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Zoom on genetics complexity in plants

Fine-tuning plant growth throughout development and in response to environmental limitations is a decisive process to optimize fitness and population survival in the wild, especially for plants being sessile organisms. The team of Olivier Loudet “Variation and Abiotic Stress Tolerance” reveled the high genetic complexity allowing shoot growth variations in response to water limitation. Published in PLoS Genetics on the 22th of April 2019, theses results open new perspectives in the discovering of genetics variations controlling stress response for interesting adaptative and agronomic traits.

As a sessiles organisms, plants have to cope with environmental fluctuations and evolved a wide range of responses well illustrated by their great phenotypic plasticity and their ability to colonize very diverse habitats, through intraspecific genetic diversity.

Thanks to the Phenoscope, a robotised platform designed to cultivate plant and perform high throughput under strictly-controlled and reproducible conditions (see below), The team of Olivier Loudet managed to decifer the basal genetics of this vegetal diversity. On the Phenoscope, more than 700 cultivated Arabidopsis thaliana plants are moving continuously and consequently in an equivalent environment. They are weighed and watered and photographed very regularly. As a sessile organism, plants have to cope with environmental fluctuations and evolved a wide range of responses well illustrated by their great phenotypic plasticity and their ability to colonize very diverse habitats, through intraspecific genetic diversity.

Quantitative genetics approaches exploiting different crosses allowed to map the individual genetic loci (QTLs’: 'Quantitative Trait Loci') controlling different parameters linked to leaf growth with a precision never reach so far. Shoot growth and morphology have been analyzed in response to moderate water limitation. The team of Olivier Loudet studied Integrative traits such as those related to vegetative growth (highlighting either cumulative growth, growth rate) for 4 crosses between Arabidopsis variants (recombinant populations, RILs: Recombinant Inbred Lines). Subsequently, by focusing all of the mapping power on a small region representing 2.5% (3 Mégabases) of the genome of the model plant Arabidopsis in an unprecedentedly phenotyping effort, the unique cross analyzed revealed an underlying very complex so-called 'genetic architecture'. For example, several independent genes had remained hidden in this region beyond a major-effect gene controlling growth variation. Taking into account this hidden effects in cartography of QTLs is important to understand the variation of quantitative characters.

To study growth natural variability in a wild type species as Arabidopsis open doors to the discovery of new variants responding to stress and controlling adaptative characters of agronomic interest. A new order of magniture in predictive or digital biology could be announced: results of this study suggest that the genetics complexity being the base of phenotypic diversity is probably very underestimated.

Focus on the ‘Phenoscope’
Deviced at the Institut Jean-Pierre Bourgin (IJPB, INRA Versailles-Grignon -Ile-de-France) and thanks to genetic ressources of the Arabidopsis thaliana Stock Center, the Phenoscope gather 4 unique robots in two culture chambers of the Plant Observatory (INRA patent) to observe plants at the vegetative stage (shoot).
It allows :
> to study more than 700 cultivated plants per robot
> to analyse large populations in controlled and reproducible conditions, being not feasible by hand and represent a bottle neck in modern biology
> or to characterize in detail a small number of different plants (genotypes) in a wide range of conditions (watering for example)
> to homogenise conditions by a continuous movement of plants (ex: typical cycle of 4 hours)
> 3 time less of repetitions necessary within each experiment
> dynamic shooting of growth with automatic extraction of characters by image analysis

The future XL Phenoscope is now being deviced: this prototype will receive plants including ones behond the flowering stage, up to the seed.

More information: https://phenoscope.versailles.inra.fr/

Communiqué de presse INRA 22/04/19

Contact:
Olivier Loudet (01 30 83 32 17)
Institut Jean-Pierre Bourgin (INRA, AgroParisTech ; ERL CNRS)
Département scientifique Biologie et amélioration des plantes
Ile-de-France-Versailles-Grignon

Contact(s) press:
Inra service de presse (01 42 75 91 86)

Associated Department:
Plant Biology and Breeding
Associated Centre:
Ile-de-France-Versailles-Grignon

Référence:
The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana. Elodie Marchadier, Mathieu Hanemian, Sébastien Tisné, Liên Bach, Christos Bazakos, Elodie Gilbault, Parham Haddadi, Laetitia Virlouvet, Olivier Loudet. PLoS Genetics. 22th Avril 2019. https://doi.org/10.1371/journal.pgen.1007954

23th April 2019


 

Crop plants could now reproduce clonally through seeds

Grown throughout the world, F1 hybrid crop varieties have highly desirable traits. However, they remain expensive to produce. This situation may be about to change. By modifying the expression of certain genes, Raphaël Mercier, the group leader of "Mécanisms of meiose" from l'IJPB, INRA, Versailles, in collaboration with the University of Californie Davis and the China National Rice Research Institute, have created hybrid. This breakthrough research has been published in Nature and Nature Biotechnology.

