Monoploid potato genotypes represent plant material that is free from the "genetic load" of lethal and severely deleterious alleles normally present in the highly heterozygous cultivated potato species. Field evaluations enabled the identification of agronomically superior monoploid potato genotypes from a population of more than 100 anther-derived monoploids. Chemical fusion and electrofusion between pairs selected from 31 superior monoploids resulted in the production of three different groups of intermonoploid somatic hybrids. The hybridity of somatic hybrid plants and calluses was confirmed through PCR-based amplification of simple sequence repeat (SSR) sequences in the potato genome. Polymorphic SSR loci between the monoploid parents of a particular group of somatic hybrids were used to separate true somatic hybrids (heterozygous at the loci) from parental somaclones regenerating from unfused protoplasts (homozygous for one parental band at the loci). One group of somatic hybrids (SH1, SH2 and SH2B) was of particular interest because it resulted from the fusion of a S. phureja monoploid to a high acetylleptinidine-producing monoploid derived from an F1 hybrid between S. chacoense and S. phureja. The leptine acetylleptinidine (ALD) is produced only by some accessions of S. chacoense Bitt. and provides resistance to feeding by the Colorado potato beetle (Leptinotarsa decemlineata Say) when present in sufficient concentrations. The somatic hybrids produced moderate levels of ALD in leaves and stems (roughly 60% that of a high ALD-producing S. chacoense clone). Pollinations of SH1, SH2 and SH2B by several diploid and tetraploid potato clones resulted in three fruit on SH2, one fruit on SH2B and no fruit on SH1. Two resulting progeny populations of SH2 [SH2A = SH2 × S. andigena 8-1 (4x); SH2P = SH2 × S. phureja 66AP11-53 (2x)] expressed higher fertility than the original somatic hybrids and were sexually crossed as both male and female parents to S. tuberosum cv. Atlantic. All of the SH2 progeny populations expressed acetylleptinidines, albeit at lower levels than the SH2 somatic hybrid, providing strong evidence that the genes controlling acetylleptinidine production are dominant. Variation for ALD expression in the SH2 progeny indicated one or a few genes with additive effect controlling the ALD trait. In addition, the choice of male parent in sexual crosses to SH2 affected subsequent ALD expression in progeny populations. The SH2 progeny represent an important first step towards transferring acetylleptinidines to cultivated potato. SH1, SH2 and SH2B appeared to be negatively affected by an unusually high ploidy (hexaploid, 6x). Field-grown plants produced many tubers (mean = 35) of low weight (mean = 10.4 g) and were stunted in appearance. Anther culture of SH2 yielded triploid regenerants (3x). These regenerants may be more phenotypically normal than the original somatic hybrids because of lower ploidy. Segregation of SSR alleles in the triploid anther culture regenerants provided evidence that the hexaploid somatic hybrid SH2 genome is comprised of four homologous genomes of CP2-103 (the high leptine-producing monoploid) and two homologous genomes of 13-14 203 (the S. phureja monoploid). / Master of Science

Microsatellites are strings of short DNA motifs (≤6 bp) repeated in tandem across genomes of both prokaryotes and eukaryotes. In 20 years, they became popular genetic markers, successfully employed in the field of genetic mapping and gene hunting, as well as to address various biological questions at the individual, family, population and species level. However, evolutionary and demographic inferences from microsatellite polymorphism are hampered by controversy and ambiguity in the mutational processes of microsatellite sequences. Drawing on new data from genome projects, I review in Chapter 1 the concept of a microsatellite life cycle, which hypothesizes that microsatellites follow a life cycle from birth, through expansion, contraction, death and potentially resurrection. To document and understand this integrative concept of evolution, which could help improve current models of microsatellite evolution, there is an implicit need to study the evolution of microsatellites above the species level. A prerequisite of such comparative studies is therefore to find microsatellite loci that are conserved between different species. The near or full completion of many vertebrate genomes and their alignment against one another offer the ultimate approach to find genomic elements conserved over a large evolutionary scale. In Chapter 2, I present a new comprehensive method to find conserved microsatellites in whole genomes. Using the multiple-alignment of the human genome against those of 11 mammalian and five non-mammalian vertebrates, I examine the genomewide conservation of microsatellites, and challenge the general assumption that microsatellites are too labile to be maintained in distant species. In Chapter 3, I present