In multiple species, genome-wide association (GWA) studies have become an increasingly prevalent method of identifying the quantitative trait loci (QTLs) that underlie complex traits. Despite this, relatively few GWA analyses using high-density genomic markers have been carried out on highly quantitative traits in wheat. We utilized single-nucleotide polymorphism (SNP) data generated via a genotyping-by-sequencing (GBS) protocol to perform GWA on multiple yield-related traits using a panel of 329 soft red winter wheat genotypes grown in four environments. In addition, the SNP data was used to examine linkage disequilibrium and population structure within the testing panel. The results indicated that an alien translocation from the species Triticum timopheevii was responsible for the majority of observed population structure. In addition, a total of 50 significant marker-trait associations were identified. However, a subsequent study cast some doubt upon the reproducibility and reliability of plant QTLs identified via GWA analyses. We used two highly-related panels of different genotypes grown in different sets of environments to attempt to identify highly stable QTLs. No QTLs were shared across panels for any trait, suggesting that QTL-by-environment and QTL-by-genetic background interaction effects are significant, even when testing across many environments. In light of the challenges involved in QTL mapping, prediction of phenotypes using whole-genome marker data is an attractive alternative. However, many evaluations of genomic prediction in crop species have utilized univariate models adapted from animal breeding. These models cannot directly account for genotype-by-environment interaction, and hence are often not suitable for use with lower-heritability traits assessed in multiple environments. We sought to test genomic prediction models capable of more ad-hoc analyses, utilizing highly unbalanced experimental designs consisting of individuals with varying degrees of relatedness. The results suggest that these designs can successfully be used to generate reasonably accurate phenotypic predictions. In addition, multivariate models can dramatically increase predictive accuracy for some traits, though this depends upon the quantity and characteristics of genotype-by-environment interaction. / Ph. D.

Des changements de méthylation de l'ADN peuvent affecter l'expression des gènes et pour certains être transmis au travers des générations. De telles " épimutations " qui concernent des groupes de cytosines à proximité ou dans les gènes sont donc une source potentielle de variation phénotypique héritable en absence de changements de la séquence de l'ADN. Chez les plantes la méthylation de l'ADN est cependant principalement observée au niveau des séquences répétées. Il reste à déterminer dans quelle mesure les changements de méthylation au niveau de ce type de séquences peuvent être héritées et affecter les phénotypes. Afin de répondre à ces questions, plus de 500 épiRIL (epigenetic Recombinant Inbred Lines) quasi-isogéniques a été générée chez Arabidopsis thaliana. Cette population a été obtenue par le croisement d'un parent sauvage et d'un parent mutant pour le gène DDM1 présentant une très forte réduction du taux de méthylation de l'ADN. Après un rétrocroisement de la F1 avec une plante sauvage, les individus sauvages pour le gène DDM1 ont été sélectionnés et propagées sur 6 générations par autofécondation. Nous avons montré par l'analyse du méthylome de plus de 100 épiRIL que l'hypométhylation induite par ddm1 présente selon les séquences affectées différents degrés de transmission au travers des générations. La réversion de l'hypométhylation concerne des régions associées à une abondance élevée en sRNA de 24 nt. Nous avons utilisé l'hypométhylation stablement transmise dans les épiRIL induite par ddm1 afin de détecter des QTL (Quantitative Trait Loci) affectant le temps de floraison et la longueur de la racine primaire, deux caractères pour lesquels les variations observées dans les épiRIL présentent une héritabilité importante. En dernier lieu, nous avons recherché par différentes approches les variations causales de ces QTL.