Methods for breeding better crops focus on two key tasks: 1) producing high performing hybrids by crossing different plant lineages and 2) attempting to preserve and perpetuate the resulting genetic combinations such that the resulting seeds carry the target traits.

To this end, agriculture has been using F1 hybrids since the 1930s. Generated by crossing two pure crop lineages that contain genes of interest, F1 hybrids combine the desirable traits exhibited by each of their parents. They display "hybrid vigour”, benefits that are greater than the sum of the individual agricultural values of the two parental lineages. In crops where individual plants have both male and female organs (e.g., maize, tomato), F1 hybrids are produced by removing the male organs and then carrying out manual pollination. In crops where individual plants are unisexual (e.g., rapeseed, beet), controlled pollination of female plants is performed. The problem is that the offspring of F1 hybrids do not display the same traits as their parents because of the dynamics of meiosis, during which chromosome exchange occurs. Each year, it is therefore necessary to reuse F1 hybrid seeds from the original parental cross to obtain the desired trait combinations.

From meiosis to mitosis
For decades, scientists have searched for a way to preserve the desirable gene combinations represented in high-performing hybrids. In particular, attention has been focused on apomixis, a process used by certain plants (such as dandelions and hawthorns) to asexually reproduce though seeds, which allows them to forgo meiosis and fertilisation. The offspring produced are thus clones of their parents—they are identical to each other. Recently, in Arabidopsis (a model plant species) and in rice, INRA researchers were able to replace meiosis with a mitosis-like process (MiMe) by inactivating three genes involved in meiosis. The result: plants produced gametes (i.e., reproductive cells) containing the same exact chromosomes as their mother plants. However, to engineer apomixis, there is an important additional step. Female gametes must be able to give rise to embryos despite being unfertilised. INRA researchers were able to surmount this hurdle thanks to two separate collaborations: one with Venkatesan Sundaresan's team at University of California Davis and a second with Kejian Wang's team at the China National Rice Research Institute. These two groups independently discovered how to induce embryogenesis without the need for female gametes to be fertilised by male gametes.

A spitting genetic image
To accomplish this feat, they used CRISPR-Cas9 to inactivate the three MiMe-related genes identified by INRA scientists. Sundaresan's team then activated a gene called BABYBOOM 1 in the female gametes. Normally, this gene is only expressed following fertilisation. In contrast, Wang's team inactivated the MATRILINEAL gene (also known as the NOT LIKE DAD gene), which is involved in the fertilisation process. In this way, both teams managed to induce fertilisation-free embryogenesis, which produced rice seeds that gave rise to plants that were identical to the hybrid mother plant. Furthermore, Sundaresan's team showed that these clones also produced clonal offspring: three generations later, identical plants were still being generated. It is therefore possible to preserve hybrid vigour in the offspring of F1 hybrids in rice!

Tremendous possibilities
In both cases, the seed production rates are too low for the processes to be immediately used for commercial seed production. However, the researchers are exploring how these rates can be boosted.

In the longer term, this discovery will revolutionise strategies for improving crops, notably by making it possible to generate clones of F1 hybrids for most species of agricultural interest. The simplicity of the process means that it should be straightforward to test a greater number of genetic combinations and thus generate new types of hybrids, which could lead to a broader diversity of crop varieties. Furthermore, farmers would be able to replant seeds from crops that they had grown themselves, knowing that the resulting plants would reliably display hybrid vigour across generations. This would be a major boon for farmers, and especially for farmers in developing countries, as the annual cost of purchasing seeds represents a significant expense. For everyone to be able to take advantage of these technological advances, the plant breeding and seed production industries will need to change their current economic models.

Seed crops are produced via sexual reproduction: the male gamete, which contains half the chromosomes of its parent cell, fertilises the female gamete, which also contains half the chromosomes of its parent cell. This resulting embryo (and the plant into which it will develop) thus contains chromosomes from both parents. During meiosis in this offspring plant, the chromosomes that it obtained from its parents will recombine. As a result, the male and female gametes produced will contain a mixture of the parental genetic information. This process is repeated each generation. In crops that self-fertilise, such as wheat, male and female gametes display homogeneity after a certain number of generations, leading to pure lineages that remain stable over time. In crops that cross-fertilise, such as maize, offspring always differ from their mother plants

In contrast, certain seed crops reproduce using apomixis—embryos develop without the need for either meiosis or fertilisation. Offspring resulting from apomixis only contain and pass along genetic information from the mother plant. Certain wild plants such as dandelions and hawthorns clonally reproduce in this way through seeds.

