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Marine bivalves are a group of species composed of clams, mussels and oysters. Bivalves are keystone species in coastal ecosystems and represent an increasingly important segment of the global aquaculture industry. Domestication of shellfish species is in the early stages, with few organized breeding programmes and a heavy reliance on wild seed. Consequently, the development and use of genomic markers may significantly assist shellfish aquaculture breeding and production. However, molecular genetic markers typically exhibit unusual patterns of segregation in bivalve species, which result in deviations from Mendelian expectations, and could potentially limit their use in parental assignment, mapping of quantitative trait loci and genomic prediction. Previous studies have suggested that segregation distortions originate at the larval stage, as a result of the linkage of markers to deleterious mutations. This high genetic load has been associated with the high fecundity of bivalve species. However, no direct evidence of a high incidence of de novo mutations has been provided. The aim of this thesis is to gain further insight into segregation distortions in bivalve species by studying the phenomenon at a genome-wide scale, using modern high-throughput sequencing technology. The studies presented in this thesis derive from experiments involving genotyping of parents and offspring from pair-crosses of three different bivalve species (the Pacific oyster Crassostrea gigas, the Blue mussel Mytilus edulis, and the GreenshellTM mussel Perna canaliculus) using high throughput sequencing and SNP arrays. The parent and offspring genotype data were used to characterize patterns of segregation distortion at a genome-wide level, followed by exploratory analyses to test hypotheses related to possible causes of this distortion. Three main findings resulted from the genome-wide analysis of segregation patterns. First, by using Restriction site Associated DNA sequencing (RAD-Seq) we observe that technical artefacts are more widespread than previously considered, contributing to apparent distortions via unreliable genotype calls. By analysing read depth data from RAD-Seq, we suggest that apparent homozygous genotype calls may actually be hemizygous, suggesting a very high frequency of null alleles which contribute to distorted segregation patterns. Bioinformatic pipelines to improve RAD-Seq locus assembly and marker genotyping for bivalve species are presented. Second, by using a high-density SNP array and RAD-Seq in pair crosses of Pacific oyster and aligning to the reference genome assembly, we find that segregation distortions cover extensive regions of the genome, and that certain genomic regions are consistently distorted in different families. Finally, following previous suggestions that the reproductive strategies of bivalve species may favour a high mutation rate, we provide preliminary evidence of a high incidence of de novo mutations that appear spontaneously (i) during male and female gamete formation and (ii) post-zygotically, during larval development. This putative high de novo mutation rate is likely to also contribute to deviations from Mendelian inheritance patterns in these species. New genomic technologies have allowed us to gain substantial insight into the intriguing yet poorly understood phenomena related to inheritance in bivalve species. The results have both fundamental and practical implications for genetic analysis interpretation and selective breeding for aquaculture in this large and highly diverse group of species.

Phytophthora root and stem rot caused by Phytophthora sojae Kaufm. & Gerd. is one of the most damaging diseases of soybean, with an estimated worldwide loss of revenue of $1-2 billion per year. Management is principally done by planting cultivars with resistance. Monogenic race specific resistance genes to P. sojae (Rps) confer resistance to pathogen strains carrying the virulence gene (Avr). The durability of a deployed gene in the field is limited by generation of new virulence pathotypes of P. sojae that can evade the Rps-mediated immunity. Rps8 was identified in the South Korean landrace PI 399073 and to facilitate its introduction in commercial cultivars, molecular markers closely linked with the locus are required. These markers can also assist in the cloning of this gene, allowing us to enrich the knowledge on: the genomic organization and structure of Rps genes and the study of soybean-P. sojae race specific interactions. In this study, resistance to P. sojae was evaluated on eight Williams (rps8/rps8) x PI 399073 (Rps8/Rps8) populations, and one PI 399073 (Rps8/Rps8) x PI 408211B (multiple Rps genes) population. In the Williams x PI 399073 crosses, phenotypic ratios were highly skewed with an excess of Rps8/Rps8 lines, maintenance of heterozygosity and few rps8/rps8 lines. A graphical genotype was generated from three Williams x PI 399073 BC4F2:3 populations as Rps8 was associated with a 2.23 Mbp region on chromosome 13. The linkage of this region with Rps8 was confirmed in BC4F4:5 generation. In a PI 399073 x PI 408211B F4:5 a different locus which conferred resistance to P. sojae isolate Butmu was identified adjacent to Rps8. This locus segregates as a single dominant gene and this region in this population was segregating in a Mendalian fashion. Male gametogenesis was evaluated in the parental genotypes and heterozygous lines at the Rps8 region. In the parent, PI 399073, a mix of abnormal meiotic products was observed. In selected heterozygous lines from one of the populations with segregation distortion, meiotic abnormalities as well as DNA in microcytes were observed. To summarize, in PI 399073, resistance to P. sojae on chromosome 13 could be comprised of more than one Rps gene and sequencing of this region will be crucial to elucidate its complexity. Markers linked with the two resistance loci can be used for the screening of breeding lines. Meiotic abnormalities may have contributed to the segregation distortion of Rps8 in the Williams x PI 399073 populations, however, further studies would be required to determine the meiotic fate of this genomic region.