Genotypes adapted to contrasting environments are expected to behave differently when placed in common controlled conditions, if their sensitivity to environmental cues or intrinsic growth behaviour are set to different thresholds, or are limited at distinct levels. This allows natural variation to be exploited as an unlimited source of new alleles or genes for the study of the genetic basis of quantitative trait variation. My doctoral work focuses on analysing natural variation for shoot growth and response to the environment in A. thaliana. Natural variation analyses aim at understanding how molecular genetic or epigenetic diversity controls phenotypic variation at different scales and times of plant development and under different environmental conditions, and how selection or demographic processes influence the frequency of those molecular variants in populations for them to get adapted to their local environment. As such, the analysis of A. thaliana natural variation can be addressed using a variety of approaches, from genetics and molecular methods to ecology and evolutionary questions. During my PhD, I got the chance to tackle several of those aspects through my contributions to three independent projects which have in common to exploit A. thaliana natural variation. The first one is the analysis of the pattern of polymorphism from a set of 102 A. thaliana accessions at the MOT1 gene coding for a molybdate transporter (an essential micronutrient) and responsible for contrasted growth and fitness among accessions in response to Mo availability in the soil. I showed at different geographical scales that MOT1 pattern of polymorphisms is not consistent with neutral evolution and shows signs of diversifying selection. This work helped reinforce the hypothesis that in some populations, mutations in MOT1 have been selected to face soils rich in Mo and potentially deleterious despite their negative effect on Mo-limiting soils. The second project consists in the characterisation and functional analysis of two putative receptor-like kinases (RLKs) identified from their effect on shoot growth specifically under mannitol-supplemented media and not in response to other osmotic constraints. The function of such RLKs in A. thaliana, which is not known to synthesize mannitol was intriguing at first but, through different experiments, we built the hypothesis that those RLKs could be activated by the mannitol produced by some pathogens such as fungi and participate to plant defensive response. The third project, in collaboration with Michel Vincentz's team from CBMEG (Brasil) and Vincent Colot (IBENS, Paris), consists in the analysis of the occurrence of natural epigenetic variants of the QQS gene in different populations from Central Asia and their possible phenotypic and adaptive consequences. Overall, these analyses of the genetic and epigenetic molecular variation leading to the biomass phenotype(s) in interaction with the environment provide clues as to how and where in the pathways adaptation is shaping natural variation.

Doctor of Philosophy / Polyphenol oxidase (PPO) catalyses undesirable darkening in wheat products such as Asian noodles. Genetic variation for PPO activity is characterized in bread wheat. Australian wheat breeding programmes recognize that reduced PPO activity is an important quality target. Despite this interest from breeders, no varieties possessing extremely low and null PPO activity exist. The development of null PPO wheat varieties is dependant on an understanding of the genetic control of the null phenotype. Knowledge of these factors will accelerate efforts to develop them. The inheritance of PPO activity was investigated in two populations that were derived from hybrids between a null PPO genotype and Australian wheat varieties Lang and QAlBis. Observed genetic ratios were consistent with two and three gene control, respectively in these populations. QTL mapping was performed in the QALBis x VAW08-A17 population. The Diversity Array Technology (DArT) approach was employed to genotype the QALBis x VAW08-A17 population. Three highly significant QTLs that control PPO activity were identified on chromosomes 2AL, 2BS and 2DL. Close associations between PPO activity and DArT marker loci wPt-7024, wPt-0094 and wPt-2544 were observed, respectively. Collectively, these loci explained 74% of the observed variation in PPO activity across seasons. Significant QTLs on chromosomes 1B and 3B were also identified that together explained an additional 17% of variation in PPO activity. The relationship between PPO activity and yellow alkaline noodles (YAN) colour stability parameters was investigated in a DM5637*B8 x H45 doubled haploid population. PPO activity and changes in YAN brightness (ΔL* 0-24h) and yellowness (Δb* 0-24h) in both seasons were analysed. Quantitative trait analyses of PPO activity, flour yellowness (b*) and YAN colour stability was also conducted in this population. QTL mapping of variation in PPO activity in the DM5637*B8 x H45 DH population identified a highly significant QTL on chromosome 2AL, which explained 52% of the observed variation across seasons. Regression analysis