Recent advances in genomics now allow for the identification of the genes and mutations that underlie the heritability of agronomically important traits in livestock. The corresponding genes are said to map to Quantitative Trait Loci (QTL), and the mutations referred to as Quantitative Trait Nucleotides (QTN). The most commonly used approach relies on positional cloning which typically proceeds in three steps: QTL mapping by linkage analysis, QTL fine-mapping by linkage disequilibrium or association analysis, and QTN identification combining haplotype analysis and functional assays. Knowledge of QTL and QTN provides insights into the genetic architecture of complex traits and physiology of production traits, and opens novel possibilities for enhanced selection referred to as Marker Assisted Selection (MAS). This thesis is devoted to QTN identification of a QTL that was previously mapped to pig chromosome 2 and fine-mapped to a 250 Kb segment encompassing the imprinted IGF2 gene. The QTL was shown to have a major post-natal effect on muscle mass and fat deposition, and to be subject to parental imprinting as only the padumnal chromosome affects the phenotype. To identify the QTN we have first generated 32 Kb and 56 Kb of finished porcine sequence encompassing the IGF2 and H19 genes, respectively. The corresponding sequences were annotated including definition of gene models, identification of interspersed repeats and determination of 97 sequence elements that are highly conserved between pig, human and mouse. We have then resequenced 28 Kb encompassing the IGF2 gene for 15 boar chromosomes for which the QTL genotype had been determined by progeny-testing or Marker Assisted Segregation Analysis (MASA). This revealed 258 polymorphisms of which only one (Int3-3072G>A) cosegregated perfectly with QTL genotype. The corresponding single nucleotide polymorphism (SNP) is a G to A transition affecting one of the highly conserved sequence elements located just downstream of differentially methylated region 1 in intron 3. We have demonstrated that the Int3-3072 A allele associated with increased muscle mass is also associated with increased IGF2 mRNA levels in post-natal striated muscle (but not in pre-natal muscle nor in pre- and post-natal liver). However, the Int3-3072G>A SNP does not alter imprinting nor allele-specific methylation. Using a luciferase reporter assay, we then demonstrated that the Int3-3072 A allele reduces the cis activity of a silencer element, and using an electrophoretic mobility shift assay (EMSA), that it abrogates binding of a nuclear factor assumed to be a trans-acting silencing factor. Taken together both genetic and functional evidence strongly support the conclusion that the Int3-3072G>A SNP is the causative SNP. The thesis is concluded by a discussion that (i) highlights the factors that make domestic animals a unique resource for the molecular dissection of complex phenotypes, (ii) comments the Asian origin of the Int3-3072A allele associated with increased muscle mass, (iii) describes recent advances in characterizing the trans-acting silencing factor binding to the Int3-3072G allele, (iv) pinpoints statistical issues related to the detection of imprinted QTL, (v) reports on the utility of the Int3-3072G>A SNP for MAS applied to pig breeding, and (vi) makes projections on how latest progress in genome analysis will affect positional identification of QTN in the near future. Grâce aux progrès récents en génomique, il est maintenant possible didentifier les gènes et mutations qui sous-tendent lhéritabilité des caractères de production chez les animaux de rente. Ces gènes se localisent au niveau de Loci de Traits Quantitatifs (QTL), et les mutations correspondantes sont qualifiées de Nucléotides de Traits Quantitatifs (QTN). La démarche expérimentale la plus couramment utilisée est le clonage positionnel. Celui-ci comprend trois étapes: cartographie de QTL par analyses de liaison génétique, cartographie fine de QTL par études dassociation exploitant le déséquilibre de liaison, et identification de QTN par combinaison danalyses haplotypiques et fonctionnelles. Lidentification de QTL et QTN non seulement révèle larchitecture génétique des phénotypes complexes que sont les caractères de production, ainsi que les rouages moléculaires qui les sous-tendent, mais ouvre également des possibilités nouvelles de sélection plus performante dite Assistée par Marqueurs (MAS). Cette thèse est consacrée à lidentification dun QTN correspondant à un QTL dabord localisé sur le chromosome 2 du porc, et ensuite cartographié finement dans un segment chromosomique de 250 Kb comprenant le gène IGF2. Le QTL en question a un effet post-natal majeur sur la croissance musculaire et le dépôt graisseux. Il est soumis à lempreinte parentale, lallèle paternel étant