O desvio de segregação, processo biológico definido pela formação de progênie cujas proporções genotípicas diferem das predições mendelianas, pode apresentar diferentes causas: a segregação não aleatória dos cromossomos durante a meiose, a seleção gamética e a viabilidade pós-zigótica diferencial. A fim de investigar a distorção de segregação em humanos, estudamos uma família com transmissão preferencial paterna de uma alteração patogênica no gene CAPN3(CAPN3 c.759_761del), previamente associada à distrofia muscular de cinturas do tipo 2A (LGMD2A). Inicialmente, definimos uma região com 2,1 Mb de extensão, presente na maior parte dos indivíduos da família. O sequenciamento direto de 14 genes contidos nesse intervalo não revelou variantes raras que pudessem estar diretamente associadas à vantagem da subpopulação de gametas portadores da alteração em CAPN3. Entretanto, a presença de variantes comuns distribuídas em cinco genes da região pode indicar que a distorção de segregação observada é consequência da interação, em nível proteico, de pequenas alterações genômicas, resultando no desempenho diferencial de tais células gaméticas. Além disso, utilizamos outra abordagem: espermatozoides de indivíduos saudáveis foram selecionados segundo sua motilidade e as frequências alélicas de cada loco em heterozigose foram comparadas entre células lentas e rápidas, a fim de identificarmos regiões suscetíveis ao desvio de segregação. Alguns resultados estatisticamente significantes foram obtidos para regiões que contêm genes envolvidos na reação acrossômica e na motilidade espermática, como PDE1C e PDE4D. Isso nos sugere que tais processos constituem alvos da seleção, o que pode culminar em formação de progênie com proporções que fogem às predições mendelianas. Esses achados são importantes porque possibilitam a ampliação de nossos conhecimentos acerca do desvio de segregação e seu impacto na espécie humana, considerando ainda possíveis efeitos na fertilidade masculina / The transmission ratio distortion (TRD), a biological process defined as a deviation from Mendelian predictions, is caused by different mechanisms: nonrandom segregation of chromosomes during meiosis or gametic and postzygotic viability selection. In order to investigate TRD in humans, we have studied a family with an overtransmitted pathogenic deletion in the CAPN3 gene (CAPN3 c.759_761del), previously associated to limb-girdle muscular dystrophy type 2A (LGMD2A). Initially, it was possible to define a 2.1 Mb region which was present in most of the individuals. The direct sequencing of 14 genes contained in this interval did not reveal rare variants that could be responsible for the advantage of gametes carrying the CAPN3 mutation. Nevertheless, common variants identified in five genes could indicate that the observed transmission distortion is caused by the interaction among proteins with small dissimilarities, resulting in differential performance of these gametic cells. Subsequently we developed another approach: spermatozoa from healthy individuals were sorted according to their motility and allelic frequencies at each locus in heterozygous state were compared in order to identify genomic regions susceptible to TRD. Surprisingly, some statistically significant results were achieved for regions containing genes involved with acrosome reaction and sperm motility, as PDE1 and PDE4, suggesting these processes are targets of the selection that ends in offspring with proportions skewed away from the Mendelian predictions. These results are important for enlarge our knowledge about TRD and its impact in humans, considering possible effects in male fertility

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.

