Karine ALIX
last updated 08/10/2024
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+33 (0)1 69 33 23 72
karine.alix@inrae.fr
Genomics, Evolution and Adaptation of Domesticated plants
AgroParisTech, Professor
Plant, genome, evolution,, Adaptation,, Inter-, and, intra-specific, hybridization,, Polyploidy,, Transposable, elements,, Small, non, coding, RNAs,, Gene, regulation
publications - orcid
Position and education
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2019-present: Professor at AgroParisTech , Paris in the Teaching Unit Evolutionary genetics and plant breeding (GEAP). Research in the team GEvAD at GQE-Le Moulon, Gif-sur-Yvette, France.
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2005-2019: Maître de Conférences (Associate Professor) in GEAP, Paris; research conducted in the team GEvAD ", at GQE-Le Moulon , Gif-sur-Yvette, France.
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2003-2004: Postdoctoral position in Pr M. Manzanares-Dauleux’s lab, IGEPP, Rennes, France. Genetics, clubroot, Brassica, Arabidopsis.
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2001-2002: Temporary position in Dr A.-M. Chèvre’s lab (IGEPP, Rennes, France): Introgression, blackleg, Brassica napus, cytogenetics, interspecific hybridization, gene flow.
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2001: Postdoctoral fellow (OECD) in Dr Pat Heslop-Harrison’s lab, Department of Biology, University of Leicester, Leicester/United Kingdom. Brassica, retrotransposons, organization, evolution.
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1999-2000: Postdoctoral position in Dr P. Roumet and Pr J. David’s lab (AGAP, Montpellier, France): peroxidases, polymorphism, S-SAP markers, durum wheat, Ph1, recombination, Triticum, Aegilops, cytogenetics
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1995-1998: PhD student in Dr J.-C. Glaszmann and Dr A. D’Hont’s lab (CIRAD, Montpellier): “The repetitive sequences of sugarcane: genome-specificities and phylogeny of the Saccharum complex”.
Management
- Head of the Teaching Unit Evolutionary genetics and plant breeding, GEAP at AgroParisTech – since 2016
Research Management and Administration
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Special adviser in the Director committee of GQE – Le Moulon, since 2020
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Appointed Member for CNECA 5 - since 2018
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Appointed member for CSS GVA, INRAE - since 2016
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Appointed member for CCSU 64-69, Univ. Paris-Saclay - since 2015
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Editor for Annals of Botany , from 2009 - IF 2020 = 4.005
Research interests
My interests include evolution of the plant genome in the context of adaptation of plants and notably of crops, with a particular focus on the processes of interspecific hybridization and polyploidy (See Annals of Botany ). I am notably interested in the dynamics of transposable elements (TEs), see New Phytologist , as well as their epigenetic control by small non coding RNAs, during the course of the evolution and adaptation of cultivated plants in comparison to their wild relatives.
Brassica is an agriculturally important genus that provides a wide range of diploid and allotetraploid species, and is particularly appropriate for studying gene expression changes and evolution of TEs that occur during speciation and polyploidization (see Plant Journal ).
Part of my research project is dedicated to the analysis of the impact of a recent polyploidization event on gene regulation as well as on the activation of TEs, using newly synthesized Brassica napus lines, in collaboration with Anne-Marie Chèvre and Mathieu Rousseau-Gueutin, IGEPP, INRAE Rennes. During her postdoctoral position (2006-2008), Anne Marmagne contributed to the study of the relationships between transcript and protein changes following allopolyploidization (see New Phytologist ). The analysis of the impact of allopolyploidy on TEs was part of Véronique Sarilar’s PhD project (2008-2011), see PMB and New Phytologist .
I also analysed the role of small non-coding RNAs in the regulation of gene expression and the control of non-coding components of the genome. During her PhD work (2010-2014), Paulina Martinez Palacios studied the mobilization of snRNAs following allopolyploidization in independent lines of newly synthesized B. napus (see MBE ).
With the help of Pierre Gérard, work is in progress to evaluate the relationships between structural and functional modifications that are triggered by a new polyploidization event, taking into consideration the central role of micro RNAs in gene regulation. This has been initiated by Quentin Charret’s MSc work (2018) thanks to a new collaboration with Hélène Touzet, CRIStAL, Université de Lille.
In relation with my interest in interspecific hybridization as a major process in plant evolution, I collaborated with Yves Vigouroux, DIADE, IRD Montpellier, in supervising Roland Akakpo’s PhD project (2015-2018). The main objective was to clarify the genetic relationships between three Dioscorea species, with D. abyssinica and D. praehensilis considered as the progenitors of the cultivated yam species D. rotundata (see BMC Genomics and Science Advances . At GQE-Le Moulon, and in collaboration with Florian Maumus, URGI, INRAE Versailles, we analysed the diversity and organisation of TEs among the three species, by exploiting NGS data to evaluate the involvement of TEs in Dioscorea genome modeling.
Recently, I began a new collaborative project with Amandine Cornille. The project aims at analyzing the contribution of TEs to the evolution of the Malus genome and the adaptation of the cultivated apple tree. During his MSc project (2020), Anthony Venon created a complete TE database for Malus by exploiting NGS data from more than 180 wild and cultivated Malus genotypes. Analysis of the differential TE profiles within a sample of ~200 Malus genomes should highlight the contribution of TEs to the domestication and adaptation of the cultivated apple tree.