identified that wPt-7024 was highly significantly associated with PPO activity in this population. A highly significant association between this marker and PPO was also identified in the QALBis x VAW08-A17 population. Collectively, the three identified QTLs (on chromosomes 2AL, 7A and 7B) explained 71% of variation in PPO activity across seasons. A highly significant (P<0.001) QTL on chromosome 2B along with significant (P<0.01) QTLs on the chromosomes 1A, 3B, 4B and 5B were found to control flour yellowness. The QTLs on 2B, 4B and 5B were detected in both seasons analysed and accounted for 90% of variation in flour b* across seasons. The study on YAN colour stability located two highly significant (P<0.001) QTLs and two significant (P<0.01) QTLs that controlled the change in brightness of yellow alkaline noodle. The 2A QTL accounted for 64% of observed variation across seasons. It was in the same location as the PPO QTL and shared a common closest marker wPt-7024. Only one significant QTL for YAN a* (0-24h) was identified. It accounted for 12% of variation across seasons and was only detected in one season. One highly significant (P<0.001) QTL and two significant (P<0.01) QTLs were identified that controlled the change in yellowness of yellow alkaline noodle. The 2A QTL accounted for 68% of observed variation across seasons. The location of this QTL corresponded with that of 2A QTLs for PPO activity and L* of YAN in this study. Furthermore, wPt-7024 was also identified as the marker with the most significant association with L*. The identification of a correlation between the characters and a common location of a highly significant QTL for each of these characters indicates that it is likely that PPO activity is directly responsible for a large proportion of the changes in brightness and yellowness of YAN. QTLs for L* and b* of YAN were detected in a common location on chromosome 1A. However, no corresponding QTL was identified that controls PPO activity, highlighting the complexity of the relationship between these traits. Resistance to three rust pathogens (Puccinia graminis, Puccinia striiformis, and Puccinia triticina) was also investigated in the DM5637*B8 x H45 DH population because they are major yield limiting diseases in wheat. Disease response data at the seedling stage were converted to genotypic scores for rust genes Sr24/Lr24, Sr36, Lr13 and Yr7 to construct a genetic linkage map. No recombination was observed between rust resistance genes Sr36, Lr13 and Yr7 in this DH population. Therefore, these genes mapped in the same position on chromosome 2B. The Lr24/Sr24 locus was incorporated into the chromosome 3D map. Interval mapping analysis identified QTLs on chromosomes 2B, 3B, 4B and 5B that control adult plant resistance (APR) to stripe rust. Two QTLs on chromosomes 2B and 3D were identified that controlled APR to leaf rust in this DH population.

<p>The domestication of the pig began about 9 000 years ago and many of the existing domestic breeds have been selected for phenotypic traits like lean meat and fast growth. Domestic pigs are phenotypically very different from the ancestral wild boar that has adapted to survive in their natural environment. Because of their divergence, crosses between domestic pigs and wild boars are suitable for constructing genetic maps and Quantitative trait locus (QTL) analyses. A cross between the Large White and the European wild boar was thus initiated in the late 1980s. A major QTL for fat deposition and growth, denoted <i>FAT1</i>, was found on chromosome 4. The aim of this thesis was to further characterise the <i>FAT1</i> locus and to identify the causative gene(s) and mutation(s). We have identified new markers and constructed a high-resolution linkage and RH map of the <i>FAT1</i> QTL interval. We also performed comparative mapping to the human genome and showed that the pig chromosome 4 is homologous to human chromosomes 1 and 8. The gene order is very well conserved between the two species. In parallel we have narrowed down the <i>FAT1</i> QTL interval by repeated backcrossing to the domestic Large White breed for six generations. The QTL could be confirmed for fatness but not for growth. Furthermore, the data strongly suggested that there might be more than one gene underlying the <i>FAT1</i> QTL. Depending on which hypothesis to consider, the one- or two-loci model, the <i>FAT1</i> interval can be reduced to 3,3 or 20 centiMorgan (cM), respectively, based on the backcross experiments. In the last study we confirm the two-loci model with one locus primarily effecting abdominal fat and another locus primarily effecting subcutaneous fat. We have identified a missense mutation in the <i>RXRG</i> gene which is in strong association with the abdominal fat QTL and the mutation is a potential candidate for that locus.</p><p>Brown adipose tissue (BAT) is a specific type of fat essential for non-shivering thermogenesis in mammals. Piglets appear to lack BAT and rely on shivering as the main mechanism for thermoregulation. Uncoupling protein 1 (<i>UCP1</i>) gene is exclusively expressed in BAT and its physiological role is to generate heat by uncoupling oxidative phosphorylation. We show that the <i>UCP1</i> gene has been disrupted in the pig lineage about 20 years ago. The inactivation of <i>UCP1</i> provides a genetic explanation for the poor thermoregulation in piglets. </p>