similar results using the alignment of the newly sequenced platypus genome against those of three mammals, the chicken and the lizard, and incorporate these data into the framework created by the 17-genome analysis. This enlarged dataset was ground for attempting to reconstruct a vertebrate phylogeny from the presence/absence of microsatellites in the different genomes. Maximum parsimony analyses resulted in a tree much similar to that of the current view of the vertebrate phylogeny, while Bayesian analyses showed some discrepancies. This work opens a way for novel theoretical developments regarding the inference of ancestral states of microsatellites. In Chapter 4, I show how knowledge on conserved microsatellite sites can help for the development of a set of comparative primers useful across the Mammalia; implementing a similar protocol, nine conserved dinucleotide repeats were genotyped in 20 unrelated individuals of 18 species (nine sister species) encompassing the mammalian phylogeny, including marsupials and monotremes, and four microsatellites were sequenced in 4 individuals per species. My results emphasize conserved microsatellites as a new resource for genetic mapping and population studies. Finally, in Chapter 5, I recount the unexpected extent of structural change among mammalian orthologous microsatellites, including change of complexity, motif replacement and overall length variability. Altogether, these findings provide a comprehensive framework that may help in many areas of research, including molecular ecology, genome mapping, population genetics, and genome and microsatellite evolution.

Microsatellites are strings of short DNA motifs (≤6 bp) repeated in tandem across genomes of both prokaryotes and eukaryotes. In 20 years, they became popular genetic markers, successfully employed in the field of genetic mapping and gene hunting, as well as to address various biological questions at the individual, family, population and species level. However, evolutionary and demographic inferences from microsatellite polymorphism are hampered by controversy and ambiguity in the mutational processes of microsatellite sequences. Drawing on new data from genome projects, I review in Chapter 1 the concept of a microsatellite life cycle, which hypothesizes that microsatellites follow a life cycle from birth, through expansion, contraction, death and potentially resurrection. To document and understand this integrative concept of evolution, which could help improve current models of microsatellite evolution, there is an implicit need to study the evolution of microsatellites above the species level. A prerequisite of such comparative studies is therefore to find microsatellite loci that are conserved between different species. The near or full completion of many vertebrate genomes and their alignment against one another offer the ultimate approach to find genomic elements conserved over a large evolutionary scale. In Chapter 2, I present a new comprehensive method to find conserved microsatellites in whole genomes. Using the multiple-alignment of the human genome against those of 11 mammalian and five non-mammalian vertebrates, I examine the genomewide conservation of microsatellites, and challenge the general assumption that microsatellites are too labile to be maintained in distant species. In Chapter 3, I present similar results using the alignment of the newly sequenced platypus genome against those of three mammals, the chicken and the lizard, and incorporate these data into the framework created by the 17-genome analysis. This enlarged dataset was ground for attempting to reconstruct a vertebrate phylogeny from the presence/absence of microsatellites in the different genomes. Maximum parsimony analyses resulted in a tree much similar to that of the current view of the vertebrate phylogeny, while Bayesian analyses showed some discrepancies. This work opens a way for novel theoretical developments regarding the inference of ancestral states of microsatellites. In Chapter 4, I show how knowledge on conserved microsatellite sites can help for the development of a set of comparative primers useful across the Mammalia; implementing a similar protocol, nine conserved dinucleotide repeats were genotyped in 20 unrelated individuals of 18 species (nine sister species) encompassing the mammalian phylogeny, including marsupials and monotremes, and four microsatellites were sequenced in 4 individuals per species. My results emphasize conserved microsatellites as a new resource for genetic mapping and population studies. Finally, in Chapter 5, I recount the unexpected extent of structural change among mammalian orthologous microsatellites, including change of complexity, motif replacement and overall length variability. Altogether, these findings provide a comprehensive framework that may help in many areas of research, including molecular ecology, genome mapping, population genetics, and genome and microsatellite evolution.