The role of hydraulics FSPMs in the context of root breeding : a case study on Pearl Millet

Developing a sustainable agricultural model is one of the great challenges of the coming years. The agricultural practices inherited from the Green Revolution of the 1960s show their limits today, and new paradigms need to be explored in the context of counter rising issues such as the multiplication of climate-change related drought episodes. Two such new paradigms are the use of functional-structural plant models to complement and rationalize breeding approaches and a renewed focus on root systems as untapped sources of plant improvement. Since the late 1980s, numerous functional and structural models of root systems were developed and used to investigate the properties of root systems in soil or lab-conditions. In this talk, we present a review on the use of multiscale functional-structural hydraulic root models in the context of drought tolerance breeding. We discuss how root models predictions can be linked to breeding studies to improve plant resistance to drought and how they can be validated to demonstrate models reliability and use. To illustrate this topic, we present a new structural model of pearl millet root system growth dynamics, combining stochastic and data-driven modules. The model is capable of simulating the development of observed root phenotypic variability of two millet genotypes chosen for their contrasted root traits. Model description, principle, assumptions, formalism and simulations will be presented during the talk

Characterization of pearl millet root architecture and anatomy reveals three types of lateral roots

Pearl millet plays an important role for food security in arid regions of Africa and India. Nevertheless, it is considered an orphan crop as it lags far behind other cereals in terms of genetic improvement efforts. Breeding pearl millet varieties with improved root traits promises to deliver benefits in water and nutrient acquisition. Here, we characterize of early pearl millet root system development using several different root phenotyping approaches that include rhizotrons and microCT. We report that early stage pearl millet root system development is characterized by a fast growing primary root that quickly colonizes deeper soil horizons. We also describe root anatomical studies that revealed 3 distinct types of lateral roots that form on both primary roots and crown roots. Finally, we detected significant variation for two root architectural traits in pearl millet inbred lines. This study provides the basis for subsequent genetic experiments to identify loci associated with interesting early root development traits in this important cereal

Glutaredoxin regulation of primary root growth is associated with early drought stress tolerance in pearl millet

Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet’s early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Sahelian climate. Using crop modeling, we demonstrate that early drought stress is an important constraint in agrosystems in the Sahel where pearl millet was domesticated. Furthermore, we show that increased pearl millet primary root growth is correlated with increased early water stress tolerance in field conditions. Genetics including genome-wide association study and quantitative trait loci (QTL) approaches identify genomic regions controlling this key root trait. Combining gene expression data, re-sequencing and re-annotation of one of these genomic regions identified a glutaredoxin-encoding gene PgGRXC9 as the candidate stress resilience root growth regulator. Functional characterization of its closest Arabidopsis homolog AtROXY19 revealed a novel role for this glutaredoxin (GRX) gene clade in regulating cell elongation. In summary, our study suggests a conserved function for GRX genes in conferring root cell elongation and enhancing resilience of pearl millet to its Sahelian environment

Author Response: Glutaredoxin regulation of primary root growth is associated with early drought stress tolerance in pearl millet

Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet’s early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Sahelian climate. Using crop modelling, we demonstrate that early drought stress is an important constraint in agrosystems in the Sahel where pearl millet was domesticated. Furthermore, we show that increased pearl millet primary root growth is correlated with increased early water stress tolerance in field conditions. Genetics including GWAS and QTL approaches identify genomic regions controlling this key root trait. Combining gene expression data, re-sequencing and re-annotation of one of these genomic regions identified a glutaredoxin-encoding gene PgGRXC9 as the candidate stress resilience root growth regulator. Functional characterization of its closest Arabidopsis homolog AtROXY19 revealed a novel role for this glutaredoxin (GRX) gene clade in regulating cell elongation. In summary, our study suggests a conserved function for GRX genes in conferring root cell elongation and enhancing resilience of pearl millet to its Sahelian environment

Exploration du système racinaire du mil et ses conséquences pour la tolérance à la sécheresse

