage et la sélection génomique à moindre coût. / Genetic recombination is a fundamental biological process, which occurs during the meiosis. It allows the good segregation of the chromosomes and contributes to maintain the genetic diversity. Recombination was already studied in a lot of different species, especially in mammals and in farm animals, such as the pig, the cattle or the sheep. In each case, a variation of the recombination rate between the individuals was observed. This variation was heritable and under genetic determinism. In some species, genetic recombination maps were also created, which allowed to localize the crossovers and to detect really tiny genomic regions where the recombination is huge: the recombination hotspots. In the Lacaune breed sheep, a lot of genotyping data are available thanks to two existing arrays: a first with a medium density of markers (about 54,000 markers) and a second with a high density of markers (about 600,000 markers). Two datasets were thus available: a familial dataset with about 6,000 animals genotyped for the 54,000 markers and a dataset of 70 unrelated Lacaune genotyped for the 600,000 markers. Genetic recombination maps were created for these two datasets. With the 70 unrelated Lacaune, about 50,000 hotspots were detected. The familial dataset allowed to observe the mammals common recombination patterns. Finally, when the two datasets were combined, selection signatures were revealed and a high density recombination map were created. Furthermore, a variation of the recombination rate within the individuals was observed and was associated to 2 main QTLs on the chromosomes 6 and 7. Already known, or not, candidate genes were proposed and sometimes studied: especially RNF212 and HEI10. Finally, a comparison with another sheep breed revealed that the genetic recombination maps were really similar, but the individual recombination rate was under a different genetic determinism. A concrete application of the genetic recombination map in genomic selection was also proposed thanks to the creation of lowdensity SNPs sets, which could be used to impute the animals and thus to improve the genotyping and the genomic selection for lessercosts.