Press release INRA 10/01/19

Contact:
Raphaël Mercier (01 30 83 39 89)
Institut Jean-Pierre Bourgin (INRA, AgroParisTech, ERL CNRS)

Contact(s) press:
Inra service de presse (01 42 75 91 86)
Associated Department:
Biologie et amélioration des plantes
Associated Centre:
Ile-de-France-Versailles-Grignon

Références:
Imtiyaz Khanday, Debra Skinner, Bing Yang, Raphael Mercier & Venkatesan Sundaresan.A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature (2019). https://doi.org/10.1038/s41586-018-0785-8 Abstract

Chun Wang, Qing Liu, Yi Shen, Yufeng Hua, Junjie Wang, Jianrong Lin, Mingguo Wu, Tingting Sun, Zhukuan Cheng, Raphael Mercier & Kejian Wang. Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes.Nature Biotechnology (2019). https://doi.org/10.1038/s41587-018-0003-0 Abstract

See also:
Raphaël Mercier, INRA award "Scientific challenge" 2016

10th January 2019


Small is big in Arabidopsis mitochondrial ribosome:
machinery translating proteins

 

Ribosomes are the molecular machines that translate messenger RNAs into proteins. They consist of two subunits. The small one decodes messenger RNA and the large one carries out the polymerization of amino acids to form the corresponding protein. Hakim Mireau, INRA senior scientistand collaborators of the group "Organelles and reproduction" from IJPB, INRA, Versailles in collaboration with the teams of Philippe Giegé (IBMP, Strasbourg university) and Yaser Hashem (IECB, INSERM, Bordeaux) has determined the specific composition and architecture of Arabidopsis mitochondrial ribosomes. This study is published in the journal Nature Plants january the 9th 2019.

Mitochondria represent the energy center of eukaryotic cells. For their metabolism as well as for their gene expression, mitochondria combine bacterial-like traits with traits that have evolved in eukaryotes. Translation is the least well-known step of mitochondrial gene expression. In plants, pentatricopeptide repeat (PPR) proteins are involved in all steps of gene expression but their function in mitochondrial translation remains unclear.

Using a biochemical approach, researchers have characterized the mitochondrial ribosome (mitoribosome) of the model plant Arabidopsis and identified its protein composition. 19 plant-specific mitoribosome proteins have been found, among which 10 are PPR proteins. Mutant analysis of genes encoding these PPR proteins, in particular using ribosome profiling, revealed their role in translation. Finally, a cryo-electron microscopy analysis revealed the unique three-dimensional architecture of these mitoribosomes. They are characterized by a very large small subunit, in particular with a new elongated domain never observed to date in other ribosomes.

This work contributes to understand the evolutionary diversity of translation systems. It illustrates remarkably how evolution has played with mitoribosomes to optimize protein synthesis in mitochondria.

Figure legend : Structural comparison between Arabidopsis mitoribosome and animal mitoribosome as well as with Arabidopsis cytosolic ribosome, which highlights the originality of this mitoribosome architecture. In particular, it is characterized by the presence of additional domains (circled in red). “SSU” represents small subunits and “LSU” large ribosomal subunits.

Contact:
Hakim Mireau  
Institut Jean-Pierre Bourgin (INRA, AgroParisTech, ERL CNRS)

Référence :
Florent Waltz F, Tan-Trung Nguyen, Mathilde Arrivé, Anthony Bochle, Johana Chicher, Philippe Hammann, Lauriane Kuhn, Martine Quadrado, Hakim Mireau, Yaser Hashem, Philippe Giegé. Small is big in Arabidopsis mitochondrial ribosome. Nature Plants doi: https://doi.org/10.1038/s41477-018-0339-y Abstract

 

9th January 2019


Recombination increased in crops by the RECQ4 gene inactivation

During the process of sexual reproduction, chromosomes exchange genetic material by recombination (crossing-over) so participating in diversity. But shuffling is limited, exchanges being scarce, genes inhibiting this mechanism. Raphaël Mercier leader of the group "Mecanism of Meiosis", IJPB, INRA, Versailles, and other scientist of INRA and CIRAD have shown that when one of these genes: RECQ4, is desactivated, the number of recombinations is 3 fold higher in crops as rice, pea and tomatoe. That breakthrough published in Nature Plants, the 26th november 2018, could allow to speed up the selection process in plant breeding and the production of plants better adapted to environment conditions (pests resistance, climate change adaptation).