Pearl millet plays an important role for food security in arid regions of Africa and India. Nevertheless, it lags far behind other cereals in terms of genetic improvement. Improving its root system could improve pearl millet tolerance to abiotic constraints (drought and low nutrient availability) and lead to a significant increase in production. The objective of this work is to characterize pearl system root system development in order to produce knowledge for breeding, mainly targeted on tolerance to drought stress occurring at the early growth stages.First, we described the dynamics of early pearl millet root system development and the anatomy of the different root types. This work revealed the existence of three anatomically distinct types for lateral roots. We also showed the existence of variability in primary root growth and lateral root density in a diversity panel derived from cultivated varieties, which opens the possibility to use this existing variability in root system breeding. Our study also revealed a large variability among the growth profiles of lateral roots.To further analyze this diversity, the growth rates of a large number of lateral roots were measured daily and a statistical model developed to classify these lateral roots into three main trends, according to their growth profiles. These three categories distinguish roots with high growth rate that keep on growing after the end of the experiment, roots with intermediate growth rates and roots with low growth rates that quickly stop growing. These different lateral root types are randomly distributed along the primary root and there seem to be no influence of root types on the intervals between successive lateral roots. The three growth types correspond, though imperfectly, to the three anatomical types evidenced in the first chapter. A similar work has been performed on maize, which was used to compare these two phylogenetically close cereals.Finally, we searched for genetic markers associated to primary root growth, a root trait potentially involved in early drought stress tolerance. A large panel of genetically fixed pearl millet inbred lines was phenotyped, confirming the presence of a large variability existing for this trait. These lines were then genotyped by sequencing. Analyses of association between phenotype and genotype are underway.This work provides a precise description of pearl millet root system that was little studied to date. Our data were used for parameterization and testing of functional structural plant models simulating root growth and water transport. The statistical tool developed for the characterization of the different lateral root growth types is an original approach that can be used on other cereals. Finally, results from our association study will reveal new information on the genetic control of root growth and open the way to marker assisted selection for root traits in pearl millet.Le mil est une céréale d’importance majeure pour la sécurité alimentaire dans les régions arides d’Afrique et d’Inde. Pourtant, elle a fait l’objet de relativement peu d’efforts d’amélioration variétale par rapport à d’autres céréales. En particulier, l’amélioration de son système racinaire pourrait permettre une amélioration de la tolérance de cette plantes aux contraintes physiques qu’elle subit (sécheresse et faible disponibilité en nutriments) et ainsi un accroissement substantiel de la production. L’objectif de ce travail est de caractériser ce système racinaire, en vue de produire des connaissances nécessaires à l’amélioration variétale, axée principalement sur la tolérance à la sécheresse en début de cycle.Dans un premier temps, nous avons décrit précisément la morphologie du système racinaire dans les premiers stades de développement, la dynamique de mise en place des différents axes racinaires ainsi que l’anatomie des différents types de racines. Ce travail a mis en évidence l’existence de trois types anatomiques distincts pour les racines latérales. Nous avons également mis en évidence l’existence de variabilité dans la dynamique de mise en place précoce du système racinaire au sein d’un panel de diversité issu de variétés cultivées, ce qui ouvre la possibilité d’utiliser cette variabilité existante pour l’amélioration du système racinaire. Notre étude a aussi révélé une grande variabilité des profils de croissances au sein des racines latérales.Pour analyser plus avant cette diversité, la croissance d’un grand nombre de racines latérales a été mesurée quotidiennement et un modèle statistique a permis de classer ces racines latérales en trois grandes tendances, selon leurs profils de croissance. Ces trois catégories distinguent des racines avec des forts taux de croissance, et dont la croissance se poursuit après la fin du suivi, des racines avec des taux de croissance intermédiaires et des racines au taux de croissance faible, qui cessent rapidement de pousser. Ces différents types de racines sont répartis aléatoirement le long de la racine primaire et il ne semble pas y avoir d’influence des types racinaires sur les intervalles entre racines latérales successives. Les trois types cinétiques correspondent, imparfaitement cependant, aux trois types anatomiques mis en évidence dans le premier chapitre. Un travail similaire a été effectué sur le maïs, ce qui a permis de comparer ces deux céréales phylogénétiquement proches.Enfin, nous avons recherché de marqueurs génétiques associés à la croissance de la racine primaire, un trait racinaire supposément impliqué dans la tolérance à la sécheresse précoce. Ce travail a nécessité le phénotypage du trait racinaire en question sur panel de lignées de mil fixées, ce qui a confirmé la présence d’une grande variabilité existante pour ce trait. Ces lignées ont ensuite été génotypées par séquençage. Les analyses d’association génotype/phénotype sont en cours.Ce travail de thèse a permis de caractériser plus précisément le système racinaire du mil, relativement mal connu jusqu’à ce jour. Il a fourni des données utiles pour la paramétrisation et le test de modèles fonctionnels de croissance et de transport d’eau. La caractérisation cinétique précise des types de racines latérales est une approche originale et pourra être utilisée chez d’autres céréales. Enfin, les données acquises par génétique d’association devraient pouvoir servir à une meilleure compréhension de la mise en place de ce système racinaire et ouvrent la voie à l’amélioration assistée par marqueurs génétiques pour des traits racinaires chez le mil