le seul à influencer le phénotype. Afin didentifier le QTN, nous avons tout dabord généré 32 Kb et 56 Kb de séquences finies, comprenant respectivement les gènes IGF2 et H19. Les séquences correspondantes ont été annotées bioinformatiquement, y compris la définition de modèles gèniques, lidentification de séquences répétées dispersées, ainsi que de 97 éléments de séquence fortement conservés chez le porc, lhomme et la souris. Nous avons ensuite re-séquencé 28 Kb chevauchant le gène IGF2 pour 15 chromosomes dont le génotype au niveau du QTL fut préalablement déterminé par testage de descendance ou Ségrégation Assistée par Marqueurs. Cet exercice a révélé 258 polymorphismes dont un seulement (Int3-3072G>A) correspondait parfaitement aux génotypes QTL. Ce polymorphisme est une transition G à A affectant un des 97 éléments hautement conservés, situé juste en aval de la région différentiellement méthylée (DMR1) dans lintron 3. Nous avons ensuite démontré que lallèle Int3-3072 A, associé à une augmentation de la masse musculaire, est également associé à une augmentation des taux dARNm IGF2 dans le muscle strié post-natal (mais non dans le muscle strié pré-natal, ni dans le foie pré- et post-natal). Par contre, le polymorphisme Int3-3072G>A naffecte ni état dempreinte ni de méthylation allèle-spécifique du gène. Nous avons ensuite démontré à laide dun test rapporteur de type luciférase que lallèle Int3-3072 A réduit lactivité dun élément silenceur agissant en cis, et à laide dun test de type EMSA quil empêche la liaison dun facteur nucléaire. Conjointement, ces données génétiques et fonctionnelles démontrent que le polymorphisme Int3-3072G>A SNP correspond bien au QTN. Nous concluons la thèse par une discussion dans laquelle nous (i) démontrons pourquoi les animaux domestiques offrent des possibilités uniques pour la dissection moléculaire de phénotypes complexes, (ii) commentons lorigine asiatique de lallèle Int3-3072A associé à une augmentation du développement musculaire, (iii) décrivons les progrès récent dans lidentification du facteur nucléaire reconnaissant spécifiquement lallèle Int3-3072G, (iv) attirons lattention sur les artéfacts statistiques associés à la détection de QTL soumis à lempreinte, et (v) discutons limpact de nouvelles technologies génomiques sur le clonage positionnel de gènes.

Wheat grain quality has a complex genetic architecture heavily influenced by the growing environment. Consistency in wheat quality not only affects the efficiency of milling and baking but also the quality of end-use products. The objectives of this study were to 1) analyze the different wheat quality parameters in Recombinant Inbred Lines (RILs) grown under different environments, and 2) to identify Quantitative Trait Loci (QTLs) associated with quality stability in RILs grown under different environments. A set of 180 RILs derived from two spring wheat lines 'Halberd' and 'Len' were grown at Uvalde and College Station TX, in the 2009/2010 growing season and at Chillicothe and College Station TX, in 2010/2011 growing seasons. The experiment was laid out in Randomized Complete Block Design (RCBD) with four replications within each location. Each line was tested for multiple quality traits that included grain hardness, protein content, dough mixing properties and bread baking quality using Single Kernel Characterization System (SKCS), Near-Infrared Reflectance Spectrometry (NIRS) analysis, mixograph and the Sodium Dodecyl Sulfate Sedimentation (SDSS) test. Genetic linkage map construction was carried out with 116 single nucleotide polymorphism (SNP) markers in the RILs. Then composite interval mapping was carried out to identify QTLs associated with quality traits. The SDSS column height was positively correlated across four environments. Similarly, it was found to have significant positive correlation with mixing tolerance and peak time within and also across locations. However, the SDSS was negatively correlated with the hardness index. The protein percent was not significant with any of the quality traits within and across environments. We were able to detect many QTLs for different quality traits but most of them were site specific. Only a few QTLs were consistent across environments. Most of the QTLs for quality traits i.e., SDSS, peak time, mixing tolerance and hardness index were identified on chromosome 1B. We were able to detect overlapped QTLs for SDSS column height and mixing tolerance on chromosome 1B. Furthermore, overlapping QTLs for mixing tolerance and peak time were detected on an unknown chromosome. We also detected overlapping QTLs for hardness index on chromosome 1B. We identified one stable QTL for SDSS column height on chromosome 4B. This QTL was detected based on the coefficient of variation (CV) for SDSS in four different environments.

