Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam

Background: Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results: The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions: Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development

Two Lateral organ boundary domain transcription factors HvCRL1 and HvCRL1L1 regulate shoot-borne root formation in Barley (Hordeum vulgare L.)

Plant-specific LOB-domain (LBD) transcription factors are crucial in post-embryonic root initiation. In cereals, the fibrous root system comprises primary and seminal roots that develop during embryogenesis and lateral- and crown roots that develop post-embryonically from root or stem, respectively. In rice, the CROWNROOTLESS1 (CRL1) LBD transcription factor is the core regulator of crown root initiation and a direct target of the auxin response factor (ARF)-mediated auxin signaling pathway. Orthologs of CRL1 have been identified and characterized in several species, where their role in crown root initiation has been validated. In barley, we identified two genes phylogenetically closely related to the rice CRL1 genes that we named HvCRL1 and HvCRL1L1. Using a crown root inducible system (CRIS), we identified that both HvCRL1 and HvCRL1L1 are expressed in response to auxin during the early steps of crown root differentiation in stem base, with HvCRL1 transcripts being accumulated quickly during the first hour of treatment. Transient activation assays in rice proto- plast showed that HvCRL1 could bind the LBD-box, a consensus DNA sequence recognized by LBD transcription factors, whereas HvCRL1L1 did not. Both genes can partially complement the crl1 rice mutant. Loss-of-function mutation in each gene drastically impairs crown root formation in barley. These data show that HvCRL1 and HvCRL1L1 are both involved in the regulation of crown root formation in barley but that these two transcription factors likely act through distinct and complementary pathways in this developmental process

Transcriptional changes during crown-root development and emergence in barley (Hordeum vulgare L.)

Background: Roots play an important role during plant growth and development, ensuring water and nutrient uptake. Understanding the mechanisms regulating their initiation and development opens doors towards root system architecture engineering. Results: Here, we investigated by RNA-seq analysis the changes in gene expression in the barley stem base of 1 day-after-germination (DAG) and 10DAG seedlings when crown roots are formed. We identified 2,333 genes whose expression was lower in the stem base of 10DAG seedlings compared to 1DAG seedlings. Those genes were mostly related to basal cellular activity such as cell cycle organization, protein biosynthesis, chromatin organization, cytoskeleton organization or nucleotide metabolism. In opposite, 2,932 genes showed up-regulation in the stem base of 10DAG seedlings compared to 1DAG seedlings, and their function was related to phytohormone action, solute transport, redox homeostasis, protein modification, secondary metabolism. Our results highlighted genes that are likely involved in the different steps of crown root formation from initiation to primordia differentiation and emergence, and revealed the activation of different hormonal pathways during this process. Conclusions: This whole transcriptomic study is the first study aiming at understanding the molecular mechanisms controlling crown root development in barley. The results shed light on crown root emergence that is likely associated with a strong cell wall modification, death of the cells covering the crown root primordium, and the production of defense molecules that might prevent pathogen infection at the site of root emergence

Sculpting the soil microbiota

Soil is a living ecosystem, the health of which depends on fine interactions among its abiotic and biotic components. These form a delicate equilibrium maintained through a multilayer network that absorbs certain perturbations and guarantees soil functioning. Deciphering the principles governing the interactions within soils is of critical importance for their management and conservation. Here, we focus on soil microbiota and discuss the complexity of interactions that impact the composition and function of soil microbiota and their interaction with plants. We discuss how physical aspects of soils influence microbiota composition and how microbiota–plant interactions support plant growth and responses to nutrient deficiencies. We predict that understanding the principles determining the configuration and functioning of soil microbiota will contribute to the design of microbiota-based strategies to preserve natural resources and develop more environmentally friendly agricultural practices

Plant microbiota controls an alternative root branching regulatory mechanism in plants

The establishment of beneficial interactions with microbes has helped plants to modulate root branching plasticity in response to environmental cues. However, how the plant microbiota harmonizes with plant roots to control their branching is unknown. Here, we show that the plant microbiota influences root branching in the model plant Arabidopsis thaliana. We define that the microbiota's ability to control some stages in root branching can be independent of the phytohormone auxin that directs lateral root development under axenic conditions. In addition, we revealed a microbiota-driven mechanism controlling lateral root development that requires the induction of ethylene response pathways. We show that the microbial effects on root branching can be relevant for plant responses to environmental stresses. Thus, we discovered a microbiota-driven regulatory pathway controlling root branching plasticity that could contribute to plant adaptation to different ecosystems

