Grain protein content (GPC) in wheat has been found to be regulated by the gene NAM-B1. Homologues to the NAM-B1 gene have been found in barley, HvNAM-1 and HvNAM-2. Previous studies have found that base mutations in the NAM-1 gene at base position 544 might have an impact on GPC. Previous studies also found that landrace of barley showed higher GPC than cultivated barley, indicating that plant improvement might have affected base mutations and therefore GPC. I wanted to study if there are any nutritional differences in Nordic barley and if those differences might correlate with haplotypes. Comparisons of barley varieties from four Nordic countries, and two varieties from the US used as low and high GPC controls, did not show any significant differences depending on their origin country and no differences regarding plant improvement status between the countries. When sequencing Nordic barley varieties, five haplotypes were found for the gene HvNAM-1, and two haplotypes for the gene HvNAM-2. A low polymorphism for both genes indicate a strong natural selection for the consensus haplotype which might be preferable for Nordic climate with a short growing season and cold temperatures. Even though it is not clear what is the cause of the low polymorphism in Nordic barley varieties, they showed a generally higher nutrient content than barley varieties of the high GPC and may be suitable for breeding for a yield with a high nutrient content.

Rice is an important human staple food for over half of the world’s population. Amylose content (AC), gelatinization temperature (GT), grain protein content (GPC), percentage grain chalkiness (PGC), and mineral content are important parameters for evaluating rice quality, which attracts customers and breeders. Only limited genes or QTLs (OsAAP6, OsGluA2, OsASN1, Chalk5, OsHMA3, etc.) are reported regulating rice GPC, PGC, and mineral content due to the lack of genetic knowledge and molecular markers. To dissect the genetic architecture of rice grain quality regulation, genome wide association studies (GWAS) were performed using two populations (USDA-mini core collection and a panel of 662 rice accessions from the 3K Rice Genomes Project). A total of 28, 11, 4, 3, 40, 3, 4, 3, and 10 QTLs were identified associated with Cd, Co, Cu, K, Mo, Ni, Rb, Sr, and Zn under flooded environment, while, 23, 7, 7, 7, and 3 QTLs were detected to be associated with Cd, Fe, Mo, Ni, and Zn under unflooded environment, respectively. Moreover, 6, 5, and 2 significant QTLs were tightly associated with kernel length, kernel rate, kernel width, respectively. Furthermore, 44, 7, 27, and 20 QTLs were identified associated with AC, GT, GPC, and PGC, respectively. Overall, 53 (~ 20.08%) of the 264 QTLs were coinciding with previously reported QTLs/genes, and 211 (~ 79.92%) were novel QTLs. A candidate gene, OsPCAT (putative cationic transporter), associated with GPC in the dry season was selected for further analysis. The OsPCAT gene belongs to the amino acid transporters (AATs) family with nine closely related members reported in Oryza Sativa. The classification and evolution of the CAT family (a subgroup of AATs family) using 61 species were studied. The over-expression lines (OsPCAT-OX) and CRISPR-Cas9 knock-out lines (OsPCAT-KO) were developed to study the function of OsPCAT gene. The preliminary results showed the GPC in OsPCAT-OX lines was increased and OsPCAT-KO lines were decreased compared to WT. Overall, a large number of new and reported QTLs associated with rice grain quality have been identified. This work lays the foundation for marker development in breeding and further investigation on rice grain quality regulation.