The domestication of the pig began about 9 000 years ago and many of the existing domestic breeds have been selected for phenotypic traits like lean meat and fast growth. Domestic pigs are phenotypically very different from the ancestral wild boar that has adapted to survive in their natural environment. Because of their divergence, crosses between domestic pigs and wild boars are suitable for constructing genetic maps and Quantitative trait locus (QTL) analyses. A cross between the Large White and the European wild boar was thus initiated in the late 1980s. A major QTL for fat deposition and growth, denoted FAT1, was found on chromosome 4. The aim of this thesis was to further characterise the FAT1 locus and to identify the causative gene(s) and mutation(s). We have identified new markers and constructed a high-resolution linkage and RH map of the FAT1 QTL interval. We also performed comparative mapping to the human genome and showed that the pig chromosome 4 is homologous to human chromosomes 1 and 8. The gene order is very well conserved between the two species. In parallel we have narrowed down the FAT1 QTL interval by repeated backcrossing to the domestic Large White breed for six generations. The QTL could be confirmed for fatness but not for growth. Furthermore, the data strongly suggested that there might be more than one gene underlying the FAT1 QTL. Depending on which hypothesis to consider, the one- or two-loci model, the FAT1 interval can be reduced to 3,3 or 20 centiMorgan (cM), respectively, based on the backcross experiments. In the last study we confirm the two-loci model with one locus primarily effecting abdominal fat and another locus primarily effecting subcutaneous fat. We have identified a missense mutation in the RXRG gene which is in strong association with the abdominal fat QTL and the mutation is a potential candidate for that locus. Brown adipose tissue (BAT) is a specific type of fat essential for non-shivering thermogenesis in mammals. Piglets appear to lack BAT and rely on shivering as the main mechanism for thermoregulation. Uncoupling protein 1 (UCP1) gene is exclusively expressed in BAT and its physiological role is to generate heat by uncoupling oxidative phosphorylation. We show that the UCP1 gene has been disrupted in the pig lineage about 20 years ago. The inactivation of UCP1 provides a genetic explanation for the poor thermoregulation in piglets.

Les résistances génétiques permettent une lutte efficace contre les maladies des plantes cultivées mais sont limitées par les capacités d'évolution des bioagresseurs ciblés. Chez le piment, le fonds génétique peut améliorer la durabilité de la résistance au PVY conférée par le gène majeur pvr23. L'objectif de ma thèse était de caractériser les facteurs génétiques de l'hôte conditionnant la durabilité du gène majeur en répondant aux questions suivantes : (i) Quels sont leurs actions sur l'évolution des populations virales ? (ii) Correspondent-ils aux QTL (quantitative trait loci) de résistance partielle ? (iii) Sont-ils répandus au sein des ressources génétiques du piment ? Différentes expérimentations incluant des tests de résistances, d'évolution expérimentale et de compétition entre différents variants viraux, ont montré que les facteurs du fonds génétique augmentant la durabilité de pvr23 agissaient en : (i) diminuant la concentration virale dans la plante, (ii) en réduisant les probabilités de mutations du PVY vers le contournement du gène pvr23 et (iii) en ralentissant la sélection des variants viraux contournants. La détection de QTL et la cartographie des facteurs génétiques affectant la fréquence de contournement de pvr23 (QTL de durabilité) a mis en évidence quatre régions du génome du piment qui, par des effets additifs ou épistatiques, expliquent 70% de la variabilité phénotypique observée. La cartographie comparée montre que trois des quatre QTL de durabilité co-localisent avec des QTL affectant la résistance partielle, suggérant que les QTL de résistance partielle ont un effet pléiotropique sur la durabilité d'un gène majeur de résistance. L'étude d'une collection de 20 accessions de piment, porteuses de pvr23 ou pvr24(allèle très proche de pvr23) dans des fonds génétiques variés, a montré que les fonds génétiques favorables à la durabilité de ces allèles de résistance sont fréquents dans les ressources génétiques du piment. Ces résultats mettent en évidence que la durabilité d'un gène majeur de résistance peut-être fortement augmentée lorsqu'il est associé à des facteurs génétiques réduisant la multiplication du pathogène. De plus, la fréquence de contournement du gène majeur s'est révélée être un caractère très héritable (h²=0.87) et la détection de QTL affectant ce caractère est possible. La sélection directe pour de tels QTL est donc envisageable et ouvre de nouvelles perspectives pour préserver la durabilité des gènes majeurs de résistance utilisés en sélection variétale.