The potential benefits of plant genetic engineering for disease and pest resistance have been widely acknowledged in many studies, and although genetically modified crops are still encountering public wariness, these benefits warrant continued exploration. Because of its intrinsic economic benefits, the development of true potato seed (TPS) cropping systems has been instituted in many regions of the world. The incorporation of transgenic resistance could further the economic gain of farmers who are seeking ways to sustain their livelihood in the most efficient way possible. It is, however, largely unresearched how sexual hybridization of a transgenic crop would affect the behavior of a transgene in the resultant progeny. In the initial part of this study, transgenic lines were developed with a Cry3Aa transgene. These plants were then used in 4x-4x reciprocal crosses and 4x-2x hybridization schemes to determine the stability of the transgene after sexual hybridization. There was no observed parent of origin effect on transgene expression; however, a highly significant, non-mendelian inheritance of the Cry3Aa transgene was seen in the maternally inherited transgene of one set of progeny from a reciprocal cross. Additional transgenic lines of potato were developed with a PVY-O coat protein transgene. These plants were challenged with PVY-O and monitored for symptoms visually and for virus serologically. One transgenic line exhibited complete resistance to PVY-O while two others showed a delay in symptom occurrence. Further examination of the expression levels of the PVY-O coat protein transgene will be necessary to determine the type and usefulness of the observed resistance.

Diploid potato populations between a primitive cultivated species, Solanum phureja, and a weedy species, S. chacoense, were used to examine the segregation of microsatellite markers and three traits in backcrosses. Two of the traits, anther culture competence and 2n pollen production, originated from S. phureja whereas the third, leptine production (a specific glycoalkaloid known to convey resistance to the Colorado potato beetle) originated from S. chacoense. Using CP2, a self-incompatible F₁ hybrid originating from a cross between S. chacoense clone 80-1 and S. phureja clone 1-3, three populations were developed: 1-3 x CP2 (PBCp), CP2 x 1-3 (PBCc), and CP2 x 80-1 (CBC). For the microsatellite study, four simple sequence repeat (SSR) primer pairs that amplified fragments within potato sequences found in the GenBank were used to look at segregation ratios in our backcross populations and to eliminate possible spurious genotypes bearing non-parental alleles in these populations. Seventeen spurious genotypes were discarded from PBCp; none was found in PBCc or CBC. Two SSR loci showed skewed segregation in PBCp (favoring transmissnion of the allele originally found in 80-1), PBCc showed normal segregation at all loci, and CBC showed distorted segregation at one locus (revealing a deficiency of homozygotes). In the study of anther culture, three components of ACR were investigated in a preliminary study: 1) embryos produced per anther (EPA), 2) embryo regeneration rate and 3) percentage of monoploids (2n=1x=12) among regenerants. CP2 was intermediate, 80-1 was low, and 1-3 was high for ACR. Only EPA was selected for further characterization in our populations. PBCp (78 genotypes) and CBC (57 genotypes), were characterized for anther culture response ACR/EPA in a series of studies. Nine high and ten low selections were identified in CBC, and ten high and ten low selections were identified in PBCp. EPA selections were used for bulk segregant analysis (BSA) using 214 RAPD primers. Two bands, one amplified by OPQ-10 and another by OPZ-4 were linked in coupling and in repulsion, respectively, to ACR in PBCp. One band amplified by OPW-14 primer was linked in coupling to ACR in CBC. One-way ANOVAs for data from remaining genotypes of the populations verified linkage of the markers to ACR/EPA. For 2n pollen production, a total of 77 PBCp genotypes was characterized; 80-1 produces low % 2n pollen, and 1-3 produces high % 2n pollen. Pollen samples were stained with propidium iodide and examined by flow cytometry. The frequency of 2n pollen varied continuously from 1.7 % to 40.6 % among the 41 genotypes that flowered sufficiently to allow three separate pollen collections. Variation due to the environment was observed where the frequency of 2n pollen appeared greater over a range of genotypes on single collection days. BSA could not be used due to limited population size and a low number of selections at the extremes of the distribution of phenotypes. The continuous variation for 2n pollen production suggests multigenic control of the trait. In the study of leptine content in reciprocal backcross populations, 87 genotypes within PBCp, and 42 genotypes within PBCc were characterized using gas chromatography of leaf samples. CP2 was intermediate, 1-3 had zero, and 80-1 was high for leptine content in the foliage. Leptines were present in low levels in 43 of 87 genotypes in PBCp, indicating simple genetic control. In PBCc, only 7 of 42 genotypes expressed leptines, generally at a higher level than in PBCp, indicating cytoplasmic inheritance. Ten high and ten nil selections within PBCp, and seven high and eight nil selections within PBCc were used for BSA using 214 RAPD primers. Three primers OPQ-2, OPT-16 and OPT-20 amplified bands segregating with high bulks in both populations. These markers were linked in coupling to leptine content in PBCp. Linkage was verified by ANOVAs for leptine content in the entire population.