Although polyploidy is believed to be a major source of evolutionary novelty, few studies have examined the genetic basis of phenotypic variation in wild polyploids. In this thesis I have studied the genetic basis of flowering time variation in the wild tetraploid crucifer Capsella bursa-pastoris, as well as the evolutionary history of this species. First, phylogenetic methods were employed to test hypotheses on the origin of C. bursa-pastoris. Based on DNA sequences from two chloroplast DNA loci and three independent nuclear genes, we found no support for the notion of C. bursa-pastoris as an autopolyploid of the diploid C. grandiflora, or an allopolyploid of C. grandiflora and C. rubella, even though some C. bursa-pastoris accessions shared alleles with C. rubella at nuclear loci. Using divergence population genetic methods, a larger sample of accessions and data for six duplicated nuclear genes, we found that allele sharing in sympatry was better explained by introgressive hybridization than by multiple origins of the tetraploid. The genetic basis of flowering time variation was examined using three approaches. A gene expression microarray study revealed that early- and late-flowering accessions differ in circadian rhythm, as well as in the gibberellin pathway affecting flowering time. Second, two QTL (Quantitative Trait Loci) for flowering time map to duplicated linkage groups. Third, polymorphisms at the candidate genes CRYPTOCHROME1 (CRY1), in one of the QTL regions, and FLOWERING LOCUS C (FLC) are associated with natural flowering time variation. Different FLC splice site polymorphisms are associated with flowering time in samples from Western Eurasia and China. The CRY1 association is only found in Europe, where alleles introgressed from C. rubella have an effect on flowering time. In conclusion, duplicated genes, introgressive hybridization and splicing variation may all have played a role in the evolution of flowering time variation in C. bursa-pastoris.

Visual quality is one of the major factors that determine the market value of field pea (Pisum sativum L.). Breeding for improved visual quality of pea seeds is currently a challenging task, because of the complexity and lack of sound genetic knowledge of the traits. The objectives of this research were to characterize the genetic basis and identify the genomic regions associated with four key visual quality traits (cotyledon bleaching in green pea, greenness in yellow pea, and seed shape and seed dimpling in both green and yellow types) in field pea. Biochemical and gene expression profiling to understand the molecular basis of post-harvest cotyledon bleaching in green pea was also addressed. Two F5:6 recombinant inbred line (RIL) populations (90 lines from Orb X CDC Striker cross, and 120 lines from Alfetta X CDC Bronco cross) were developed and evaluated for visual quality traits in two locations in Saskatchewan, Canada in 2006 and 2007. The four quality traits evaluated all displayed a continuous range of expression with moderate to high heritability. Two genetic linkage maps utilizing 224 markers (29 simple sequence repeat (SSR) (from Agrogene) and 195 amplified fragment length polymorphism (AFLP)) and 223 markers (27 SSR and 196 AFLP ) were constructed for the Orb X CDC Striker population and the Alfetta X CDC Bronco population, respectively. Multiple quantitative traits (QTL) mapping detected major QTLs on linkage group (LG) IV and LG V, as well as location- and year-specific QTLs on LG II and LG III associated with green cotyledon bleaching resistance. Nine QTLs controlling yellow seed lightness, three for yellow seed greenness, 15 for seed shape and nine for seed dimpling were detected. Among them, 5 QTLs located on LG II, LG IV and LG VII were consistent in at least two environments. The QTLs and their associated markers will be useful tools to assist pea breeding programs attempting to pyramid positive alleles for the traits. The bleaching resistant cultivar CDC Striker had a slower rate of chlorophyll degradation in cotyledons and a higher carotenoid to chlorophyll ratio in seed coats than the bleaching susceptible cultivar Orb when seed samples were exposed to high intensity light. An oligo-nucleotide microarray (Ps6kOLI1) was utilized to investigate the gene expression profiles of CDC Striker and Orb seed coats at different developmental stages. It clearly indicated that the expression of genes involved in the production and accumulation of secondary metabolites was significantly different between these cultivars. The results of both biochemical and gene expression studies suggested the bleaching resistance in CDC Striker was not due to the accumulation of chlorophyll pigments in the cotyledons, but rather due to the ability of seed coats to protect them from photooxidation. Accumulation of specific carotenoids which could bind with the reaction center protein complex more effectively and accumulation of phenolic secondary metabolites which could enhance the antioxidant properties and structural integrity of the seed coats may lead to the bleaching resistant phenotype. Therefore, breeding green pea cultivars with higher seed coat antioxidant properties would improve both visual and nutritional quality. This research has provided several insights into molecular approaches to improve field pea visual quality for food markets.