Doctor of Philosophy / Polyphenol oxidase (PPO) catalyses undesirable darkening in wheat products such as Asian noodles. Genetic variation for PPO activity is characterized in bread wheat. Australian wheat breeding programmes recognize that reduced PPO activity is an important quality target. Despite this interest from breeders, no varieties possessing extremely low and null PPO activity exist. The development of null PPO wheat varieties is dependant on an understanding of the genetic control of the null phenotype. Knowledge of these factors will accelerate efforts to develop them. The inheritance of PPO activity was investigated in two populations that were derived from hybrids between a null PPO genotype and Australian wheat varieties Lang and QAlBis. Observed genetic ratios were consistent with two and three gene control, respectively in these populations. QTL mapping was performed in the QALBis x VAW08-A17 population. The Diversity Array Technology (DArT) approach was employed to genotype the QALBis x VAW08-A17 population. Three highly significant QTLs that control PPO activity were identified on chromosomes 2AL, 2BS and 2DL. Close associations between PPO activity and DArT marker loci wPt-7024, wPt-0094 and wPt-2544 were observed, respectively. Collectively, these loci explained 74% of the observed variation in PPO activity across seasons. Significant QTLs on chromosomes 1B and 3B were also identified that together explained an additional 17% of variation in PPO activity. The relationship between PPO activity and yellow alkaline noodles (YAN) colour stability parameters was investigated in a DM5637*B8 x H45 doubled haploid population. PPO activity and changes in YAN brightness (ΔL* 0-24h) and yellowness (Δb* 0-24h) in both seasons were analysed. Quantitative trait analyses of PPO activity, flour yellowness (b*) and YAN colour stability was also conducted in this population. QTL mapping of variation in PPO activity in the DM5637*B8 x H45 DH population identified a highly significant QTL on chromosome 2AL, which explained 52% of the observed variation across seasons. Regression analysis identified that wPt-7024 was highly significantly associated with PPO activity in this population. A highly significant association between this marker and PPO was also identified in the QALBis x VAW08-A17 population. Collectively, the three identified QTLs (on chromosomes 2AL, 7A and 7B) explained 71% of variation in PPO activity across seasons. A highly significant (P<0.001) QTL on chromosome 2B along with significant (P<0.01) QTLs on the chromosomes 1A, 3B, 4B and 5B were found to control flour yellowness. The QTLs on 2B, 4B and 5B were detected in both seasons analysed and accounted for 90% of variation in flour b* across seasons. The study on YAN colour stability located two highly significant (P<0.001) QTLs and two significant (P<0.01) QTLs that controlled the change in brightness of yellow alkaline noodle. The 2A QTL accounted for 64% of observed variation across seasons. It was in the same location as the PPO QTL and shared a common closest marker wPt-7024. Only one significant QTL for YAN a* (0-24h) was identified. It accounted for 12% of variation across seasons and was only detected in one season. One highly significant (P<0.001) QTL and two significant (P<0.01) QTLs were identified that controlled the change in yellowness of yellow alkaline noodle. The 2A QTL accounted for 68% of observed variation across seasons. The location of this QTL corresponded with that of 2A QTLs for PPO activity and L* of YAN in this study. Furthermore, wPt-7024 was also identified as the marker with the most significant association with L*. The identification of a correlation between the characters and a common location of a highly significant QTL for each of these characters indicates that it is likely that PPO activity is directly responsible for a large proportion of the changes in brightness and yellowness of YAN. QTLs for L* and b* of YAN were detected in a common location on chromosome 1A. However, no corresponding QTL was identified that controls PPO activity, highlighting the complexity of the relationship between these traits. Resistance to three rust pathogens (Puccinia graminis, Puccinia striiformis, and Puccinia triticina) was also investigated in the DM5637*B8 x H45 DH population because they are major yield limiting diseases in wheat. Disease response data at the seedling stage were converted to genotypic scores for rust genes Sr24/Lr24, Sr36, Lr13 and Yr7 to construct a genetic linkage map. No recombination was observed between rust resistance genes Sr36, Lr13 and Yr7 in this DH population. Therefore, these genes mapped in the same position on chromosome 2B. The Lr24/Sr24 locus was incorporated into the chromosome 3D map. Interval mapping analysis identified QTLs on chromosomes 2B, 3B, 4B and 5B that control adult plant resistance (APR) to stripe rust. Two QTLs on chromosomes 2B and 3D were identified that controlled APR to leaf rust in this DH population.