This thesis concerns Precision Agriculture (PA) technology which involves methods developed to optimise grain yield by examining data quality and modelling protein/yield relationship of wheat and sorghum fields in central and southern Queensland. An important part of developing strategies to optimisise grain yield is the understanding of PA technology. This covers major aspects of PA which includes all the components of Site- Specific Crop Management System (SSCM). These components are 1. Spatial referencing, 2. Crop, soil and climate monitoring, 3. Attribute mapping, 4. Decision suppport systems and 5. Differential action. Understanding how all five components fit into PA significantly aids the development of data analysis methods. The development of PA is dependent on the collection, analysis and interpretation of information. A preliminary data analysis step is described which covers both non-spatial and spatial data analysis methods. The non-spatial analysis involves plotting methods (maps, histograms), standard distribution and statistical summary (mean, standard deviation). The spatial analysis covers both undirected and directional variogram analyses. In addition to the data analysis, a theoretical investigation into GPS error is given. GPS plays a major role in the development of PA. A number of sources of errors affect the GPS and therefore effect the positioning measurements. Therefore, an understanding of the distribution of the errors and how they are related to each other over time is needed to complement the understanding of the nature of the data. Understanding the error distribution and the data give useful insights for model assumptions in regard to position measurement errors. A review of filtering methods is given and new methods are developed, namely, strip analysis and a double harvesting algoritm. These methods are designed specifically for controlled traffic and normal traffic respectively but can be applied to all kinds of yield monitoring data. The data resulting from the strip analysis and double harvesting algorithm are used in investigating the relationship between on-the-go yield and protein. The strategy is to use protein and yield in determining decisions with respect to nitrogen managements. The agronomic assumption is that protein and yield have a significant relationship based on plot trials. We investigate whether there is any significant relationship between protein and yield at the local level to warrent this kind of assumption. Understanding PA technology and being aware of the sources of errors that exist in data collection and data analysis are all very important in the steps of developing management decision strategies.

Agriculture is, after fossil fuels, the second largest producer of greenhouse gas emissions, which are responsible for global climate change, and it is necessary to look for ways to reduce this environmental load. Cereals are the most cultivated crops in the world, so it is appropriate to examine their share of this load. The aim of the thesis was to evaluate and compare the environmental aspects of the cultivation of selected cereals (wheat, rye and barley) in the conventional and ecological farming system. The resulting environmental load was first calculated on 1 kg of grain, and then the load was recalculated to a load of 1 kg of protein contained in grain of selected cereals. Protein content in grain is one of the grain quality indicators. A simplified LCA method has been used for the environmental load calculations. This method is used for environmental impact assessments and covers the whole life cycle of the product.

Le rendement en grains (Rdt) et la teneur en protéines (%Prot) sont deux cibles majeures dans les programmes de sélection variétale chez le blé car ces caractères contribuent à la valeur économique de cette culture. Malheureusement, leur amélioration simultanée est empêchée par la relation négative %Prot-Rdt. Il a été montré que l’écart à cette relation (“Grain Protein Deviation”, GPD) est déterminé en partie génétiquement et serait utile pour modifier cette relation négative mais ses bases biologiques restent mal comprises à ce jour. Nous avons montré que le GPD est principalement relié à la variabilité génétique pour l’absorption d’azote post-floraison (ABSN) dans les conditions agro-climatiques du Nord-Ouest de l’Europe. Nous proposons que la variabilité génétique pour l’accès à l’azote du sol (architecture et fonctionnement racinaire) ou pour la régulation de ABSN par le statut azoté (transport et assimilation de l’azote) pourrait expliquer le GPD. Etant donné que le retardement de la sénescence durant la période post-floraison peut résulter en une augmentation de ABSN, nous avons analysé les déterminants génétique des relations entre durée de sénescence des feuilles après floraison et Rdt ou %Prot, observées au niveau phénotypique, en utilisant des données acquises sur une population de cartographie de blé cultivée au sein d’un large réseau expérimental. Une association positive entre durée de sénescence des feuilles après floraison et %Prot ou Rdt a été observée selon les environnements étudiés. Nous faisons l’hypothèse que l’impact d’un retardement de la sénescence des feuilles après floraison pourrait être modulé selon la disponibilité en azote durant cette période, ce qui conduirait à modifier la relation %Prot-Rdt selon les environnements étudiés. Enfin, des données obtenues sur trois populations de