Recombination is a natural mechanism common to all organisms practicing sexual reproduction, as plants, fungi or animals. Genetic diversity within species takes its origin in chromosomes shuffling. Plant breeding, as practiced since ten thousand years, consisting in crossing two plants chosen for interesting and complementary characters is based on this mechanism. Then, to obtain a new tasty tomato variety resistant to a biopest, successive crosses are performed to select the suitable combination of characters (genes involved in taste and resistance). But this process takes a very long time, consequence of the low number of crossing-over i.e. - exchange points of genetic material (CO), during reproduction. In average, between 1 to 3 CO occur for each cross. Consequently, it is impossible for example to associate 6 interesting genes in a single generation, constituting an important curb to plant breeding.

But what limits the number of recombinations ?
To understand this the limitation of the number of recombination, scientists from INRA identified and studied, in the model plant Arabidopsis thaliana, genes involved in the control of recombination level. They discovered that REQ4, one of them, harbor a high anti-crossing-over activity. Recombination frequency is twice to four fold higher when RECQ4 is inactivated!

But what happens in cultivated plants?
It has been evaluated by the consortium associating INRA and CIRAD, studying the following important crops: pea, tomato and rice. The RECQ4 gene has been successfully switched of in these species, increasing by an average of three the number of crossing-over and consequently increasing chromosome shuffling and diversity for each generation. INRA, as an applied research Institute will focus now of integrating such a tool in plant breeding programs.

But why recombinations are so infrequent?
More recently, what explains the active mechanisms as RECQ4 which limits this process, and then the rhythm of diversity, within the majority of living organisms with sex reproduction? The question is still open. The most shared theory by scientists to explain this phenomenon is that the evolution of species happens in a quite globally stable environment. Consequently, combinations selected within the previous generations are well adapted to the environment where new individual develop themselves. Diversity being necessary to adapt to survive, to shuffle cards, as we could say jeopardize the equilibrium within each generation, is probably not the most optimum solution. In brief, diversity is needed but not too much.

Communiqué de presse INRA 26/11/18

Contact:
Raphaël Mercier (01 30 83 39 89) Institut Jean-Pierre Bourgin (INRA, AgroParisTech, ERL CNRS)

Contact(s) press:
Inra service de presse (01 42 75 91 86)
Scientific department associated:
Biologie et amélioration des plantes
Center associated:
Versailles-Grignon

Référence:
Delphine Mieulet, Gregoire Aubert, Cecile Bres, Anthony Klein, Gaëtan Droc, Emilie Vieille, Celine Rond-Coissieux, Myriam Sanchez, Marion Dalmais, Jean-Philippe Mauxion, Christophe Rothan, Emmanuel Guiderdoni and Raphael Mercier, Unleashing meiotic crossovers in crops, Nature Plants doi: https://doi.org/10.1101/343509 Abstract

See also:
Raphaël Mercier, INRA award "Scientific challenge" 2016

26th november 2018


Séminars
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___________________________________________________

Tuesday 25th June 2019
_______________________________________________
_____

11:00 AM

Invited Speaker

Pr. Bernard CARROLL
The University of Queensland,
Autralie

Mechanisms of gene silencing in Arabidopsis


Invited by:

Registration compulsory except for INRA Versailles member up to 24/05/19 12:00 AM

_____________________________________

Seminars location except other indications
___________________________________

Amphitheatre, Building 10
INRA Centre de Versailles-Grignon
Route de St Cyr (RD10)
F-78026 Versailles Cedex
France

_______________________________

Page Intranet séminaires IJPB



Events
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Workshop Plant Performance under Stress

24th June 2019, INRA, Versailles, France

This workshop in organised as part of the EIG-Concert Japan Project “Improving crop yield by enhanced plant performance under stress conditions” (IPSC). IPSC takes a comprehensive systems biology approach, combining phenotypic, transcriptomic, and metabolomic datasets to investigate plant responses to environmental factors including biotic and abiotic stresses.

This second workshop organised by the IPSC project takes place at the Institut Jean-Pierre Bourgin (IJPB), a multidisciplinary research institute associated to INRA, AgroParisTech and CNRS, and located on the INRA Versailles campus, next to the palace park. IJPB is one of the largest plant biology research centres in Europe and part of the Laboratory of Excellence Saclay Plant Sciences (SPS).