In durum wheat (<i>Triticum turgidum</i> L. var <i>durum</i>), grain protein concentration (GPC) and gluten quality are among the important factors influencing pasta-making quality. Semolina with high protein content produces pasta with increased tolerance to overcooking and greater cooked firmness. However, genetic improvement of GPC is difficult largely because of its negative correlation with grain yield, and a strong genotype x environment interaction. Therefore, identification of quantitative trait loci (QTL) for high GPC and the associated markers is a priority to enhance selection efficiency in breeding durum wheat for elevated GPC. At a physiological level, GPC is influenced by several factors including nitrogen remobilization from vegetative organs and direct post-anthesis nitrogen uptake (NUP) from the soil. Understanding the relationship between elevated GPC and nitrogen remobilization, and post-anthesis NUP will enable durum wheat breeders to develop varieties that not only produce high yield and high GPC, but also exhibit better nitrogen use efficiency. The objectives of this study were: (1) to identify and validate QTL for elevated GPC in two durum wheat populations; and (2) to determine if elevated GPC is due to more efficient nitrogen remobilization and/or greater post-anthesis NUP. A genetic map was constructed with SSR and DArT® markers in a doubled haploid population from the cross Strongfield x DT695, and GPC data were collected in replicated trials in six Canadian environments from 2002 to 2005. Two stable QTL for high GPC, QGpc.usw-B3 on chromosome 2B and QGpc.usw-A3 on 7A, were identified. Strongfield, the high GPC parent, contributed the alleles for elevated GPC at both QTL. These two QTL were not associated with variation in grain weight (seed size) or grain yield. QGpc.usw-A3 was validated in a second Strongfield-derived population as that QTL was significant in all six testing environments. Averaged over five locations, selection for QGpc.usw-A3 resulted in a +0.4% to +1.0% increase in GPC, with only small effects on yield in most environments. A physiological study of grain protein accumulation revealed that regardless of the growing condition, nitrogen remobilization was the major contributor for grain nitrogen in durum genotypes evaluated, accounting for an average of 84.3% of total GPC. This study confirmed that introgression of Gpc-B1 into Langdon resulted in increased GPC, and this GPC increase was due to higher N remobilization. Strongfield expressed greater N remobilization than DT695 and the semi-dwarf cultivar Commander, but N remobilization was not the determining factor for Strongfields elevated GPC. Strongfield expressed greater post-anthesis NUP than DT695. Similarly, a selection of six high-GPC doubled haploid (DH) lines from the cross DT695 x Strongfield expressed significantly greater post-anthesis NUP than six low-GPC DH selections, supporting the hypothesis that elevated GPC in Strongfield is derived from greater post-anthesis NUP. All six high-GPC DH selections carried the Strongfield allele at QGpc.usw-A3, suggesting this QTL maybe associated with post-anthesis NUP.

L'ametller, Prunus amygdalus Batsch, és una espècie diploide que pertany al gènere Prunus. Encara que l'autoincompatibilitat (AI) és un caràcter important des del punt de vista evolutiu en el món vegetal, l'autocompatibilitat (AC) és un caràcter agronòmic crític per a assegurar la producció. D'aquesta manera, l'AC s'ha convertit en un dels principals objectius dels programes de millora d'ametller en tot el món. L'AC ha estat identificada en diverses varietats d'ametller, encara que sol ser excepcional. Els mètodes que s'han aplicat per a determinar l'AC són l'observació dels tubs pol·línics, i el quallat de fruits després de pol·linitzacions controlades. No obstant això, les noves tècniques moleculars s'han aplicat cada vegada més al llarg de les dues últimes dècades. Amb això s'ha aconseguit de determinar el genotip de les varietats i seleccions d'una manera molt ràpida i eficaç. L'AC ha estat relacionada amb la presència de l'al·lel Sf, el qual pertany a la sèrie al·lèlica S, i és dominant sobre els altres al·lels d'AI. Com a conseqüència d'això, sempre s'havia considerat que l'AI/AC era un caràcter qualitatiu, controlat per un únic locus, anomenat el locus S.Només un 25% dels individus procedents de l'encreuament 'Vivot' &#1048751; 'Blanquerna' ha estat AC, molt menys de l'esperat, un 50%. Les dues versions diferents de l'haplotip Sf, una activa i AI (Sfa) i l'altra inactiva i AC (Sfi), han mostrat el reconeixement