cartographie cultivées dans un large réseau expérimental ont permis de suggérer, après méta-analyse de QTL, des régions génomiques potentiellement utiles en sélection pour améliorer la %Prot sans diminuer le Rdt. Ceci a permis de mettre en avant des régions situées sur les chromosomes 2A et 3B. En particulier, la région située sur le 2A pourrait être reliée à la présence d’un gène codant pour une glutamine synthétase chloroplastique qui a été associée à la variabilité génétique pour %Prot chez le blé tendre dans une étude antérieure. / Grain yield (GY) and grain protein concentration (GPC) are two major targets in wheat breeding programs as these traits contribute to the economic value of the wheat crop. Unfortunately, their simultaneous improvement is hampered by the genetic negative GPC-GY relationship. It has been shown that the deviation to this relationship (“Grain Protein Deviation”, GPD) has a genetic basis and might be useful to shift this negative relationship but its biological bases remain unclear. GPD was shown to be mainly related to the genetic variability for post-anthesis nitrogen (N) uptake (PANU) in the North-West European agro-climatic conditions. We proposed that the genetic variability for the access to N in the soil (root architecture and functioning) or for the regulation of PANU by the plant N status (N transport and assimilation) could explain GPD. As delaying leaf senescence during the post-anthesis period might result in increasing PANU, we analysed the genetic determinants of the phenotypic relationships between leaf senescence duration after anthesis and GPC or GY using data obtained on a wheat mapping population grown in a large mutli-environment trial network. A positive association was found between leaf senescence duration and GPC or GY depending onthe environment. We suggested that the impact of delaying leaf senescence after anthesis on GY or GPC might be modulated by the N availability during the post-anthesis period and would lead to modify the GPC-GY relationship depending on the considered environments. Finally, data obtained on three connected mapping populations grown in a large mutli-environment trial network were used to suggest by meta-QTL analysis potential genomic regions possibly useful in wheat breeding to improve GPC without reducing GY. This put forward genomic regions located on the 2A and 3B chromosomes as potentially interesting targets to improve GPC. In particular, the region on the 2A might be related to a chloroplastic glutamine synthetase gene previously shown to be associated with genetic variability for GPC in bread wheat.

La concentration en protéines des grains est un critère qualitatif majeur qui conditionne la valeur économique et technologique du blé tendre (Triticum aestivum L.). Cependant, la forte relation négative existant entre concentration en protéines et rendement en grains implique que l’amélioration de la concentration en protéines par une approche génétique soit complexe à atteindre sans impacter négativement le rendement. Pour contourner cette difficulté, il a été proposé qu’une sélection variétale basée sur l’écart à cette relation négative (nommé Grain Protein Deviation ; GPD) permette d’améliorer la concentration en protéines indépendamment du rendement. Au niveau physiologique, le GPD est fortement corrélé à la capacité des génotypes à absorber de l’azote après floraison indépendamment de la quantité d’azote déjà absorbée à floraison, suggérant que la satiété en azote soit à la base de son établissement. Envisager une sélection sur la base du GPD nécessite cependant d’acquérir des connaissances approfondies des mécanismes impliqués dans la régulation de l’absorption d’azote par la satiété en azote, qui permettraient de cibler précisément des traits simples à quantifier et robustement associés à cette capacité accrue d’accumulation de protéines dans les grains.Cette étude se base sur deux expérimentations conduites en conditions contrôlées et une expérimentation au champ. Dans chacune de ces expérimentations, différents niveaux de fertilisation ont été appliqués en pré-floraison afin d’obtenir des statuts azotés contrastés à floraison. L’effet du statut azoté à floraison sur l’absorption post-floraison a ensuite été observé dans différentes conditions de disponibilités d’azote après floraison. Des mesures physiologiques et moléculaires ont été réalisées en parallèle des mesures d’absorption d’azote.Nous avons mis en évidence que l’absorption d’azote post-floraison présente une dynamique élaborée qui suppose qu’elle est soumise à des régulations complexes. Parmi celles-ci, le statut azoté des plantes à floraison conditionne en grande part la quantité d’azote absorbée dans les jours qui suivent la floraison (PANUprécoce , de floraison à floraison + 250 degrés-jour). La quantité de PANUprécoce se présente comme un déterminant fort de la concentration en protéines des grains du fait de la forte corrélation positive observée entre ces deux traits en conditions contrôlées et au champ, et ce indépendamment du niveau de rendement. L’étude de deux génotypes robustement contrastés pour le GPD a montré qu’à statuts azotés équivalents, la quantité de PANUprécoce est sujette à des effets génétiques qui tendent à confirmer l’impact de la variabilité génétique de satiété en azote sur l’établissement du GPD.Ces travaux ont permis de proposer des marqueurs du GPD potentiellement valorisables en sélection. Au niveau physiologique, la