The project DomIsol funded by ANR began in 2020, with Maud Tenaillon as PI. The main objective of our scientific consortium is to characterize the molecular determinants of the genetic barriers that have been progressively established between domesticated plants and their wild relatives. From different plant systems, we will define the evolutionary genomics of such a reproductive divergence. I will notably focus on the Brassica oleracea system, for which knowledge at the structural and functional levels of the mechanisms responsible for genetic incompatibilities between wild and cultivated cabbages, should help in exploring genetic resources for breeding.
Collaborations
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At GQE-Le Moulon: Pierre Gérard, Amandine Cornille, Matthieu Falque, Johann Joets, Maud Tenaillon, Clémentine Vitte
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At IDEEV : Thierry Robert, ESE
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Yves Vigouroux , DIADE, IRD Montpellier
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Florian Maumus , URGI - INRA Versailles
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Hélène Touzet, CRIStAL – Université de Lille
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Anne Marmagne - IJPB, INRA Versailles
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Anne-Marie Chèvre , Mathieu Rousseau-Gueutin - IGEPP, INRA Rennes]
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Martin Crespi and Christine Lelandais - IPS2, Gif-sur-Yvette
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Erwin Van Dijk and Claude Thermes - I2BC, Gif-sur-Yvette
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Pat Heslop-Harrison - University of Leicester, UK.
Teaching
For students at AgroParisTech, (cursus Ingénieurs)
First year
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Population genetics
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Stakes and challenges « the wild biodiversity and the cultivated biodiversity: the current situation »
Second year
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Plant genetics and breeding
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(i) What we can learn from genome exploration, (ii) Adaptation of plants to environment, (iii) The new challenges of plant breeding
Third year
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Specialization in Production and Innovation in Plant Systems: Genomics, plant biotechnologies and seed biology; Genetics and plant breeding
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Specialization in Biotechnologies (Biotechs): Genomics, hight throughput in biology and bioinformatics
For Master students at Université Paris-Saclay
Master 1, Biologie Intégrative et Physiologie (BIP);
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Responsible for the common course - Course dedicated to genome evolution and organisation
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M1 BIP, specialization in plant biology ; responsible for this programme with Dr M. Garmier - (i) Genomics of cultivated plants and bioinformatics, (ii) Genetics for agronomy and plant breeding
Master 2 Plant Science : responsible for the Professional programme IQPV (Innovation en qualité et productions végétales) with Dr H. Vanacker - Courses specialized in genomics, genetics and plant breeding.
Publications
2023
- Tenaillon MI., Burban E., Huynh S., Wojcik A., Thuillet AC., Manicacci D., Gérard PR., Alix K. , Belcram H., Cornille A., Brault M., Stevens R., Lagnel J., Dogimont C., Vigouroux Y., Glémin S.. (2023) Crop domestication as a step toward reproductive isolation. American Journal of Botany, 7 (110) e16173
2021
- Kalendar R., Sabot F., Rodriguez F., Karlov GI., Natali L., Alix K. . (2021) Editorial: Mobile Elements and Plant Genome Evolution, Comparative Analyzes and Computational Tools. Front. Plant Sci., (12) 735134
2019
- Martinez Palacios P., Jacquemot MP., Tapie M., Rousselet A., Diop M., Remoué C., Falque M., Lloyd A., Jenczewski E., Lassalle G., Chévre AM., Lelandais C., Crespi M., Brabant P., Joets J., Alix K. . (2019) Assessing the Response of Small RNA Populations to Allopolyploidy Using Resynthesized Brassica napus Allotetraploids. Mol Biol Evol, 4 (36) 709-726
- Scarcelli N., Cubry P., Akakpo R., Thuillet AC., Obidiegwu J., Baco MN., Otoo E., Sonké B., Dansi A., Djedatin G., Mariac C., Couderc M., Causse S., Alix K. , Chaïr H., François O., Vigouroux Y.. (2019) Yam genomics supports West Africa as a major cradle of crop domestication. Sci. Adv., 5 (5) eaaw1947
2018
- Dard-Dascot C., Naquin D., d'Aubenton-Carafa Y., Alix K. , Thermes C., van Dijk E.. (2018) Systematic comparison of small RNA library preparation protocols for next-generation sequencing. BMC genomics, 1 (19) 118
2017
- Akakpo R., Scarcelli N., Chaïr H., Dansi A., Djedatin G., Thuillet AC., Rhoné B., François O., Alix K. , Vigouroux Y.. (2017) Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes. BMC Genomics, 1 (18) 782
- Alix K. , Gérard PR., Schwarzacher T., Heslop-Harrison JSP.. (2017) Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants. Ann Bot, 2 (120) 183-194
2013
- Jenczewski E., Chèvre AM., Alix K. , Chen ZJ., Birchler JA.. (2013) Chromosomal and gene expression changes in Brassica allopolyploids. , 171-186
- Sarilar V., Martinez-Palacios P., Rousselet A., Ridel C., Falque M., Eber F., Chevre AM., Joets J., Brabant P., Alix K. . (2013) Allopolyploidy has a moderate impact on restructuring at three contrasting transposable element insertion sites in resynthesized Brassica napus allotetraploids. The New phytologist, 2 (198) 593-604