The overall accuracy, efficiency and profitability of livestock improvement strategies can be greatly increased by incorporating quantitative genetics into livestock selection and breeding. Since the introduction of quantitative genetics, a range of traits describing the animal e.g. in terms of health, growth, fecundity, production, have been extensively evaluated in terms of genetics and are now commonly manipulated through breeding to achieve specific selection goals. An industry led enquiry as to the possibility of including spine traits in genetic selection to increase back length in sheep was the basis of the present thesis. Collecting information on spine traits (spine length, vertebrae length and vertebrae number) is of particular interest and use to the sheep breeding industry as there may be the potential to increase meat yield from the highly valuable longissimus thoracis et lumborum (LTL or loin), located parallel to the spine, with little associated change in production costs. The thesis focusses on the use of X-ray computed tomography (CT) scanning as a technique which would allow spine traits to be measured in vivo, hence being useful for genetic selection. The topogram scans produced from the CT scanning procedure were analysed to derive spine trait information for the thesis. The scans were from Scottish Blackface (maternal breed stock), Texel (terminal sire breed), Texel cross Mule and Poll Dorset cross Mule (three-way cross slaughter lambs) so as to represent the divergent genotypes found across the different levels of the United Kingdom’s (UK) three-tier crossbreeding structure of sheep. The present study explored as a first step intra- and inter-operator repeatability of assessment of spine traits from CT derived topograms, as a means to investigate the suitability of the approach for widespread uptake within industry where operators will vary. The results showed that there was high repeatability for intra- and inter-operator assessment of spine trait measurements verifying that the CT method could be accepted as a reliable alternative (to slaughter for example) to quantify spine traits. To determine whether spine traits are similar across the range of breeds representing the key genotypes and crosses in the UK sheep industry, numerous CT topograms were analysed. The results showed marked variation in spine traits within and between Scottish Blackface, Texel, Texel cross Mule and Poll Dorset cross Mule breeds and crosses. For example, the Texel breed was found to have the largest within-breed range for thoracolumbar vertebrae number (17 – 21; the majority possessing 19), but the spine length of these animals was, on average, significantly shorter than the other breed/cross groups. The present study concluded that the significant differences between the breeds and breed types for the particular spine traits were possibly indicative of a genetic control for these traits. Furthermore, investigation into the phenotypic correlations between spine and production traits revealed some directional associations which may prove beneficial for meat production. For example, Scottish Blackface lambs which had a longer length of a specific spine region had an associated decrease in the volume of carcass fat. Texel lambs which had a longer length of a specific spine region had a slightly larger loin muscle area, at a given weight. The present study also examined animals from a population of Texel lambs already heavily selected for increased muscling. The Texel muscling quantitative trait locus (TM-QTL), segregating in these animals and generally in the UK’s Texel sheep population, is expressed through a polar overdominance pattern of inheritance and its effect on the loin (localised muscle hypertrophy) is commonly utilised in the selection and breeding of Texel sheep to improve meat production. Examination of topograms from lambs bearing the whole range of TM-QTL genotypes showed little evidence to suggest that the change in loin shape/increased loin muscling, as a result of the TM-QTL and its inheritance, has led to any associated change in the underlying spine characteristics. This suggests that selection for increased muscling associated with the TM-QTL may be achieved independently of changes in the spine traits studied. The potential to breed for certain spine traits to increase vertebrae number and hence chops or loin yield can be enhanced by establishing the genetic parameters for the traits. The present study employed a collection of performance trait records from Texel lambs to provide the basis for genetic analysis. The results showed different levels of heritability for the different spine traits but also high standard errors. For example, heritability of vertebrae number was dependent on vertebra location: for thoracic vertebrae heritability was high (ℎ2 = 0.99; SE = 0.42), for lumbar vertebrae heritability was low (ℎ2 = 0.08; SE = 0.12), whereas in contrast, thoracolumbar vertebrae heritability was moderate (ℎ2 = 0.44; SE = 0.27). Phenotypic and genetic correlations between all combinations of traits were also obtained. Accurate predictions of the size and direction of response to selection can be achieved through such genetic analysis of traits. The more that is known of the genetic characteristics of traits and their genetic correlations with other economically important traits, the more efficiently it can be built into breeding programmes improving the overall performance of stock. The results of this study showed that providing spine measurements can contribute to the diversity of trait information available to breeders. The present study also suggests that there may be opportunities to select for increased spine length/vertebrae number which would benefit the sheep industry in terms of increased chop number/loin yield. Although more data are needed prior to implementation. Practical uptake of selection for spine traits would be enhanced due to the straightforward nature of the measurements and the high operator repeatability.

