Tradicionalmente los programas de mejora del melocotón (Prunus persica (L.) Batsch) se centraron fundamentalmente en la obtención de genotipos elite de alta productividad, resistentes a plagas y patógenos, adaptados a diferentes zonas agroecológicas y que produzcan frutos de gran tamaño y buen aspecto. Como resultado, muchos de estos programas han obtenido cultivares de excelentes características agronómicas. No obstante, el mejoramiento selectivo hacia caracteres agronómicos puede ir en detrimento de la calidad organoléptica del fruto como fue demostrado en el caso de fresa y tomate donde algunos aromas se perdieron en el proceso de mejora (Klee and Giovannoni, 2011; Olbricht et al., 2008). En melocotón, la disminución de la calidad del fruto ha sido percibida por los consumidores y además es la mayor causa de insatisfacción de los mismos (Bruhn et al., 1991). Un probable consecuencia de esto puede ser el bajo consumo de melocotón en comparación con otras frutas como el plátano y la manzana (Crisosto, 2006). Estudios pioneros han establecido que el aroma es uno de los atributos principales por los cuales los consumidores juzgan la calidad del melocotón (Bruhn, 1995). El aroma está definido íntegramente por los compuestos volátiles orgánicos (VOCs) los cuales también contribuyen al sabor del fruto en combinación con azucares y ácidos orgánicos. Los volátiles del melocotón han sido estudiados con anterioridad, describiéndose un poco más de 100 compuestos incluyendo: lactonas, esteres, terpenos, aldehídos, ácidos carboxílicos y alcoholes entre otros [(Aubert and Milhet, 2007) y referencias incluidas]. La identificación de regiones génicas y genes candidatos para el control de los aromas del fruto resulta un punto fundamental para su posterior implementación en programas de mejora con el fin de obtener melocotones de mayor calidad. En este sentido nos propusimos la identificación de QTLs (del inglés ``Quantitative trait loci'') y genes candidatos involucrados en la producción de los compuestos volátiles del melocotón. El desarrollo reciente de un conjunto técnicas analíticas de mayor potencia permitió el advenimiento de una nueva plataforma tecnológica, la metabolómica, que contempla el análisis global de los metabolitos de un organismo permitiendo abordar la evaluación de calidad de una forma más exhaustiva. Dentro de ellas, la tecnología HS-SPME-GC-MS (del inglés ``Head Space-Solid Phase Microextraction-Gas Chromatography-Mass Spectroscopy'') es actualmente el método de elección para el análisis de volátiles debido a su alta sensibilidad, reproducibilidad y robustez (Tikunov et al., 2005). Además el análisis en conjunto de los datos derivados de la metabolómica con otras tecnologías de alto rendimiento para el análisis de expresión de genes, como lo son los microarrays, ha permitido el descubrimiento de genes implicados la producción de diversos metabolitos en Arabidopsis y tomate (Mounet et al., 2009; Saito and Matsuda, 2010; Carrera et al. 2012). En una primera instancia nos propusimos el desarrollo de una plataforma de alto rendimiento basada en HS-SPME-GC-MS para la identificación y cuantificación de compuestos volátiles en fruto de melocotón. Se ensayarán diferentes protocolos para la extracción de los compuestos volátiles con el fin de identificar el más adecuado (es decir el más sensible manteniendo la reproducibilidad y con una robustez satisfactoria). Una vez desarrollado un protocolo adecuado se analizará en paralelo la evolución de los compuestos volátiles y la expresión de genes mediante microarrays durante la maduración de diferentes genotipos de melocotón con el objetivo de identificar patrones comunes de co-regulación entre metabolitos y genes durante el desarrollo del fruto. Por último, se propuso la identificación de regiones génicas implicadas en la producción de volátiles mediante análisis de QTLs. / Sánchez, G. (2013). Cartografiado de QTL y genes candidatos asociados a metabolitos determinantes de la calidad de fruto en melocotón [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/34511