O desvio de segregação, processo biológico definido pela formação de progênie cujas proporções genotípicas diferem das predições mendelianas, pode apresentar diferentes causas: a segregação não aleatória dos cromossomos durante a meiose, a seleção gamética e a viabilidade pós-zigótica diferencial. A fim de investigar a distorção de segregação em humanos, estudamos uma família com transmissão preferencial paterna de uma alteração patogênica no gene CAPN3(CAPN3 c.759_761del), previamente associada à distrofia muscular de cinturas do tipo 2A (LGMD2A). Inicialmente, definimos uma região com 2,1 Mb de extensão, presente na maior parte dos indivíduos da família. O sequenciamento direto de 14 genes contidos nesse intervalo não revelou variantes raras que pudessem estar diretamente associadas à vantagem da subpopulação de gametas portadores da alteração em CAPN3. Entretanto, a presença de variantes comuns distribuídas em cinco genes da região pode indicar que a distorção de segregação observada é consequência da interação, em nível proteico, de pequenas alterações genômicas, resultando no desempenho diferencial de tais células gaméticas. Além disso, utilizamos outra abordagem: espermatozoides de indivíduos saudáveis foram selecionados segundo sua motilidade e as frequências alélicas de cada loco em heterozigose foram comparadas entre células lentas e rápidas, a fim de identificarmos regiões suscetíveis ao desvio de segregação. Alguns resultados estatisticamente significantes foram obtidos para regiões que contêm genes envolvidos na reação acrossômica e na motilidade espermática, como PDE1C e PDE4D. Isso nos sugere que tais processos constituem alvos da seleção, o que pode culminar em formação de progênie com proporções que fogem às predições mendelianas. Esses achados são importantes porque possibilitam a ampliação de nossos conhecimentos acerca do desvio de segregação e seu impacto na espécie humana, considerando ainda possíveis efeitos na fertilidade masculina / The transmission ratio distortion (TRD), a biological process defined as a deviation from Mendelian predictions, is caused by different mechanisms: nonrandom segregation of chromosomes during meiosis or gametic and postzygotic viability selection. In order to investigate TRD in humans, we have studied a family with an overtransmitted pathogenic deletion in the CAPN3 gene (CAPN3 c.759_761del), previously associated to limb-girdle muscular dystrophy type 2A (LGMD2A). Initially, it was possible to define a 2.1 Mb region which was present in most of the individuals. The direct sequencing of 14 genes contained in this interval did not reveal rare variants that could be responsible for the advantage of gametes carrying the CAPN3 mutation. Nevertheless, common variants identified in five genes could indicate that the observed transmission distortion is caused by the interaction among proteins with small dissimilarities, resulting in differential performance of these gametic cells. Subsequently we developed another approach: spermatozoa from healthy individuals were sorted according to their motility and allelic frequencies at each locus in heterozygous state were compared in order to identify genomic regions susceptible to TRD. Surprisingly, some statistically significant results were achieved for regions containing genes involved with acrosome reaction and sperm motility, as PDE1 and PDE4, suggesting these processes are targets of the selection that ends in offspring with proportions skewed away from the Mendelian predictions. These results are important for enlarge our knowledge about TRD and its impact in humans, considering possible effects in male fertility

<p>Speciation has occurred countless times throughout history, and yet the genetic mechanisms that lead to speciation are still missing pieces. Here, we describe the genetics of two processes that can act alone or together to cause speciation: hybrid sterility and meiotic drive. We use the <italic>Drosophila pseudoobscura/D, persimilis</italic> species as a model system to study these processes. We expanded on a prior study and saw little variation in strength of previously known hybrid sterility alleles between distinct strains of <italic>D. persimilis</italic> and the Bogota subspecies of <italic>D. pseudoobscura</italic>. Introgression of an autosomal, noninverted hybrid sterility allele from the USA subspecies of <italic>D. pseudoobscura</italic> into <italic>D. persimilis</italic> demonstrated that the <italic>D. pseudoobscura</italic> copy of a <italic>D. persimilis</italic> hybrid sterility factor also causes hybrid male sterility in a <italic>D. pseudoobscura bogotana</italic> background. This allelism suggests that the introgressed allele is ancestral, but was lost in the Bogota lineage, or that gene flow between <italic>D. pseudoobscura</italic> USA and <italic>D. persimilis</italic> moved the sterility-conferring allele from <italic>D. persimilis</italic> into <italic>D. pseudoobscura</italic>. To further understand the genetic basis of speciation, we asked if meiotic drive in <italic>D. persimilis</italic> is associated with hybrid sterility seen in <italic>D. persimilis/D. pseudoobscura</italic> hybrids. QTL mapping of both traits along the right arm of the X chromosome, where both drive and hybrid sterility loci are found, suggest that some of the causal loci overlap and may be allelic.</p> / Dissertation