Functional characterization of genes regulated by the CROWN ROOT LESS 1 transcription factor involved in crown root initiation and development in rice

Le but de cette thèse est de préciser les mécanismes moléculaires agissant en aval du facteur de transcription CROWN ROOT LESS 1 (CRL1) qui régule la formation des racines coronaires (RC). Nous avons pu identifier dans un premier temps une nouvelle séquence d’ADN reconnue par CRL1 nommé CRL1-box différente de la LBD-box qui était le seul motif cis-régulateur précédemment décrit pour la famille des facteurs de transcription (FT) de type LATERAL ORGAN BOUNDARIES DOMAIN (LBD). Nous avons ensuite identifié un groupe de gènes régulés par CRL1, et avons montré l’implication de deux d’entre eux, OsROP et OsbHLH044, dans le développement des RC. OsbHLH044 est un facteur de transcription répresseur et semble être aussi impliqué dans la sénescence cellulaire ainsi que la réponse aux stress. Enfin, nous avons mis en évidence une cascade de régulation liant positivement CRL1 avec QUIESCENT-CENTER-SPECIFIC HOMEOBOX (QHB) un gène impliqué dans la différenciation et le maintien du centre quiescent via le facteur de transcription OsHOX14. En addition nous avons mis en évidence une boucle de rétroaction négative de QHB sur ses activateurs CRL1 et OsHOX14, qui pourrait être impliquée dans la structuration du primordia de racine coronaire.The aim of this thesis is to specify the molecular mechanisms acting downstream of the CROWN ROOT LESS 1 transcription factor (CRL1) that regulates coronary root (CR) formation. We were able to identify at first a new CRL1 recognized DNA sequence named CRL1-box different from the LBD-box which was the only cis-regulatory motif previously described for the LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factor (TF) family. We then identified a group of genes regulated by CRL1, and showed the involvement of two of them, OsROP and OsbHLH044, in the development of CR. OsbHLH044 is a repressive transcription factor and appears to be also involved in cell senescence as well as stress response. Finally, we demonstrated a regulatory cascade linking CRL1 with QUIESCENT-CENTER-SPECIFICHOMEOBOX (QHB), a gene involved in the differentiation and maintenance of the quiescent center, via the OsHOX14 transcription factor. In addition we have demonstrated a negative feedback loop of QHB on its activators CRL1 and OsHOX14, which could be involved in structuring the coronary root primordi

Utilisation de l’indice de biodiversité potentielle

Entretenir sa forêt: Fiche techniquePeu de temps après la création de l’IBP en 2008, le CRPF Midi-Pyrénées a proposé cette méthode à un propriétaire tarnais qui réalisait son PSG et souhaitait mieux intégrer la biodiversité ordinaire dans sa gestion courante. C’est ce travail qui est ici relaté. Notons qu’en complément à l’IBP, le propriétaire a utilisé ultérieurement la démarche BIOFIL 1, développée par le CRPF Midi-Pyrénées et permettant notamment de mieux repérer à l’échelle de la forêt leséléments de biodiversité remarquables

Industrie et environnement : une nouvelle préoccupation, le management écologique

Industrial civilization is clearly the main responsable for environmental hazards. Therefore the growing ecological concept among industrialists lead to an ecological way of management. As far as possible they try to reduice the nuissances for the general well being. German industrialists made the first steps, opening the way with bäum association. Some firms, like madaus adopted strongly ecological concepts which became a full part of their firm culture.Si l'industrialisation est en grande partie responsable de la détérioration de l'environnement, la prise de conscience écologique est très forte chez les industriels qui, par un management écologique de leur entreprise essaient de maîtriser au mieux les nuisances, pour le bien de tous. Les industriels allemands sont les pionniers en la matière avec le mouvement B.A.U.M.. Certaines firmes, comme MADAUS, adoptent complètement les concepts écologiques qui sont intégrés dans la «culture d'entreprise».Biguet L., Gachelin Charles, Gonin Patrick, Mathieu B., Roussel Isabelle. Industrie et environnement : une nouvelle préoccupation, le management écologique. In: Hommes et Terres du Nord, 1991/4. Environnement. pp. 256-260