croissance des tiges après floraison se présente comme un marqueur prometteur du GPD car ce trait est fortement corrélé à la PANUprécoce. Au niveau moléculaire, la concentration en nitrates des racines, également soumise à des effets génétiques, est proposée comme marqueur potentiel du fait de son rôle probable dans la régulation expressionnelle des gènes impliqués dans l’absorption et l’assimilation d’azote. / Grain protein concentration is one of the major qualitative criteria of bread wheat (Triticum aestivum L.) economic and technological value. However, the negative relationship existing between protein concentration and grain yield implies that grain protein concentration improvement is complex to achieve without detrimental effect on grain yield. Breeding programs based on the deviation to this negative relationship (Grain protein deviation of GPD) have been proposed to be a suitable strategy to improve grain nitrogen concentration without detrimental effects on yield. At a physiological level, GPD is strongly correlated with genotypes aptitude to uptake nitrogen after flowering independently of the nitrogen amount already taken up before this stage, suggesting that satiety for nitrogen could be involved in its establishment. Breeding for GPD implies however a more detailed knowledge of the processes implied in nitrogen uptake regulation by nitrogen plant satiety. This would allow targeting traits both simple to measure and robustly associated with this increased capacity to accumulate proteins in grains.The present study is based on two experiments carried on under controlled conditions and a third led under field conditions. In all experiments, various levels of pre-flowering fertilization were applied in order to obtain contrasted plant nitrogen status at flowering. Nitrogen status effect on post-flowering nitrogen uptake was observed under various post-flowering N availability conditions. Physiological and molecular measurements were carried out in parallel with uptake measurements.We highlighted that post-flowering nitrogen uptake has an elaborate dynamic, suggesting the involvement of complex regulations. Among these, plant nitrogen status at flowering determines to a great extent the amount of nitrogen taken up during the days following flowering (early PANU, from flowering to flowering +250 °C.days-1). Early PANU appears to be a strong determinant of grain protein concentration, as strong positive correlations were observed between these two traits both under controlled conditions and field conditions, independently of grain yield level. The study of two genotypes strongly contrasted for GPD highlighted that, despite comparable N status, early PANU is subjected to strong genetic variations which tend to identify N satiety as a determinant of GPD.The present study identified robust markers of GPD of potential use in plant breeding. At a physiological level, post flowering stem elongation appears to be a promising marker of GPD since this trait is strongly correlated with early PANU. At a molecular level, root nitrate concentration, a trait submitted to genetic variations, is also proposed as a marker of GPD because of its role in the expression regulation of the genes governing nitrogen uptake and assimilation.

Lentil (Lens culinaris Med.) is an important component of the human diet in the world, but in the meantime, Europe produces only 26% of the lentils it consumes. This is partly due to strong agronomic weaknesses that reduce yield such as lodging, bruchid beetles and weeds, especially in organic farming. Intercropping, the simultaneous growing of two or more species in the same field is tested here as an option to reduce these drawbacks and develop organic lentil production. The aims of this thesis were to (1) assess the potential of lentil-spring wheat intercrops to produce organic lentil, (2) understand the mechanisms that explain their performances, and (3) evaluate the profitability of such intercrops. A two-year field experiment was carried out in southwestern France in 2015 and 2016 under organic farming rules. Four lentil and two wheat cultivars were grown as sole crops and intercrops in multiple additive and substitutive designs. Our results showed that the total intercrop attainable grain yield was higher than the mean of sole crops. Yet, lentil yield in intercrop was lower than in sole crop as the result of a strong competition for resources from wheat in early lentil growth stages reducing the number of branches per plant of lentil. This led to lower gross margins of intercrops. However, lentil lodging was strongly reduced in intercrops thus its mechanical harvest efficiency increased. This led to similar mechanically harvested yields of lentil in intercrop and sole crop. Consequently, after mechanical harvest and grain cleaning, the marketable gross margin of intercrops was higher than that of sole crops. Our results suggest that (1) intercrop had no effect on bruchids, (2) the most effective intercrop is when lentil is at sole crop density and wheat at 15-20%, (3) intercrop performance is due to complementary use of N pools through legume N2 fixation and (4) the intensity of interspecific interactions depends on year, wheat density and genotypes. Our work indicates that lentil-spring wheat intercrop can develop organic lentil production but a better understanding of Genotype x Environment x Cropping system interactions may be useful to design optimized managements.

La lentille (Lens culinaris Med.) est une composante importante des régimes alimentaires de nombreuses populations à travers le monde mais sa consommation en Europe est relativement faible. L’Europe produit seulement 26% de sa consommation de lentille et ce déficit est en partie causé par d’importants verrous agronomiques comme la verse, les bruches et la compétition des adventices qui réduisent ses rendements, notamment en agriculture biologique. Les associations de cultures, définies comme la culture simultanée d’au moins deux espèces différentes sur une même surface pendant une durée significative, sont considérées comme une option pour lever ces verrous agronomiques et ainsi développer la production de lentille en agriculture biologique. Les objectifs de cette thèse étaient de (1) évaluer le potentiel des associations de lentille et de blé de printemps pour produire de la lentille en conditions d’agriculture biologique et (2) comprendre les principaux mécanismes sous-jacents à la performance des associations. Des essais agronomiques ont été mis en place en 2015 et 2016 en conditions d’agriculture biologique. Quatre variétés de lentille et de blé de printemps ont été conduites en culture pures et en plusieurs associations de type substitutif et additif. Nos résultats montrent que le rendement moyen des associations avant récolte mécanique était plus élevé que le rendement moyen des cultures pures. Néanmoins, le rendement de lentille en association était inférieur à celui de la lentille en culture pure en raison d’une compétition forte et précoce du blé pour les ressources qui a causé la diminution nombre de ramifications par plante de la lentille. Le prix de la lentille étant environ quatre fois plus élevé que celui du blé, la marge brute des associations avant récolte était inférieure à celle de la lentille en culture pure. Cependant, la verse de la lentille a été fortement réduite en association, entrainant une augmentation de l’efficacité de sa récolte mécanique. En conséquence les rendements de lentille issus de la récolte mécanique se sont avérés similaires en association et en culture pure. Enfin, après tri et nettoyage des graines, la marge brute des associations sur le rendement commercialisable était supérieure à celle des cultures pures. Nos résultats montrent que (1) les associations n’ont pas eu d’effet sur le taux de bruchage des lentilles, (2) l’association la plus performante est constituée de lentille à densité équivalente à la culture pure dans laquelle on ajoute 15-20% de blé, (3) la performance des associations est due à une utilisation complémentaire de l’azote rendue possible par la fixation symbiotique de l’azote par la lentille et (4) l’intensité des compétitions entre espèces dépendent de l’année, de la densité de blé et des génotypes. En conclusion, nos travaux indiquent que les associations de lentille et de blé de printemps peuvent permettre de développer la production de lentille en agriculture biologique mais qu’une meilleure compréhension des interactions de type génotype x environnement x conduite pourrait permettre de mettre au point des couverts encore plus performants. / Lentil (Lens culinaris Med.) is an important component of the human diet in the world, but in the meantime, Europe produces only 26% of the lentils it consumes. This is partly due to strong agronomic weaknesses that reduce yield such as lodging, bruchid beetles and weeds, especially in organic farming. Intercropping, the simultaneous growing of two or more species in the same field is tested here as an option to reduce these drawbacks and develop organic lentil production. The aims of this thesis were to (1) assess the potential of lentil-spring wheat intercrops to produce organic lentil, (2) understand the mechanisms that explain their performances, and (3) evaluate the profitability of such intercrops. A two-year field experiment was carried out in southwestern France in 2015 and 2016 under organic farming rules. Four lentil and two wheat cultivars were grown as sole crops and intercrops in multiple additive and substitutive designs. Our results showed that the total intercrop attainable grain yield was higher than the mean of sole crops. Yet, lentil yield in intercrop was lower than in sole crop as the result