Exploring pearl millet root system and its outcome for drought tolerance

Le mil est une céréale d’importance majeure pour la sécurité alimentaire dans les régions arides d’Afrique et d’Inde. Pourtant, elle a fait l’objet de relativement peu d’efforts d’amélioration variétale par rapport à d’autres céréales. En particulier, l’amélioration de son système racinaire pourrait permettre une amélioration de la tolérance de cette plantes aux contraintes physiques qu’elle subit (sécheresse et faible disponibilité en nutriments) et ainsi un accroissement substantiel de la production. L’objectif de ce travail est de caractériser ce système racinaire, en vue de produire des connaissances nécessaires à l’amélioration variétale, axée principalement sur la tolérance à la sécheresse en début de cycle.Dans un premier temps, nous avons décrit précisément la morphologie du système racinaire dans les premiers stades de développement, la dynamique de mise en place des différents axes racinaires ainsi que l’anatomie des différents types de racines. Ce travail a mis en évidence l’existence de trois types anatomiques distincts pour les racines latérales. Nous avons également mis en évidence l’existence de variabilité dans la dynamique de mise en place précoce du système racinaire au sein d’un panel de diversité issu de variétés cultivées, ce qui ouvre la possibilité d’utiliser cette variabilité existante pour l’amélioration du système racinaire. Notre étude a aussi révélé une grande variabilité des profils de croissances au sein des racines latérales.Pour analyser plus avant cette diversité, la croissance d’un grand nombre de racines latérales a été mesurée quotidiennement et un modèle statistique a permis de classer ces racines latérales en trois grandes tendances, selon leurs profils de croissance. Ces trois catégories distinguent des racines avec des forts taux de croissance, et dont la croissance se poursuit après la fin du suivi, des racines avec des taux de croissance intermédiaires et des racines au taux de croissance faible, qui cessent rapidement de pousser. Ces différents types de racines sont répartis aléatoirement le long de la racine primaire et il ne semble pas y avoir d’influence des types racinaires sur les intervalles entre racines latérales successives. Les trois types cinétiques correspondent, imparfaitement cependant, aux trois types anatomiques mis en évidence dans le premier chapitre. Un travail similaire a été effectué sur le maïs, ce qui a permis de comparer ces deux céréales phylogénétiquement proches.Enfin, nous avons recherché de marqueurs génétiques associés à la croissance de la racine primaire, un trait racinaire supposément impliqué dans la tolérance à la sécheresse précoce. Ce travail a nécessité le phénotypage du trait racinaire en question sur panel de lignées de mil fixées, ce qui a confirmé la présence d’une grande variabilité existante pour ce trait. Ces lignées ont ensuite été génotypées par séquençage. Les analyses d’association génotype/phénotype sont en cours.Ce travail de thèse a permis de caractériser plus précisément le système racinaire du mil, relativement mal connu jusqu’à ce jour. Il a fourni des données utiles pour la paramétrisation et le test de modèles fonctionnels de croissance et de transport d’eau. La caractérisation cinétique précise des types de racines latérales est une approche originale et pourra être utilisée chez d’autres céréales. Enfin, les données acquises par génétique d’association devraient pouvoir servir à une meilleure compréhension de la mise en place de ce système racinaire et ouvrent la voie à l’amélioration assistée par marqueurs génétiques pour des traits racinaires chez le mil.Pearl millet plays an important role for food security in arid regions of Africa and India. Nevertheless, it lags far behind other cereals in terms of genetic improvement. Improving its root system could improve pearl millet tolerance to abiotic constraints (drought and low nutrient availability) and lead to a significant increase in production. The objective of this work is to characterize pearl system root system development in order to produce knowledge for breeding, mainly targeted on tolerance to drought stress occurring at the early growth stages.First, we described the dynamics of early pearl millet root system development and the anatomy of the different root types. This work revealed the existence of three anatomically distinct types for lateral roots. We also showed the existence of variability in primary root growth and lateral root density in a diversity panel derived from cultivated varieties, which opens the possibility to use this existing variability in root system breeding. Our study also revealed a large variability among the growth profiles of lateral roots.To further analyze this diversity, the growth rates of a large number of lateral roots were measured daily and a statistical model developed to classify these lateral roots into three main trends, according to their growth profiles. These three categories distinguish roots with high growth rate that keep on growing after the end of the experiment, roots with intermediate growth rates and roots with low growth rates that quickly stop growing. These different lateral root types are randomly distributed along the primary root and there seem to be no influence of root types on the intervals between successive lateral roots. The three growth types correspond, though imperfectly, to the three anatomical types evidenced in the first chapter. A similar work has been performed on maize, which was used to compare these two phylogenetically close cereals.Finally, we searched for genetic markers associated to primary root growth, a root trait potentially involved in early drought stress tolerance. A large panel of genetically fixed pearl millet inbred lines was phenotyped, confirming the presence of a large variability existing for this trait. These lines were then genotyped by sequencing. Analyses of association between phenotype and genotype are underway.This work provides a precise description of pearl millet root system that was little studied to date. Our data were used for parameterization and testing of functional structural plant models simulating root growth and water transport. The statistical tool developed for the characterization of the different lateral root growth types is an original approach that can be used on other cereals. Finally, results from our association study will reveal new information on the genetic control of root growth and open the way to marker assisted selection for root traits in pearl millet