Selfish genes that bias their own transmission during gametogenesis can spread rapidly in populations, even if they contribute negatively to the fitness of their host. Driving X chromosomes provide a clear example of this type of selfish propagation. These chromosomes, which are found in a broad range of taxa including plants, mammals, and insects, can have important evolutionary and ecological consequences. In this thesis, I report a new case of X chromosome drive (X drive) in a widespread woodland fly, Drosophila testacea. I show that males carrying the driving X (SR males) sire 80-100% female offspring, and that the majority of sons produced by SR males are sterile and appear to lack a Y chromosome. This suggests that meiotic defects involving the Y chromosome may underlie X drive in this species. Abnormalities in sperm cysts of SR males reflect that some spermatids are failing to develop properly, confirming that drive is acting during gametogenesis. Further, I show that SR males possess a diagnostic X chromosome haplotype that is perfectly associated with the sex ratio distortion phenotype. Phylogenetic analysis of X-linked sequences from D. testacea and related species strongly suggests that the driving X arose prior to the split of D. testacea and its sister species, D. neotestacea and D. orientacea. Suppressed recombination between the XST and XSR due to inversions on the XSR likely explains their disparate evolutionary histories. By screening wild-caught flies using progeny sex ratios and a diagnostic X-linked marker, I demonstrate that the driving X is present in wild populations at a frequency of ~10% and that autosomal suppressors of drive are segregating in the same population. Both SR males and homozygous females for the driving X have reduced fertility, which helps to explain the persistence of the driving X over evolutionary timescales. The testacea species group appears to be a hotspot for X drive, and D. testacea is a promising model to compare driving X chromosomes in closely related species, some of which may even be younger than the chromosomes themselves. / Graduate / 2019-04-16

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. / Master of Science

Diploid potato populations between a primitive cultivated species, <I>Solanum phureja</I>, and a weedy species, <I>S. chacoense</I>, were used to examine the segregation of microsatellite markers and three traits in backcrosses. Two of the traits, anther culture competence and 2<I>n</I> pollen production, originated from <I>S. phureja</I> whereas the third, leptine production (a specific glycoalkaloid known to convey resistance to the Colorado potato beetle) originated from <I>S. chacoense</I>. Using CP2, a self-incompatible F₁ hybrid originating from a cross between <I>S. chacoense</I> clone 80-1 and <I>S. phureja</I> 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 (2<I>n</I>=1<I>x</I>=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 % 2<I>n</I> pollen, and 1-3 produces high % 2<I>n</I> 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 2<I>n</I> 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. / Ph. D.

Doctor of Philosophy / Department of Plant Pathology / John F. Leslie / Members of the genus Fusarium are widely distributed in many geographic regions of the world. This genus includes plant pathogens of many important cereal crops, e.g., wheat, maize, rice and sorghum, and of other native and economically important plants. From culture collections at Kansas State University and Universiti Sains Malaysia, strains from Southeast Asia, primarily from Malaysia and Thailand, associated with mango malformation disease, bakanae disease of rice, and stalk rot of sorghum were analyzed in sexual crosses and molecular diagnostics, e.g., Amplified Fragment Length Polymorphisms (AFLPs). Fusarium proliferatum was recovered from all three crops, with each crop also yielding some species unique to the crop, e.g. F. fujikuroi from rice, F. thapsinum from sorghum, and F. mangiferae from mango. These results are consistent with hypotheses that F. proliferatum has a wide host range while other species have much more limited host preferences. The absence from our samples of species associated with these diseases in other parts of the world suggests policies should be developed to reduce the chances of introduction of novel pathogens into Southeast Asia. Fusarium fujikuroi and F. proliferatum are closely related. They usually can be separated by sexual cross-fertility and DNA sequence analysis. However, some strains can cross irregularly and with poor fertility to produce viable interspecific hybrids. From a laboratory cross between F. fujikuroi FGSC8932 and F. proliferatum FGSC7615, 533 progeny were collected. These progeny were characterized for their AFLP genotype, mating type, gibberellic acid production, and pathogenicity on rice, onions, and apples. A recombination-based map from this interspecific cross was constructed. QTLs associated with gibberellic acid production, rice pathogenicity, and onion pathogenicity were identified. Gene segregation amongst the progeny of the F. fujikuroi × F. proliferatum cross was distorted towards F. proliferatum. Both novel and transgressive pathogenicity phenotypes were detected. Overall, this research demonstrates the potential threats that can result from an interspecific cross. These threats include pathogens with novel toxin profiles, new pathogenicity phenotypes, and more virulent strains. The variation observed among the progeny may enable isolation and characterization of genetic factors that have a role in pathogenicity, toxin production, and host specificity.

No description available.