Nitrogen (N) is a central nutrient in cropping systems. However, a considerable N fraction is lost through runoffs and leaching with detrimental consequences for environment and controversial effects on human health. Increasing the plant N uptake by optimizing the degree of root branching for exploring a larger soil volume in search of the mobile nitrate resource may contribute to limit soil leaching and subsequently to rely more efficiently on the soil mineralization and fertilizer inputs. Rapeseed (Brassica napus L.) is a major oil crop that highly depends on N fertilization. This doctoral thesis aims at exploring the diversity of root morphology in recently selected cultivars and in a large set of rapeseed inbred lines, and at understanding the genetic control on root morphology and how it is impacted by N nutrition.Firstly, a panel of twenty-eight European recently selected cultivars of winter oilseed rape were tested in laboratory and field conditions. Upon hydroponic culture, these hybrids showed a great diversity for biomass production and root morphological traits. Differences in root and shoot dry biomasses and lateral root length were mainly explained by the genotype, while differences in primary root length by the nutrition. The cultivars were tested in a pluriannual field trial. The observed variation for yield and seed quality traits attributed to the genotype was more important than the year or the genotype x year interaction effects. The total root length measured in laboratory could predict the proportion of nitrogen taken-up from the field and reallocated to the seeds. The genetic interrelationship between cultivars, established with polymorphic markers, indicated a very narrow genetic base. Positive correlations were found between the genetic distance measures, root morphological trait distances during nitrogen depletion conditions, and agronomic performance. Secondly, three cultivars previously selected from a root morphology screen at a young developmental stage were field tested with two nitrogen applications. The purpose was to examine the relationship between root morphology and Nitrogen Uptake Efficiency (NUpE) and to test the predictiveness of canopy optical indices for seed quality and yield. A tube-rhizotron system was used to incorporate below-ground root growth information. One-meter length clear tubes were installed in soil at an angle of 45°. The root development was followed with a camera at key growth stages in autumn (leaf development) and spring (stem elongation and flowering). Autumn was a critical time window to observe the root development and exploration in deeper horizons (36-48 cm) was faster without any fertilization treatment. Analysis of the rhizotron images was challenging and it was not possible to clearly discriminate between cultivars. Canopy reflectance and leaf optical indices were measured with proximal sensors. The Normalized Difference Vegetation Index (NDVI) was a positive indicator of biomass and seed yield while the Nitrogen Balance Index (NBI) was a positive indicator of above-ground biomass N concentration at flowering and seed N concentration at harvest.Thirdly, the natural variability offered by a diversity set of 392 inbred lines was screened to apprehend the genetic control of root morphology in rapeseed and how it is impacted by nitrogen nutrition. Seedlings grew hydroponically with low (0.2 mM) or elevated (5 mM) nitrate supplies. Low nitrate supply triggered the primary root and lateral root growth, while elevated supply promoted shoot biomass production. A considerable variation degree in the root morphological traits was observed across the diversity set, and there was no trade-off between abundant lateral root branching and shoot biomass production. Root traits were mainly dependent on the genotype and highly heritable. A genome wide association study identified some genomic regions associated with biomass production and root morphological traits. A total of fifty-nine QTLs were identified and thirty of them were integrated into seven clusters on chromosomes A01 and C07. Some candidate genes were identified with Arabidopsis orthologs related to root growth and development, nitrogen nutrition or hormone regulation.This study provides promising routes for redesigning the root system architecture by uncovering nitrogen-interactive genomic regions shaping root morphology. A perspective is to develop genetic markers associated with root morphological traits that could be used for assisted breeding. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished