Gametophytic self-incompatibility limits the ability to derive inbred lines of potato through self-pollination and is prevalent in diploid potato. Within a population of F1 hybrids between two genotypes used in potato genome sequencing, we observed fruit set on many greenhouse-grown plants. Subsequently, after controlled self-pollinations, we confirmed fruit set in 32 of 103 F1 plants. Our goal was to identify genes responsible for self-compatibility in this population and to advance selfed progeny to develop highly homozygous inbred lines. The F1 population was genotyped using a single nucleotide polymorphism (SNP) array. Polymorphic and robust SNPs were analyzed by Fisher\'s Exact Test to identify allelic states segregating with the self-compatible phenotype. Filtering 1966 SNPs to retain only those with p-values less than 0.0001 yielded 95 highly significant SNPs, with all SNPs on anchored scaffolds located on chromosome 12. Candidate genes encoding for multiple notable proteins including an S-protein homologue were identified near highly significant SNPs on the Potato Genome Browser. Seeds obtained after self-pollination of self-compatible individuals were used to advance the population for three generations. SNP chip genotyping of the S3 generation revealed entirely different SNPs segregating for self-compatibility on nine different chromosomes. Comparison of the allelic state of SNPs in the F1 and S3 generations revealed a heterozygosity reduction by 80%, with fixation of many SNPs including those surrounding the S-protein homologue. We conclude that the genes responsible for segregation of self-compatibility in the S3 generation are different from those in the F1 generation. / Master of Science

<p>A fundamental goal in the diverse field of evolutionary biology is reconstructing the historical processes that facilitated lineage diversification and the current geographic distribution of species diversity. Oceanic islands provide a view of evolutionary processes that may otherwise be obscured by the complex biogeographic histories of continental systems, and have thus provided evolutionary biology with some of its most lasting and significant theories. The Indian Ocean island of Madagascar is home to an extraordinarily diverse and endemic biota, and reconstructing the historical processes responsible for this diversity has consumed countless academic careers. While the flowering plant genus <italic>Coffea</italic> is but one lineage contributing to Madagascar's staggering floral diversity, it is representative of the common evolutionary theme of adaptive radiation and local endemism on the island. In this dissertation, I employ the genus <italic>Coffea</italic> as a model for understanding historical biogeographic processes in the Indian Ocean using methods of molecular phylogenetics and population genetics. In the molecular phylogenetic study of <italic>Coffea</italic> presented in chapter 2, I show that Madagascan <italic>Coffea</italic> diversity is likely the product of at least two independent colonization events from Africa, a result that contradicts current hypotheses for the single origin of this group. </p><p>Species of <italic>Coffea</italic> are known to exhibit self-incompatibly, which can have a dramatic affect on the geographic distribution of plant genetic diversity. In chapter 3, I identify the genetic mechanism of self-incompatibility in <italic>Coffea</italic> as homologous to the canonical eudicot S-RNase system. Baker's Rule suggests that self-incompatible lineages are very unlikely to colonize oceanic islands, and in chapter 4, I test this hypothesis by characterizing the strength of self-incompatibility and comparing S-RNase polymorphism in <italic>Coffea</italic> populations endemic to isolated Indian Ocean islands (Grande Comore and Mauritius) with that of Madagascan/African species. My findings suggest that while island populations show little evidence for genetic bottleneck in S-RNase allelic diversity, Mauritian endemic <italic>Coffea</italic> may have evolved a type of "leaky" self-incompatibility allowing self-fertilization at some unknown rate. Through the application of traditional phylogenetic methods and novel data from the self-incompatibly locus, my dissertation contributes a wealth of new information regarding the evolutionary and biogeographic history of <italic>Coffea</italic> in the Indian Ocean.</p> / Dissertation

abstract: Isolation-by-distance is a specific type of spatial genetic structure that arises when parent-offspring dispersal is limited. Many natural populations exhibit localized dispersal, and as a result, individuals that are geographically near each other will tend to have greater genetic similarity than individuals that are further apart. It is important to identify isolation-by-distance because it can impact the statistical analysis of population samples and it can help us better understand evolutionary dynamics. For this dissertation I investigated several aspects of isolation-by-distance. First, I looked at how the shape of the dispersal distribution affects the observed pattern of isolation-by-distance. If, as theory predicts, the shape of the distribution has little effect, then it would be more practical to model isolation-by-distance using a simple dispersal distribution rather than replicating the complexities of more realistic distributions. Therefore, I developed an efficient algorithm to simulate dispersal based on a simple triangular distribution, and using a simulation, I confirmed that the pattern of isolation-by-distance was similar to other more realistic distributions. Second, I developed a Bayesian method to quantify isolation-by-distance using genetic data by estimating Wright’s neighborhood size parameter. I analyzed the performance of this method using simulated data and a microsatellite data set from two populations of Maritime pine, and I found that the neighborhood size estimates had good coverage and low error. Finally, one of the major consequences of isolation-by-distance is an increase in inbreeding. Plants are often particularly susceptible to inbreeding, and as a result, they have evolved many inbreeding avoidance mechanisms. Using a simulation, I determined which mechanisms are more successful at preventing inbreeding associated with isolation-by-distance. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2015

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No description available.

Yes / Rapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to genomic regions of high sequence divergence and high repeat content, which are typical characteristics for loci under strong long-term balancing selection. Studying genetic diversity at such loci therefore remains challenging. Here, we investigate the feasibility and error rates associated with targeted long-read sequencing of a locus under balancing selection. For this purpose, we generated bacterial artificial chromosomes (BACs) containing the Brassicaceae S-locus, a region under strong negative frequency-dependent selection which has previously proven difficult to assemble in its entirety using short reads. We sequence S-locus BACs with single-molecule long-read sequencing technology and conduct de novo assembly of these S-locus haplotypes. By comparing repeated assemblies resulting from independent long-read sequencing runs on the same BAC clone we do not detect any structural errors, suggesting that reliable assemblies are generated, but we estimate an indel error rate of 5.7×10−5. A similar error rate was estimated based on comparison of Illumina short-read sequences and BAC assemblies. Our results show that, until de novo assembly of multiple individuals using long-read sequencing becomes feasible, targeted long-read sequencing of loci under balancing selection is a viable option with low error rates for single nucleotide polymorphisms or structural variation. We further find that short-read sequencing is a valuable complement, allowing correction of the relatively high rate of indel errors that result from this approach. / This study was supported by a grant from the Swedish Research Council to T.S.

L’auto-incompatibilité est une barrière génétique qui permet à une plante de reconnaître et rejeter son propre pollen tout en acceptant le pollen d’individus moins apparentés d’un point de vue génétique. Chez les Brassicacées, l’auto-incompatibilité est contrôlée par un locus hautement polymorphe appelé le locus S, qui contient les déterminants mâle et femelle. Le stigmate exprime le déterminant femelle de l’auto-incompatibilité, S-LOCUS RECEPTOR KINASE (SRK). Chez Brassica oleracea, la localisation subcellulaire d’SRK est unique en son genre : le récepteur est localisé principalement au niveau des endosomes et dans une moindre mesure à la membrane plasmique.Nous avons étudié la fonction de la localisation endosomale de SRK chez Arabidopsis thaliana. Premièrement, nous avons réintroduit l’auto-incompatibilité chez Arabidopsis thaliana grâce à l’expression d’un allèle fonctionnel de SRK en provenance d’Arabidopsis lyrata (une espèce auto-incompatible). Deuxièmement, nous avons montré qu’un mutant perte de fonction de DYNAMIN-RELATED PROTEIN1A, une protéine requise pour l’endocytose, abolissait l’auto-incompatibilité. Nos résultats suggèrent que l’endocytose est requise pour l’auto-incompatibilité, et que SRK pourrait activer sa voie de signalisation depuis les endosomes. / Self-incompatibility is a genetic barrier by which a plant recognizes and rejects its own pollen while allowing pollen from more distantly related plants to germinate. In the Brassicacea family, it is controlled by a highly polymorphic locus called the S-locus, which contains the male and female determinants of self-incompatibility. The stigma expresses the female determinant of self-incompatibility, the plant receptor kinase (PRK) S-LOCUS RECEPTOR KINASE (SRK). In Brassica oleracea, SRK has a unique subcellular localization among PRK: the receptor is mostly localized in endosomes and to a lesser extent at the plasma membrane.We investigated the function of the endosomal localization of SRK in Arabidopsis thaliana. Firstly, we reintroduced self-incompatibility in Arabidopsis thaliana by expression of a functional SRK allele from Arabidopsis lyrata (a self-incompatible species). Secondly, we showed that a loss-of-function mutant of DYNAMIN-RELATED PROTEIN1A, a protein required for endocytosis, abolished self-incompatibility. Our results suggest that endocytosis is required for self-incompatibility, and that SRK may be signaling from endosomal compartments.

The olive (Olea europaea L.) is one of the most ancient fruit trees and has been cultivated for its oil in the Mediterranean area for thousands of years. Today, the consumption of olive oil and table olives is increasing both in traditional producing countries and the entire world. Most olive cultivars are self-incompatible and do not produce a commercial yield after self pollination. In this thesis, inflorescence architecture and sexual compatibility relationships of some olive cultivars, and gene expression in olive pistils during flowering were studied. To study the inflorescence architecture of olive, 45 inflorescences in each of the cultivars Manzanillo, Mission, and Frantoio were checked every morning from flower opening to petal fall. The flower position on the inflorescence had a highly significant effect on the opening day in all cultivars. Terminal flowers and the flowers located on the primary branches opened earlier than flowers located on the secondary branches. Flower position also had a highly significant effect on gender in Manzanillo and Mission. In Manzanillo, the secondary branches had fewer perfect flowers than the primary branches. In Mission, the secondary branches had no perfect flowers at all. In Manzanillo, perfect flowers had significantly longer petal persistence than staminate flowers. To study flower competition within the inflorescence, the distal halves, on which the flowers tend to be perfect, of 120 inflorescences in three trees of Manzanillo were removed about one month before full bloom. This resulted in a highly significant increase in the percentage of perfect flowers on the proximal halves. The effects of shoot orientation and inflorescence location on inflorescence characteristics in the cultivars Frantoio, Kalamata, and Koroneiki were also studied. For each cultivar, inflorescence characteristics in three sections of shoots (top, middle, and base) and four sides of the three selected trees (north, south, east, and west) were recorded. The statistical analysis showed that basal inflorescences were shorter and with fewer flowers but with the same percentage of perfect flowers. Shoot orientation did not have any influence on these characteristics in any of the cultivars. Sexual compatibility was assessed using two methods. In the first method, controlled crossings were performed in the cultivars Frantoio, Koroneiki, and Kalamata. The pistils were harvested one week after hand pollination and stained with 0.1% aniline blue. The styles and ovules were separated, mounted in 80% glycerol, and observed under a fluorescence microscope. In Frantoio and Koroneiki, the number of ovules penetrated by a pollen tube was used to estimate the level of sexual compatibility. In Kalamata, the numbers of ovules penetrated by pollen tubes were not significantly different between treatments; therefore, the number of pollen tubes in the lower style was used. All the cultivars studied were self- incompatible. Frantoio (as a host) was incompatible with Koroneiki and Barnea but partially compatible with Mission. Koroneiki (as a host) was incompatible with Barnea but partially compatible with Frantoio and Mission. Kalamata (as a host) was compatible with Barnea, incompatible with Mission and Koroneiki in 2004, but partially compatible with them in 2005. In the second method, eight microsatellite markers were used for genotyping three Kalamata mother trees, 40 embryos per mother tree, and all the potential pollen donors. Genotyping data were analysed using FaMoz software, and the number of embryos assigned to each putative pollen donor was determined. Paternity analysis showed that Kalamata (as a host) was self-incompatible, compatible with Barnea, Benito, and Katsourela, but incompatible with Arbequina, Azapa, and Picual. To study the gene expression in olive pistils during flowering, a genomic approach was initiated using cDNA subtractive array analysis. Total RNA was isolated from olive pistils at two developmental stages, where self-incompatibility (SI) genes are expected to be differentially expressed: 1) small green flower buds (expression of SI genes not expected) and 2) large white flower buds containing receptive pistils just prior to opening (expression of SI genes expected). From each stage, cDNA libraries were prepared and put through forward and reverse subtractive hybridisations to enrich for differentially expressed cDNAs in stage 2. Macroarrays were prepared by printing 2304 differentially expressed cDNAs onto nylon membranes and hybridised with forwardand reverse-subtracted probes. The analysis identified 90 up-regulated cDNA clones highly expressed in receptive pistils. Further subtracted and unsubtracted hybridisations confirmed up-regulation of the majority of these cDNAs. Gene expression profiles across different tissues showed that most of the genes were pistil-specific. The expression pattern of the genes showed high similarity in Kalamata, Frantoio, Barnea, and Pendolino. All the screened genes were sequenced and their similarities were searched in the NCBI database. The most redundant and interesting up-regulated clones were those similar to a receptor protein kinase-like protein. Some versions of this protein play a role in the sporophytic SI system of Brassica and the gametophytic SI system of Papaver and rye. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1325369 / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

The olive (Olea europaea L.) is one of the most ancient fruit trees and has been cultivated for its oil in the Mediterranean area for thousands of years. Today, the consumption of olive oil and table olives is increasing both in traditional producing countries and the entire world. Most olive cultivars are self-incompatible and do not produce a commercial yield after self pollination. In this thesis, inflorescence architecture and sexual compatibility relationships of some olive cultivars, and gene expression in olive pistils during flowering were studied. To study the inflorescence architecture of olive, 45 inflorescences in each of the cultivars Manzanillo, Mission, and Frantoio were checked every morning from flower opening to petal fall. The flower position on the inflorescence had a highly significant effect on the opening day in all cultivars. Terminal flowers and the flowers located on the primary branches opened earlier than flowers located on the secondary branches. Flower position also had a highly significant effect on gender in Manzanillo and Mission. In Manzanillo, the secondary branches had fewer perfect flowers than the primary branches. In Mission, the secondary branches had no perfect flowers at all. In Manzanillo, perfect flowers had significantly longer petal persistence than staminate flowers. To study flower competition within the inflorescence, the distal halves, on which the flowers tend to be perfect, of 120 inflorescences in three trees of Manzanillo were removed about one month before full bloom. This resulted in a highly significant increase in the percentage of perfect flowers on the proximal halves. The effects of shoot orientation and inflorescence location on inflorescence characteristics in the cultivars Frantoio, Kalamata, and Koroneiki were also studied. For each cultivar, inflorescence characteristics in three sections of shoots (top, middle, and base) and four sides of the three selected trees (north, south, east, and west) were recorded. The statistical analysis showed that basal inflorescences were shorter and with fewer flowers but with the same percentage of perfect flowers. Shoot orientation did not have any influence on these characteristics in any of the cultivars. Sexual compatibility was assessed using two methods. In the first method, controlled crossings were performed in the cultivars Frantoio, Koroneiki, and Kalamata. The pistils were harvested one week after hand pollination and stained with 0.1% aniline blue. The styles and ovules were separated, mounted in 80% glycerol, and observed under a fluorescence microscope. In Frantoio and Koroneiki, the number of ovules penetrated by a pollen tube was used to estimate the level of sexual compatibility. In Kalamata, the numbers of ovules penetrated by pollen tubes were not significantly different between treatments; therefore, the number of pollen tubes in the lower style was used. All the cultivars studied were self- incompatible. Frantoio (as a host) was incompatible with Koroneiki and Barnea but partially compatible with Mission. Koroneiki (as a host) was incompatible with Barnea but partially compatible with Frantoio and Mission. Kalamata (as a host) was compatible with Barnea, incompatible with Mission and Koroneiki in 2004, but partially compatible with them in 2005. In the second method, eight microsatellite markers were used for genotyping three Kalamata mother trees, 40 embryos per mother tree, and all the potential pollen donors. Genotyping data were analysed using FaMoz software, and the number of embryos assigned to each putative pollen donor was determined. Paternity analysis showed that Kalamata (as a host) was self-incompatible, compatible with Barnea, Benito, and Katsourela, but incompatible with Arbequina, Azapa, and Picual. To study the gene expression in olive pistils during flowering, a genomic approach was initiated using cDNA subtractive array analysis. Total RNA was isolated from olive pistils at two developmental stages, where self-incompatibility (SI) genes are expected to be differentially expressed: 1) small green flower buds (expression of SI genes not expected) and 2) large white flower buds containing receptive pistils just prior to opening (expression of SI genes expected). From each stage, cDNA libraries were prepared and put through forward and reverse subtractive hybridisations to enrich for differentially expressed cDNAs in stage 2. Macroarrays were prepared by printing 2304 differentially expressed cDNAs onto nylon membranes and hybridised with forwardand reverse-subtracted probes. The analysis identified 90 up-regulated cDNA clones highly expressed in receptive pistils. Further subtracted and unsubtracted hybridisations confirmed up-regulation of the majority of these cDNAs. Gene expression profiles across different tissues showed that most of the genes were pistil-specific. The expression pattern of the genes showed high similarity in Kalamata, Frantoio, Barnea, and Pendolino. All the screened genes were sequenced and their similarities were searched in the NCBI database. The most redundant and interesting up-regulated clones were those similar to a receptor protein kinase-like protein. Some versions of this protein play a role in the sporophytic SI system of Brassica and the gametophytic SI system of Papaver and rye. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1325369 / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

Fundação de Amparo a Pesquisa do Estado de Minas Gerais / The distyly is a floral polymorphism controlled genetically, where the populations present individuals with pin flowers, that possess long styles and short stamens, and individuals with thrum flowers, that possess short styles and long stamens. Their populations tend to be isoplethyc and anomalies in the distribution of pin and thrum flowers in the populations have usually been associated with the habitat fragmentation and environmental disturbances. Besides morphological characteristics of styles/stigmas anthers/pollen grains, these flowers can also present secondary differences in their morphology. Heterostylous plants usually possess a self-incompatibility system, where fruit-set occurs only after cross pollination between morphs (legitimate cross pollination). Palicourea rigida is a typically distylous species of the Rubiaceae, a family that contains the largest number of distylous species. The species is widely distributed in the Brazilian Cerrados and it is pollinated by hummingbirds. The objective of the present work was to study different populations from P. rigida comparing the distribution of pin vs. thrum individuals and other characteristics associated to heterostyly in order to verify if there were asymmetries between floral morphs and differences among areas that could be associated to environmental conditions or recent changes. The work was carried out in the Parque Estadual da Serra Caldas Novas - PESCAN (GO) and in RPPN of the Clube Caça e Pesca Itororó de Uberlândia - CCPIU (MG) where populations of P. rigida were studied in 2005 and 2006. Density, height and pin/thrum ratio were assessed for flowering individuals in both areas. Flower morphs were investigated for differences in floral morphology, nectar production, reproductive success and site of self incompatibility reactions. In spite of differences in density and individuals height, both populations were isoplethyc, with ratio between floral morphs not significantly different from 1:1. The populations were different probably due to their conservation histories, but such differences do not seem to have affected other characteristics associated to distyly. The anisoplethy was observed for populations of the species in Brasília and for other species of Palicourea. Besides the reciprocal herkogamy, with differences marked between pin/thrum styles and stamens, there were differences in the size of the anthers, stigmas and corolla that were larger in thrum flowers. The nectar production varied in volume and concentration in the two populations, but there was not a pattern that could be associated to each one of the floral morphs. There were no differences in reproductive success, which were high for the two morphs and for both populations, in spite of the species to be remarkably self-incompatible. There were differences in the site of incompatibility barriers between floral morphs that corroborated previous observations for the species and for many other species of Rubiaceae. The incompatibility reaction was more marked and interrupted pollen tube growth in the stigma of thrum flowers, while it was more variable and occurred along the style in pin flowers. All the pistils of flowers collected from both floral morphs in the study areas showed a profusion of pollen grains and pollen tubes, which indicates high pollination efficiency. The main floral visitor and pollinator, in both studied areas, was the hummingbird Eupetomena macroura. The high fruit-set indicates that the pollinators transported enough compatible pollen grains between floral morphs, although they commonly presented territorial behavior. The reproductive success was considered high, specially when compared with other self-incompatible species of the Cerrado. / A distilia é um polimorfismo floral controlado geneticamente, onde as populações apresentam indivíduos com flores longistilas, que possuem estiletes longos e estames curtos, e indivíduos com flores brevistilas, que possuem estiletes curtos e estames longos. Suas populações tendem a ser isopléticas, ou seja, com indivíduos dos dois morfos na proporção 1:1, e as anomalias referentes à distribuição dos morfos nas populações têm sido normalmente associadas à fragmentação de habitats e perturbações ambientais. Além das características morfológicas de estiletes/estigmas e anteras/grãos-de-pólen, estas flores podem ainda apresentar diferenças secundárias na morfologia. Plantas heterostílicas geralmente possuem um sistema de auto-incompatibilidade, onde só há formação de frutos nos cruzamentos entre morfos. Palicourea rigida é uma espécie tipicamente distílica de Rubiaceae, família que contém o maior número de espécies distílicas registradas. A espécie é amplamente distribuída nos cerrados brasileiros e é polinizada por beija-flores. O objetivo do presente trabalho foi estudar diferentes populações de P. rigida comparando a distribuição dos morfos florais e as características associadas à heterostilia para verificar se existem assimetrias entre os morfos e diferenças entre as áreas que pudessem ser associadas às condições ou mudanças ambientais. O trabalho foi realizado no Parque Estadual da Serra de Caldas Novas - PESCAN (GO) e na RPPN do Clube Caça e Pesca Itororó de Uberlândia - CCPIU (MG) onde foram avaliadas populações de P. rigida nos anos de 2005 e 2006. As populações foram caracterizadas quanto à densidade, altura e razão entre morfos dos indivíduos floridos. Quanto aos morfos florais, foram investigadas diferenças na morfometria, produção de néctar, sucesso reprodutivo e reações de incompatibilidade. Apesar de diferirem em densidade e altura dos indivíduos, ambas as populações foram isopléticas, com razão entre morfos não significativamente diferente de 1:1. As populações se mostraram distintas provavelmente devido à suas histórias de conservação, mas tais diferenças não parecem ter afetado as características associadas à distilia. A anisopletia foi observada para populações da espécie em Brasília e para outras espécies de Palicourea. Além da hercogamia recíproca, com diferenças marcadas entre estiletes e estames dos dois morfos, ainda houve diferenças no tamanho das anteras, dos estigmas e da corola que foram maiores em flores brevistilas. A produção de néctar variou em volume e concentração nas duas populações, mas não houve um padrão que pudesse ser associado a cada um dos morfos. Não houve diferenças quanto ao sucesso reprodutivo, que foi alto para os dois morfos e em ambas as populações, apesar da espécie ser marcadamente auto-incompatível. O sucesso reprodutivo foi considerado alto, sobretudo quando comparado com outras espécies auto-incompatíveis do Cerrado. Todos os pistilos de flores coletadas ao acaso dos dois morfos nas áreas de estudo mostraram grãos-de-pólen e tubos polínicos em profusão, o que indica alta eficiência de polinização. Houve diferença nos locais de formação das barreiras de incompatibilidade entre os morfos que corroboraram as observações anteriores para a espécie e o encontrado para várias outras Rubiaceae. De uma maneira geral a reação de incompatibilidade foi mais marcada e interrompeu o crescimento dos tubos polínicos no estigma do morfo brevistilo, enquanto foi mais variável e ocorreu ao longo do estilete no morfo longistilo. O principal visitante floral e polinizador, em ambas as áreas estudadas, foi o beija-flor Eupetomena macroura. A alta produtividade de frutos indica que os polinizadores efetivamente transportaram quantidades suficientes de grãos-de-pólen compatíveis entre os morfos, apesar de comumente apresentarem comportamento territorial. / Mestre em Ecologia e Conservação de Recursos Naturais