per part de la Sfa- RNasa dels pistils de 'Vivot' dels tubs pol·línics amb el Sfi de 'Blanquerna'. Aquests resultats suggereixen la presència d'un locus modificador no lligat al locus S, el qual seria el responsable del control de l'AI/AC en aquesta població. Encara que darrerament s'hagi aprofundit en l'estudi del locus S a nivell molecular, aquest mecanisme no està encara del tot determinat, pel que se suggereix que d'altres gens serien un requisit per a l'AI. En aquesta tesi s'ha localitzat per primera vegada en la família de les rosàcies dos nous loci, situats fora del locus S, els quals es troben en els grups de lligament 6 i 8. Amb aquests resultats, podríem suggerir que l'AI és un caràcter quantitatiu i no qualitatiu, com s'acceptava fins ara.D'altra banda, la construcció d'una llibreria genòmica (fòsmid) de 'Vivot' i 'Blanquerna' ens ha permès de comprovar que tant les Sf-RNases com les SFBf eren completament idèntiques, a pesar de tenir dues expressions tan diferents. Com no ha estat possible de trobar cap mutació entre ambdós Sf, s'ha suggerit la implicació de la metilació de l'ADN en aquesta població. La metilació pot produir canvis en els fenotips o en l'expressió els gens, sense alterar però les seqüències de l'ADN. Els assaigs realitzats en aquesta tesi suggereixen que l'ADN metilat seria el responsable d'aquesta activació i/o inactivació de l'haplotip Sf. De fet, s'ha pogut comprovar que quan la seqüència de la Sf-RNasa és metilada, aquesta inactiva l'expressió, així que aquesta inhibició es traduiria en una expressió AC, com és el cas de 'Blanquerna'. En el cas contrari, si la seqüència d'ADN no és metilada, com és el cas de 'Vivot', la RNasa roman activa i a conseqüència la planta és AI.A més, s'ha construït l'estructura en 3D de les RNases dels a&#320;lels Sf, S23 i S8 mitjançant tècniques bioinformàtiques. La principal diferència trobada ha estat que en l'estructura del Sf hi havia un llaç més llarg que en les altres dues RNases AI. En la bibliografia s'ha descrit que els llaços grans són susceptibles a la degradació proteòlica, pel que aquest mateix fenomen podria passar en aquestes RNases. / El almendro, Prunus amygdalus Batsch, es una especie diploide que pertenece al género Prunus. Aunque la autoincompatibilidad (AI) es un carácter importante en el reino vegetal desde el punto de vista evolutivo, la autocompatibilidad (AC) es un caràcter agronómico muy crítico para asegurar la producción. De este modo, la AC se ha convertido en uno de los principales objetivos de los programas de mejora de almendro en todo el mundo. Aunque la AC ha sido identificada en algunas variedades de almendro, es muy poco frecuente.Los métodos que se han utilizado para determinar la AC en el almendro son la observación de los tubos polínicos y el cuajado de frutos después de polinizaciones controladas. Sin embargo, las nuevas técnicas moleculares se han ido aplicando cada vez más durante estas dos últimas décadas. De este modo, se ha conseguido determinar el genotipo de las variedades y selecciones de una manera muy rápida y eficaz. La AC ha sido relacionada con la presencia del alelo Sf, el cual pertenece a la serie alélica S, y es dominante sobre los otros alelos de AI.Por ello siempre se había considerado que la AI/AC era un carácter cualitativo. En el transcurso de esta tesis, sólo un 25% de los individuos procedentes del cruzamiento 'Vivot' &#1048751; 'Blanquerna' ha sido AC, mucho menos de lo esperado, un 50%. Las dos diferentes versiones del haplotipo Sf, una activa y AI (Sfa) y la otra inactiva y AC (Sfi) han mostrado un mutuo reconocimiento, por lo que la Sfa-RNasa del estilo de 'Vivot' ha impedido el crecimiento del tubo polínico Sfi de 'Blanquerna'. Estos resultados sugieren la presencia de un locus modificador no ligado al locus S, el cual sería responsable del control de la AI/AC en esta población. Aunque últimamente se ha profundizado mucho en el estudio del locus S a nivel molecular, su mecanismo de acción sigue sin estar del todo determinado, por lo que se sugiere que otros genes externos son necesarios en la AI. En esta tesis se han localizado por primera vez en la familia de las rosáceas dos nuevos loci situados fuera del locus S, los cuales se encuentran en el grupo 6 y 8. Con estos resultados, podríamos sugerir que la AI es uncarácter cuantitativo y no cualitativo, como se conocía hasta la fecha.Por otro lado, la construcción de una librería genómica (fósmido) en 'Vivot' y 'Blanquerna' ha permitido comprobar que tanto las secuencias de las Sf-RNasas como de los SFBf eran completamente idénticas, a pesar de tener dos expresiones tan distintas. Como no ha sido posible encontrar ninguna mutación entre ambos Sf, se ha sugerido la implicación de la metilación del ADN en esta población. La metilación puede producir cambios en los fenotipos o en la expresión de los genes sin alterar las secuencias del ADN. Los ensayos llevados a cabo en esta tesis sugieren que el ADN metilado sería el responsable de la activación y/o inactivación del haplotipo Sf. De hecho, se ha podido comprobar que cuando la secuencia de laSf-RNasa es metilada, ésta inactiva la expresión, por lo que esta inhibición se traduciría en unaexpresión AC, como es el caso de 'Blanquerna'. En el caso contrario, si la secuencia de ADN no es metilada, como es el caso de 'Vivot', la RNasa permanece activa y a consecuencia la planta será AI.Además, se ha construido la estructura en 3D de las RNasas de los alelos Sf, S23 y S8 mediante herramientas bioinformáticas. La principal diferencia encontrada fue que en la estructura del Sf, había un lazo más largo que en las otras dos RNasas AI. En la bibliografía se ha descrito que los lazos grandes son susceptibles a la degradación proteólica, por lo que este mismo fenómeno podría estar pasando en estas RNasas. / Almond, Prunus amygdalus Batsch, is a diploid species of the genus Prunus. Although self-incompatibility (SI) is an important trait in plants from the evolutionary point of view, self-compatibility (SC) is a critical agronomic trait in order to ensure the production of an economic crop. Thus, SC has become one of the main objectives worldwide of almond breeding programmes. SC has been identified in several almond cultivars, although it happens rarely. Traditionally tests of pollen tube growth and fruit set after controlled pollinations have been carried out for determining SC cultivars in almond. However, molecular methods have been developed in the last two decades to speed up the genotype determination in cultivars and selections in order to facilitate orchard management and breeding processes. SC has been sofar only related with the presence of the Sf allele, allelic with the S series of SI alleles and dominant over SI. As a consequence, SC/SI has always been considered as a qualitative trait,controlled by a single multi-allelic locus, called the S-locus.The presence of SC of the seedling in the family 'Vivot' &#1048751; 'Blanquerna' has been 25%, much less than expected, 50%. The two different versions of the Sf haplotype, one active and being SI (Sfa) and the other inactive thus being SC (Sfi), have shown the recognition of the Sfi-pollen tubes of 'Blanquerna' by the Sfa-RNase of 'Vivot'. These results suggest the presence of a modifier locus unlinked to the S-locus which would control the SI/SC recognition mechanism. The molecular nature of the S-locus has been widely studied in many species. Although the S-locus encodes genes determining the S-specificity, other non-Sspecific genes or modifier genes are required for the S-RNase-based SI reaction. Two additional loci located outside the S-locus are here described for the first time in the rosaceous family. Thus, we may suggest that SI is a quantitative trait rather than a qualitative one.In addition, the construction of a fosmid library in 'Vivot' and 'Blanquerna' has allowed to confirm that the alignment of their Sf-RNases and SFBf were identical. As it was not possible to find any difference between both versions of the Sf haplotype, it was decided to further investigate about DNA methylation, which is involved in changes in phenotype or gene expression caused by mechanisms other than changes in the DNA sequence. Thus, our experiments have allowed suggesting that DNA methylation could be responsible of the activation/inactivation of the Sf haplotype. In fact, when the Sf-RNase sequence is methylated,an inhibition of the expression takes place, as it happens in 'Blanquerna'. Thus, this nactivation would be traduced into self-compatibility. In the case of Sf-RNase sequences with non-methylated cytosines, as it happens in 'Vivot', the RNase would remain active and, as a consequence, it would be self-incompatible.On the other hand, we have constructed the three-dimensional structures of the almond Sf, S23 and S8 RNases trough molecular modelling tools. The main structural difference found between all RNases was that the Sf structure showed an extended looping region. The amino acid residues forming this long loop could be prone to degradation and/or inactivation and as aconsequence this Sf-RNase could be less stable and thus would allow its pollen tube growthtrough its own pistil.

The seed size and shape of lentil are important traits because they determine the market class, cooking time, and can influence quality and yield of milled lentils. Understanding the genetic control of seed size and shape can help breeders develop varieties with improved seed size and shape characteristics such as seed diameter, seed thickness and seed plumpness. The objectives were to determine the heritability of seed size and shape and identify the genomic regions controlling these traits. This involved i) developing a linkage map for the LR-18 population (CDC Robin x 964a-46) using a recently developed single nucleotide polymorphism (SNP) assay; ii) analyzing the LR-18 population for seed size and shape QTLs; iii) analyzing an association mapping panel for seed size and shape QTLs. Phenotyping trials were grown at two different locations in Saskatchewan, Canada. The mapping population was grown in two different years while the association panel was only grown in one. Seed diameter and thickness were measured using sieves and this data were used to calculate seed plumpness. Days to flowering was also recorded to determine if it had any effect on seed size or shape. A linkage map consisting of 537 SNPs, 10 SSRs and 4 morphological markers on seven linkage groups was constructed and used for the QTL analysis. The heritability estimates were high for seed diameter and seed plumpness (0.92 and 0.94, respectively) while for seed thickness and days to flowering they were more moderate (0.60 and 0.45, respectively). QTL analysis revealed QTLs on five of the seven linkage groups. The association mapping study revealed similar heritability estimates of 0.97, 0.62, 0.94, and 0.62 for seed diameter, seed thickness, seed plumpness and flowering time, respectively. There were 31 different significant marker trait associations, however only 5 of those were significant for both locations. Four of those five markers did not map in the LR-18 linkage map so their genomic locations are still to be determined. Results showed that there are key regions in the genome that control seed size and shape and flowering time in lentil. These markers could be used for marker-assisted selection or for further candidate gene analysis.

In durum wheat (<i>Triticum turgidum</i> L. var <i>durum</i>), grain protein concentration (GPC) and gluten quality are among the important factors influencing pasta-making quality. Semolina with high protein content produces pasta with increased tolerance to overcooking and greater cooked firmness. However, genetic improvement of GPC is difficult largely because of its negative correlation with grain yield, and a strong genotype x environment interaction. Therefore, identification of quantitative trait loci (QTL) for high GPC and the associated markers is a priority to enhance selection efficiency in breeding durum wheat for elevated GPC. At a physiological level, GPC is influenced by several factors including nitrogen remobilization from vegetative organs and direct post-anthesis nitrogen uptake (NUP) from the soil. Understanding the relationship between elevated GPC and nitrogen remobilization, and post-anthesis NUP will enable durum wheat breeders to develop varieties that not only produce high yield and high GPC, but also exhibit better nitrogen use efficiency. The objectives of this study were: (1) to identify and validate QTL for elevated GPC in two durum wheat populations; and (2) to determine if elevated GPC is due to more efficient nitrogen remobilization and/or greater post-anthesis NUP. A genetic map was constructed with SSR and DArT® markers in a doubled haploid population from the cross Strongfield x DT695, and GPC data were collected in replicated trials in six Canadian environments from 2002 to 2005. Two stable QTL for high GPC, QGpc.usw-B3 on chromosome 2B and QGpc.usw-A3 on 7A, were identified. Strongfield, the high GPC parent, contributed the alleles for elevated GPC at both QTL. These two QTL were not associated with variation in grain weight (seed size) or grain yield. QGpc.usw-A3 was validated in a second Strongfield-derived population as that QTL was significant in all six testing environments. Averaged over five locations, selection for QGpc.usw-A3 resulted in a +0.4% to +1.0% increase in GPC, with only small effects on yield in most environments. A physiological study of grain protein accumulation revealed that regardless of the growing condition, nitrogen remobilization was the major contributor for grain nitrogen in durum genotypes evaluated, accounting for an average of 84.3% of total GPC. This study confirmed that introgression of Gpc-B1 into Langdon resulted in increased GPC, and this GPC increase was due to higher N remobilization. Strongfield expressed greater N remobilization than DT695 and the semi-dwarf cultivar Commander, but N remobilization was not the determining factor for Strongfields elevated GPC. Strongfield expressed greater post-anthesis NUP than DT695. Similarly, a selection of six high-GPC doubled haploid (DH) lines from the cross DT695 x Strongfield expressed significantly greater post-anthesis NUP than six low-GPC DH selections, supporting the hypothesis that elevated GPC in Strongfield is derived from greater post-anthesis NUP. All six high-GPC DH selections carried the Strongfield allele at QGpc.usw-A3, suggesting this QTL maybe associated with post-anthesis NUP.

Visual quality is one of the major factors that determine the market value of field pea (Pisum sativum L.). Breeding for improved visual quality of pea seeds is currently a challenging task, because of the complexity and lack of sound genetic knowledge of the traits. The objectives of this research were to characterize the genetic basis and identify the genomic regions associated with four key visual quality traits (cotyledon bleaching in green pea, greenness in yellow pea, and seed shape and seed dimpling in both green and yellow types) in field pea. Biochemical and gene expression profiling to understand the molecular basis of post-harvest cotyledon bleaching in green pea was also addressed. Two F5:6 recombinant inbred line (RIL) populations (90 lines from Orb X CDC Striker cross, and 120 lines from Alfetta X CDC Bronco cross) were developed and evaluated for visual quality traits in two locations in Saskatchewan, Canada in 2006 and 2007. The four quality traits evaluated all displayed a continuous range of expression with moderate to high heritability. Two genetic linkage maps utilizing 224 markers (29 simple sequence repeat (SSR) (from Agrogene) and 195 amplified fragment length polymorphism (AFLP)) and 223 markers (27 SSR and 196 AFLP ) were constructed for the Orb X CDC Striker population and the Alfetta X CDC Bronco population, respectively. Multiple quantitative traits (QTL) mapping detected major QTLs on linkage group (LG) IV and LG V, as well as location- and year-specific QTLs on LG II and LG III associated with green cotyledon bleaching resistance. Nine QTLs controlling yellow seed lightness, three for yellow seed greenness, 15 for seed shape and nine for seed dimpling were detected. Among them, 5 QTLs located on LG II, LG IV and LG VII were consistent in at least two environments. The QTLs and their associated markers will be useful tools to assist pea breeding programs attempting to pyramid positive alleles for the traits. The bleaching resistant cultivar CDC Striker had a slower rate of chlorophyll degradation in cotyledons and a higher carotenoid to chlorophyll ratio in seed coats than the bleaching susceptible cultivar Orb when seed samples were exposed to high intensity light. An oligo-nucleotide microarray (Ps6kOLI1) was utilized to investigate the gene expression profiles of CDC Striker and Orb seed coats at different developmental stages. It clearly indicated that the expression of genes involved in the production and accumulation of secondary metabolites was significantly different between these cultivars. The results of both biochemical and gene expression studies suggested the bleaching resistance in CDC Striker was not due to the accumulation of chlorophyll pigments in the cotyledons, but rather due to the ability of seed coats to protect them from photooxidation. Accumulation of specific carotenoids which could bind with the reaction center protein complex more effectively and accumulation of phenolic secondary metabolites which could enhance the antioxidant properties and structural integrity of the seed coats may lead to the bleaching resistant phenotype. Therefore, breeding green pea cultivars with higher seed coat antioxidant properties would improve both visual and nutritional quality. This research has provided several insights into molecular approaches to improve field pea visual quality for food markets.

Sexual selection was defined by Darwin in 1871 as selection acting solely on reproduction success. It is known to act on males resulting in extravagant ornamentations or other attributes, but in recent years more studies have shown that sexual selection also act on females. There is empirical evidence in several taxa that the secondary sexual ornament also acts as a measurement on the females’ reproductive quality, it is an honest trait. In Gallus gallus the comb has been found to be an honest ornament. Quantitative Trait Loci have been found on chromosome 1 and 3 for comb- and egg size. The honesty of the comb is hypothesized to be caused by either a pleiotropic effect gene linkage. In this study an 8th generation Advanced Interline Cross was used to guarantee maximum recombination of alleles to observe phenotypic effects. 177 females were detained during 4 weeks to measure fecundity. Egg number, mean egg weight and total egg size were correlated to comb size: length, area and weight. Correlation between comb size and total egg weight were found to be negative, suggesting the comb to be a dishonest signal. The phenotypic measurements observed in this study suggest that the genes for egg production and comb size are linked, and this linkage has been broken in the F8 analysed in this study.