Grain legume-based rotations managed under conventional tillage need cover crops to mitigate soil organic matter losses

International audienceInserting legumes in low-input innovative cropping systems can represent a good strategy to reduce current N fertilizer dependency while enhancing ecosystem services. However, although the impact of the use of legumes as cover crops has been broadly studied, very little is known about the effects of grain legume-based rotations on soil organic carbon (SOC) and nitrogen (SON). A cropping system experiment with three 3-year rotations with different levels of inclusion of grain legumes: GL0, GL1 and GL2 (none, one, and two grain legumes, respectively), with (CC) or without (BF, bare fallow) cover crops was established in SW France (Auzeville) under temperate climate. Durum wheat was present in all the rotations to act as an indicator of their performance. Soil organic C and SON were quantified before the beginning of the experiment and after 3 and 6 years (i.e., after one and two complete 3-yr rotations). Aboveground C and N inputs to the soil, and C and N harvest indexes and grain yield of the cash crops were also measured. Inserting grain legumes in the rotations significantly affected the amount of C and N inputs and consequently SOC and SON. After two cycles of the 3-yr rotation, the GL1 and GL2 treatments showed a greater decrease in SOC and SON when compared to GL0. However, the inclusion of cover crops in the rotations led to mitigate this loss. Durum wheat produced significantly greater grain yields in GL1 when compared to GL0, while GL2 presented intermediate values. In turn, the incorporation of cover crops did not reduce C and N harvest indexes or the grain yield of the different cash crops. We concluded that, in such conventionally-tilled grain legume-based rotations, the use of cover crops was efficient to mitigate SOC and SON losses and then increase N use efficiency at the cropping system level without reducing productivity

Impact of the combination of several lateral root growth and anatomies on root system water uptake

Water uptake is a challenge for crops growing in regions where sandy soils and low rainfalls are frequent. Plant species evolving in these regions, such as pearl millet which has been domesticated in Sahelian Africa, provide interesting models to identify and analyze mechanisms of tolerance to water limitations. The objective of this work was to understand how the root architectural traits of young pearl millet plants improve water uptake under challenging conditions with modeling approach. We followed the growth of pearl millet root systems on a daily basis during two weeks and observed a large variability among lateral root growth profiles. To further analyze this diversity, a statistical model was designed to classify these roots on the basis of their growth profiles. Three categories of lateral roots were identified in this way, which corresponded to distinct anatomies previously described on pearl millet. We used the MECHA model to predict hydraulic properties of the different root categories based on their anatomy and the RootTyp model to simulate typical root system architectures. These data were then used to simulate water uptake by the root system with the R-SWMS model. Comparison of the simulated conductance with measurements done in pressure chamber validated the relevance of this association of models for water flux simulations. We performed various simulations to assess (i) the value of combinations of different root categories within a root system, (ii) the relative contribution of each category to water uptake and (iii) the impact of their relative proportions on global water uptake, in the context of dry and sandy soils