of a strong competition for resources from wheat in early lentil growth stages reducing the number of branches per plant of lentil. This led to lower gross margins of intercrops. However, lentil lodging was strongly reduced in intercrops thus its mechanical harvest efficiency increased. This led to similar mechanically harvested yields of lentil in intercrop and sole crop. Consequently, after mechanical harvest and grain cleaning, the marketable gross margin of intercrops was higher than that of sole crops. Our results suggest that (1) intercrop had no effect on bruchids, (2) the most effective intercrop is when lentil is at sole crop density and wheat at 15-20%, (3) intercrop performance is due to complementary use of N pools through legume N2 fixation and (4) the intensity of interspecific interactions depends on year, wheat density and genotypes. Our work indicates that lentil-spring wheat intercrop can develop organic lentil production but a better understanding of Genotype x Environment x Cropping system interactions may be useful to design optimized managements.

Les associations d'espèces sont définies comme la culture simultanée d'au moins deux espèces sur la même parcelle pendant une période significative de leur croissance. Ce système permettrait d'améliorer l'utilisation des ressources du milieu (eau, azote, lumière…) et ainsi d'augmenter le rendement et la qualité des grains par rapport aux cultures monospécifiques. L'objectif de notre travail était d'analyser le fonctionnement et d'évaluer la performance des associations blé dur - pois d'hiver et blé dur - féverole d'hiver pour aider à la conception d'itinéraires techniques adaptés à différents objectifs de production. Pour cela nous avons testé, au cours de trois années d'expérimentations, différentes combinaisons de variétés de blé dur, disponibilités en azote, structures de couverts et densités de plantes. Nos résultats ont confirmé l'intérêt de ces systèmes pour améliorer le rendement et la teneur en protéines du blé dur comparativement aux cultures monospécifiques mais également pour la réduction des ravageurs, maladies et de l'enherbement dans certaines conditions. Ces systèmes sont ainsi particulièrement bien adaptés aux situations à faible disponibilité en azote en raison de la complémentarité entre céréale et légumineuse pour l'utilisation de l'azote (minéral du sol et fixation symbiotique) mais aussi pour la captation de l'énergie lumineuse. In fine, ce travail a permis de proposer des prototypes d'itinéraires techniques d'associations adaptés à différents objectifs de production, grâce notamment à l'analyse dynamique des compétitions et complémentarités entre espèces au sein du couvert et en particulier de l'élaboration du rendement du blé dur en association. / Intercropping is the simultaneous growing of two or more species in the same field for a significant period. Such systems are known to use available resources (water, light, nitrogen…) more efficiently than their corresponding sole crops and consequently to increase yield and grain protein concentration particularly in low N input systems. The aim of our work was to analyse the functioning of durum wheat - winter pea and durum wheat - winter faba bean intercrops. A 3-year field experiment was carried out with different fertilizer-N levels, wheat cultivars and plant densities. The intercrop efficiency was studied in order to further design low inputs cropping systems for specific objectives. Our results confirm that intercropping is more suited to low-N-input systems because it takes advantage of complementary N sources (soil mineral N and N2 fixation) and light use between species of the intercrop. Thus, intercrops were more efficient than sole crops for yield, they increased durum wheat grain protein concentration and in certain cases reduced weeds, pests and diseases. Finally, our work indicates that intercrops can be optimized for specific objectives by the choice of crop species, cultivars, N fertilization and plant densities in order to maximize resource capture and minimize competition. Indeed, intercrop efficiency is determined by the complementary resource use between the two species as well as the relative strength of the intra- and interspecific dynamic competitive interactions.