Erythrocytes infected by mature forms of the Plasmodium falciparum parasite adhere to other components of the vascular space, a behavior considered critical to the pathogenesis of severe malaria. Adhesion is mediated by the P. falciparum erythrocyte membrane protein 1 (PfEMP1), a highly variant antigen expressed by the parasite and subject to switching during the course of an infection. The host ligands of PfEMP1 include CD36, ICAM-1 and the ABO antigens. By employing a series of population- and family-based association studies from multiple African populations, we examined whether variation in the genes underlying these molecules affects susceptibility to severe malaria. Our results suggest that a common frameshift mutation in the ABO glycosyltransferase, responsible for blood group O, is associated with protection from severe malarial phenotypes (P=2x10⁻⁷), particularly severe malarial anaemia. However, we found no significant disease associations with variation in either the ICAM1 or CD36 genes. We focused on two particular functional polymorphisms, the missense ICAM-1Kilifi and the CD36 nonsense mutation T1264G. We genotyped both markers in around 10,000 individuals, but neither demonstrated an association with severe malarial phenotypes. Malaria has been a profound selection pressure shaping human genetic diversity. The last decade has seen the development of several haplotype-based methods to detect signatures of recent positive evolutionary selection. These techniques are potentially invaluable tools in our hunt for genetic variants that protect from life threatening malaria. We used simulations and empirical data from the International HapMap Project to demonstrate the validity of searching for long regions of haplotype homozygosity, as an approach to finding alleles undergoing selective sweeps. We analysed genetic data from a range of populations, particularly those utilized by HapMap, to investigate whether our candidate genes were associated with signals of recent positive selection. We characterized the distribution of a selection event associated with the CD36 1264G allele, focused in Central-West Africa, and demonstrated a novel signal of low population differentiation at the ABO gene, suggestive of longstanding balancing selection. Our work confirms that variation in the host ligands of PfEMP1 modulates severe malaria susceptibility, and highlights the value of using signals of selection, along with functional experiments and genetic association studies, to dissect the biology of severe malaria.

Fusarium verticillioides è l’agente responsabile della Fusariosi della Spiga del mais, contamina la granella con fumonisine, micotossine responsabili di diverse patologie umane e animali. Per la resistenza alla fusariosi e all’accumulo di fumonisine esiste variabilità tra genotipi diversi ma non sono ancora disponibili ibridi immuni. L’obiettivo di questo lavoro è stato quello di individuare marcatori associati alla resistenza a F. verticillioides. Mediante un bioassay è stato testato un association panel per la resistenza a F. verticillioides. Al fine di identificare i marcatori di resistenza sono stati applicati un approccio GWAS e uno per geni candidati. L’analisi GWAS è stata eseguita con 227K SNPs restituendo 206 marcatori significativi. Da un lavoro di RNASequencing sono stati individuati i geni coinvolti nella risposta a F. verticillioides mentre i geni R sono stati recuperati della letteratura scientifica. Genotipi resistenti (CO433 e CO441) e suscettibili (CO354 e CO389) sono stati scelti per individuare polimorfismi nei geni candidati da associare ai fenotipi rilevati mediante il bioassay. Quattro marcatori sono risultati significativi. Infine, la correlazione tra l’incidenza della fusariosi rilevata in campo e mediante bioassay è stata analizzata in una popolazione di 172 RIL derivanti da CO441 x CO354, tuttavia, non è stata individuata alcuna corrispondenza. / Fusarium verticillioides is the causal agent of Fusarium ear rot (FER) in maize and contaminates grains with fumonisin, a family of mycotoxins involved in several human and animal diseases. Quantitative genetic variation exists for resistance to FER and fumonisin contamination among genotypes, however, resistant maize hybrids are currently not available. The aim of this work was the identification of genetic markers associated to resistance against F. verticillioides. A bioassay was used to screen inbred lines of the maize association population for FER resistance, GWAS and candidate gene approaches were applied to identify markers. GWAS was performed using a 227K SNP matrix and resulting in 206 significant markers. Genes involved in F. verticillioides response in developing maize kernels were retrieved from a previous RNASequencing study while maize R genes were retrieved from scientific literature. Resistant (CO433 and CO441) and susceptible genotypes (CO389 and CO354) were selected to amplify and sequence candidate genes. Polymorphisms detected were used to find association with phenotypes scored using the bioassay. Four significant markers were found. Finally, the correlation between FER phenotypes scored in field experiments and bioassay phenotypes was investigated. A population of 172 RILs (CO441 x CO354), was tested. No correlation was found.

La maladie de Parkinson (MP) est une affection neurodégénérative invalidante et incurable. Il est maintenant clairement établi que d’importants déterminants génétiques prédisposent à son apparition. La recherche génétique sur des formes familiales de la MP a mené à la découverte d’un minimum de six gènes causatifs (SNCA, LRRK2, Parkin, PINK1, DJ-1 and GBA) et certains, par exemple LRRK2, contiennent des variations génétiques qui prédisposent également aux formes sporadiques. La caractérisation des protéines codées par ces gènes a mené à une meilleure compréhension des mécanismes moléculaires sousjacents. Toutefois, en dépit de ces efforts, les causes menant à l’apparition de la MP restent inconnues pour la majorité des patients. L’objectif général des présents travaux était d’identifier des mutations prédisposant à la MP dans la population canadienne-française du Québec à partir d’une cohorte composée principalement de patients sporadiques. Le premier volet de ce projet consistait à déterminer la présence de mutations de LRRK2 dans notre cohorte en séquençant directement les exons contenant la majorité des mutations pathogéniques et en effectuant une étude d’association. Nous n’avons identifié aucune mutation et l’étude d’association s’est avérée négative, suggérant ainsi que LRRK2 n’est pas une cause significative de la MP dans la population canadienne-française. La deuxième partie du projet avait pour objectif d’identifier de nouveaux gènes causatifs en séquençant directement des gènes candidats choisis à cause de leurs implications dans différents mécanismes moléculaires sous-tendant la MP. Notre hypothèse de recherche était basée sur l’idée que la MP est principalement due à des mutations individuellement rares dans un grand nombre de gènes différents. Nous avons identifié des mutations rares dans les gènes PICK1 et MFN1. Le premier code pour une protéine impliquée dans la régulation de la transmission du glutamate tandis que le second est un des acteurs-clés du processus de fusion mitochondriale. Nos résultats, qui devront être répliqués, suggèrent que le séquençage à grande échelle pourrait être une méthode prometteuse d’élucidation des facteurs de prédisposition génétiques à la MP ; ils soulignent l’intérêt d’utiliser une population fondatrice comme les canadiens-français pour ce type d’étude et devraient permettre d’approfondir les connaissances sur la pathogénèse moléculaire de la MP. / Parkinson’s disease (PD) is a complex neurological disorder with significant genetic predisposing factors which are extremely heterogeneous. Investigations of familial forms of the disorder revealed causative mutations in six different genes, namely SNCA, LRRK2, Parkin, PINK1, DJ-1 and GBA, and functional analyses of these gene products pinpointed dysfunction of key molecular pathways involved in the neurodegenerative process of the disorder. Further sequencing and genome-wide association studies indicated that some of these genes, including LRRK2, also contain variants predisposing to sporadic forms of PD. Despite these significant breakthroughs, the vast majority of PD genetic predisposing factors remain unknown. Our goal was to identify mutations predisposing to PD in the French Canadian (FC) population from a cohort mostly composed of late-onset sporadic cases. We therefore sequenced the two exons of LRRK2 that contain most of the pathogenic mutations and we performed a case-control association study. Sequencing analysis did not reveal any reported or novel mutations and the case-control association study did not provide any positive signal, thus indicating that common variants in LRRK2 are unlikely to be a significant cause of late-onset PD in the FC population. Because of the allelic and non-allelic genetic heterogeneity observed for PD, we hypothesized that dozens of genes may carry rare pathogenic mutations. The second part of this research project was therefore aimed at identifying new PD causative genes by direct sequencing of genes functionally associated with the known causative gene pathways. Our screening uncovered several rare mutations likely pathogenic in the PICK1 and the MFN1 genes. PICK1 is involved in internalization of AMPA receptors whereas MFN1 is one of the core components of the mitochondrial fusion/fission machinery. Although these observations will need to be replicated, our findings support the previously suspected pathogenic role for glutamate excitotoxicity and imbalanced mitochondrial dynamics in Parkinson’s disease. They further emphasize the value of inbred populations in genetic studies of PD and provide new clues to the molecular pathogenesis of the disorder.

O emprego de \"Total Genome Scan\" em modelos genéticos de doenças complexas tem sido fundamental para seleção de regiões cromossômicas envolvidas com traços complexos. Em nosso laboratório, identificamos cinco regiões cromossômicas associadas ao traço quantitativo pressão arterial (BP-QTL) que explicam 43% da variação da pressão arterial numa progênie obtida a partir de animais espontaneamente hipertensos (SHR) e \"Brown Norway\" (BN). Os BP-QTLs foram, então, validados por desenvolvimento de linhagens congênicas, incluindo uma para o cromossomo 4 (SHR.BN4) cuja substituição das sequências SHR pelo do animal BN levou a redução da pressão arterial sistólica basal (~14 mm Hg). O objetivo deste trabalho foi identificar as variantes genéticas candidatas neste intervalo cromossômico com base em diferenças no padrão de expressão gênica e na presença de alterações genéticas não sinônimas \"missense\" ou em regiões regulatórias conservadas que possam estar envolvidas na gênese da hipertensão. Identificamos 533 genes com expressão renal, dentre os 682 do intervalo, sendo que 28 apresentaram padrão de expressão diferente entre amostras de animais adultos (congênico vs. SHR) e seis apresentaram alterações não sinônimas \"missense\". É importante salientar que dos genes diferentemente expressos, encontramos alterações estruturais em regiões conservadas com potencial de participar na regulação em 11. Em conjunto, utilizamos uma plataforma integrada para selecionar 34 genes candidatos no cromossomo 4, dos quais 17 genes serão priorizados, para ser investigados quanto sua contribuição na hipertensão arterial do SHR e na hipertensão primária humana / Total genome scan in genetic models of complex diseases have been instrumental to select candidate genes underlying complex traits. We previously mapped 5 blood pressure related quantitative trait loci (BP-QTLs) that explain about 43% of the BP variance in a progeny derived from Spontaneous Hypertensive Rat (SHR) and Brown Norway (BN) rats. The BP-QTLs were then validated by derivation of congenic strains, including one for chromosome 4 (SHR.BN4) in which a segment from BN replaced the SHR sequences reducing basal systolic BP (~14 mm Hg). The aim of this project is to identify the candidate genetic variants within the chromosome interval based on differences in renal gene expression patterns and structural changes in both non-synonymous missense or within adjacent regulatory sequences that may contribute to hypertension. We identified 533 genes with renal expression, out of 682 in the interval, in which 28 presented differences in expression pattern in adult samples (congenic vs. SHR) and six presented non-synonymous missense alterations. In addition, 11 out of 28 differentially expressed genes showed structural alterations in adjacent conserved regions that potentially contribute to gene regulation. Taken together, using the proposed combination of strategies, we selected 34 hypertensive candidate genes in chromosome 4, in which 17 will be prioritized, to be further explored to assess their contribution to hypertension in the SHR and to essential hypertension in humans

<p>This dissertation explains why behavioral genetic research can be better informed by using characteristics in the human iris as biomarkers for personality, and is divided into five parts. Part I gives an introduction to the classical twin method and an overview of the findings that have led most developmental researchers to recognize that the normal variation of personality depends on a complex interplay between genetic and environmental factors. Part II highlights empirical findings that during the last twenty years have gradually moved genetic and environmental theory and research to evolve toward one another, and also presents the theory of genetics and experience that currently is used to explain how the interplay between genes and the environment works. Part III explains why, from a developmental perspective, it is of interest to identify candidate genes for personality, and gives a brief overview of genes that have been associated with personality. Problems associated with genetic research on the molecular level and how these apply to personality are also highlighted. Part IV examines molecular research on the iris and the brain, which suggests that genes expressed in the iris could be associated with personality, and explains how the use of iris characteristics can increase power to test candidate genes for personality by taking advantage of the self-organizing properties of the nervous system. The empirical foundation for the questions posed in this dissertation and also the empirical results are presented here. Part V discusses the associations found between iris characteristics and personality, and exemplifies how iris characteristics can be used within the theoretical frameworks presented in parts I, II, III and IV. In other words, Part V explains how iris characteristics – in addition to identify as well as test candidate genes for personality – can be used to investigate how people’s experiences in themselves are influenced by genetic factors.</p>

<p>Domestication has led to genetic changes that affect quantitative traits in farm animals. Both candidate gene analysis using association tests and genome scans based on linkage analysis have been performed to understand the molecular basis underlying quantitative genetic variation in horses, pigs and chickens. To test a possible association of polymorphisms in the <i>PRKAG3</i> gene, previously found to be associated with excess glycogen content in pig skeletal muscle, with quantitative traits in the horse, the major coding part of the equine <i>PRKAG3</i> sequence was identified. Bioinformatic characterization of the equine <i>PRKAG3</i> gene was conducted. A single nucleotide polymorphism (SNP) causing a missense mutation (Pro258Leu) was found. Screening this SNP showed that the Leu258 allele was more frequent in breeds with heavy muscularity. To assess previously reported associations between polymorphisms in the <i>MC4R</i> gene and obesity-related traits further, we conducted linkage analysis between the <i>MC4R</i> locus and fatness-related traits using a Wild BoarxLarge White intercross. No significant association between segregation at the <i>MC4R</i> locus and fatness was detected in this pedigree. A genome scan of quantitative trait loci (QTLs) has been performed in an intercross between chicken lines divergently selected for growth. Divergent parental lines have been established by selecting for high and low 56-day body weight for over 40 generations. The selection has led to approximately a 9-fold difference in 56-day body weight between lines and resulted in correlated responses for a number of traits including appetite, immune response, body composition and metabolic traits. Phenotypic data on growth and other correlated traits were collected from more than 800 F2 individuals. Genome scans using 145 markers on 26 linkage groups have identified QTLs affecting growth and correlated responses to selection for 56-day body weight. No major QTL explaining a large portion of phenotypic variation in growth was revealed in this study. </p>

Domestication has led to genetic changes that affect quantitative traits in farm animals. Both candidate gene analysis using association tests and genome scans based on linkage analysis have been performed to understand the molecular basis underlying quantitative genetic variation in horses, pigs and chickens. To test a possible association of polymorphisms in the PRKAG3 gene, previously found to be associated with excess glycogen content in pig skeletal muscle, with quantitative traits in the horse, the major coding part of the equine PRKAG3 sequence was identified. Bioinformatic characterization of the equine PRKAG3 gene was conducted. A single nucleotide polymorphism (SNP) causing a missense mutation (Pro258Leu) was found. Screening this SNP showed that the Leu258 allele was more frequent in breeds with heavy muscularity. To assess previously reported associations between polymorphisms in the MC4R gene and obesity-related traits further, we conducted linkage analysis between the MC4R locus and fatness-related traits using a Wild BoarxLarge White intercross. No significant association between segregation at the MC4R locus and fatness was detected in this pedigree. A genome scan of quantitative trait loci (QTLs) has been performed in an intercross between chicken lines divergently selected for growth. Divergent parental lines have been established by selecting for high and low 56-day body weight for over 40 generations. The selection has led to approximately a 9-fold difference in 56-day body weight between lines and resulted in correlated responses for a number of traits including appetite, immune response, body composition and metabolic traits. Phenotypic data on growth and other correlated traits were collected from more than 800 F2 individuals. Genome scans using 145 markers on 26 linkage groups have identified QTLs affecting growth and correlated responses to selection for 56-day body weight. No major QTL explaining a large portion of phenotypic variation in growth was revealed in this study.

In this thesis we have studied genetic elements potentially contributing to the pathophysiology of psychiatric disorders, focusing on different sources of human genome variability, including SNPs and CNVs, which can affect not only coding genes but also RNA regulatory elements, such as miRNAs. First, we have interrogated different candidate genes for psychiatric disorders overlapping with known CNVs, finding 14 different genes variable in copy number in psychiatric disorders but not in control individuals. Then, narrowing the analysis on mood disorders, we explored GSK3&#946; gene considering both SNPs and a partially overlapping CNV. The GSK3&#946; promoter and intron 1 region was found significantly associated with an earlier onset of the major depressive disorder. Finally, we have found evidence possibly pointing to a precise post-transcriptional regulation of circadian rhythms by miRNAs in mood disorder patients. Concretely, a variant in the precursor form of miR-182 could play an important role in fine-tuning its target sites involved in the control of sleep/wake cycles. Overall, we have provided evidence of different types of genome variation on neuronal genes or miRNA regulatory regions that can potentially contribute to the development of psychiatric disorders. / En aquesta tesi hem estudiat elements genètics que podrien contribuir potencialment en la fisiopatologia dels trastorns psiquiàtrics, centrant-nos en diferents fonts de variabilitat genòmica humana, incloent els SNPs i els CNVs, els quals poden afectar no només a gens codificants sinó també a elements reguladors, com els miRNAs. Primer, vam interrogar diferents gens candidats per trastorns psiquiàtrics solapats amb CNVs coneguts, trobant que 14 gens eren variables en el número de còpia en pacients però no en individus controls. Després, restringint l'anàlisi a trastorns afectius, vam explorar el gen GSK3&#946; considerant SNPs així com també un CNV que se solapa parcialment amb el gen. Vam trobar la regió del promotor i de l'intró 1 del gen GSK3&#946; associada de manera significativa amb una inferior edat d'inici del trastorn de depressió major. Finalment, hem trobat evidències que possiblement indiquen una precisa regulació post-transcriptional dels ritmes circadians per miRNAs en pacients amb trastorns afectius. Concretament, una variant en la forma precursora del miR-182 podria jugar un paper important en la fina regulació dels seus gens diana implicats en el control dels cicles de son i vigília. En general, hem aportat evidències de què diferents tipus de variació genòmica en gens neuronals o regions reguladores com els miRNAs podrien contribuir potencialment en el desenvolupament de trastorns psiquiàtrics.

The purpose of the present study is to gain a more complete understanding of the impact of human and physical resource allocations and their interaction on students&rsquo / mathematical literacy skills across Turkey, member and candidate countries of European Union through the Programme for International Student Assessment (PISA) 2003. Hierarchical linear modeling (HLM) techniques were used separately for three different cultural settings using the database of Programme for International Student Assessment (PISA) 2003. The results indicated that students in Turkey, member and candidate countries of European Union who performed higher on the mathematical literacy assessment tended to have the following characteristics: (1) enrolled at higher grade levels, (2) more educational resources at home, (3) higher levels of mathematics self-efficacy, (4) lower levels of mathematics anxiety, (5) more positive self-concept in mathematics, (6) less preferences for memorization strategies, and (7) more positive disciplinary climate in mathematics lessons. As the performance of schools were considered, the higher average mathematics self-efficacy of students, the higher the mean school mathematical literacy performance. The influence on mathematical literacy assessment varied from school to school with respect to grade level and disciplinary climate in mathematics lessons in Turkey and European Union countries, with respect to grade level, mathematics self-efficacy, and disciplinary climate in mathematics in European Union candidate countries. Moreover, school size and mathematics student-teacher ratio at school influenced the disciplinary climate in mathematics lessons in Turkey / academic selectivity of the school influenced the grade level and mathematics self-efficacy in the candidate countries of European Union.