Program et flyer

Scientific committee:
IPSC consortium:
Prof. Stephan Pollmann, Center for Plant Biotechnology and Genomics, Madrid, Spain
Prof. Hitoshi Sakakibara, Nagoya University, Japan
Prof. Jutta Ludwig-Müller, Technische Universität Dresden, Dresden, Germany
Prof. Ralf Oelmüller, University Jena, Jena, Germany
Prof. Jesús Vicente-Carbajosa, Center for Plant Biotechnology and Genomics, Madrid, Spain
Dr. Anne Krapp, Institut Jean-Pierre Bourgin, INRA-AgroParisTech, Versailles, France

Local committee:
Corine Enard, IJPB
Maria-Jesus Lacruz, IJPB
Adrien Léonardi, IJPB
Hervé Frémineur, IJPB
Stéphane Raude, IJPB
Philippe Poré, INRA, Versailles
Alia Dellagi, IJPB
Anne Krapp, IJPB

Contact and more information: Workshop Plant Performance under Stress website

9 mai 2019


EMBO Workshop on Meiosis

25th-29th August 2019, La Rochelle, France

The reduction-division process in Meiosis is essential for sexual life. Starting out with a diploid chromosome content, meiosis ends up with haploid products, ready to fuel the cycle of sexual reproduction. This halving of the genetic content is obtained by a remarkable series of specific mechanisms that have evolved from the mitotic divisions. The meiosis field unravels the processes behind this particular cell division in a variety of organisms from fungi, to plants, various animals and human. Studies of these specific mechanisms will be at the heart of the EMBO Workshop on Meiosis including initiation of recombination, formation of crossovers between homologous chromosomes, chromosome dynamics, cell cycle, kinetochore attachment, chromosome segregation and consequences on fertility and diseases. We choose conservation and diversities of the mechanisms as a focus for the 2019 meeting to learn from a point of view of evolution and population genetics on less well studied organisms.

Programme and Poster

Scientific Committee:
Christine Mézard, Institut Jean-Pierre Bourgin, INRA, Versailles, France
Harmit Malik, Fred Hutchinson Cancer Research, Seattle, USA
Matt Neale, University of Sussex, Brighton, United Kingdom
Melina Schuh, Max Planck Institute for Biophysical Chemistry, Berlin, Germany
Kikue Tachibana-Konwalski, Institute of Molecular Biotechnology, Vienna, Austria

Local Committee: Christine Mézard, Mathilde Grelon, Corine Enard, Hervé Frémineur, Stéphane Raude, Stéphanie Zimmerman
Institut Jean-Pierre Bourgin, INRA, Versailles, France


Contact and more information: Embo Workshop on Meiosis website

2nd May 2019


The 23RD International Conference on Plant Growth Substances

25th-29th June 2019, Paris, France

The International Plant Growth Substances Association (IPGSA) Conference welcomes researchers, academics and students from university and industry interested in the hormones, growth substances and signaling processes of plants. Held once every three years, the IPGSA conference has long provided a stimulating platform for scientists to share and discuss their latest research. The scientific advisory committee is formed of leading scientists appointed by IPGSA Council members elected from diverse countries and therefore promises to deliver an exciting program. We welcome you to the heart of Paris, and to a University venue which will ensure a rewarding experience to all.

Programme

Scientific Committee:
Christine Beveridge, Univ Queensland, Brisbane, Australia
Miguel Blazquez, IBMCP, Valencia, Spain
Siobhan Braybrook, Univ California, Los Angeles, USA
Mark Estelle, Univ California, San Diego, USA
Annie Marion-Poll, Institut Jean-Pierre Bourgin, INRA, Versailles, France
Catherine Rameau,Institut Jean-Pierre Bourgin, INRA, Versailles, France
Hitoshi Sakakibara, RIKEN, Yokohama, Japan
Daoxin Xie, Tsinghua Univ, Beijing, China

Local Committee:
Sandrine Bonhomme, Institut Jean-Pierre Bourgin, INRA, Versailles
François-Didier Boyer, Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette
Annie Marion-Poll, Institut Jean-Pierre Bourgin, INRA, Versailles
Catherine Rameau, Institut Jean-Pierre Bourgin, INRA, Versailles
Marie-Jeanne Sellier, Saclay Plant Sciences, Ile de France
Sébastien Thomine, SFBV President, CNRS, Gif-sur-Yvette

Contact and more information: IPGSA 2019 website

2dn May 2019


 

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