Karine ALIX

Evolutionary genomics of cultivated plants

     
  • Plant
  • genome
  • evolution,
  • Adaptation,
  • Inter-
  • and
  • intra-specific
  • hybridization,
  • Polyploidy,
  • Transposable
  • elements,
  • Small
  • non
  • coding
  • RNAs,
  • Gene
  • regulation

 AgroParisTech, Professor

 karine.alix@inrae.fr —   +33 (0)1 69 33 23 72


 Genomics, Evolution and Adaptation of Domesticated plants

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 Publications    

  • Génétique Quantitative et Évolution - Le Moulon
  • Université Paris-Saclay, INRAE, CNRS, AgroParisTech
  • IDEEV
  • 12 route 128
  • 91190 Gif-sur-Yvette
Karine ALIX

Position and education

  • 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.

  • 2005-2019: Maître de Conférences (Associate Professor) in GEAP, Paris; research conducted in the team GEvAD", at GQE-Le Moulon, Gif-sur-Yvette, France.

  • 2003-2004: Postdoctoral position in Pr M. Manzanares-Dauleux’s lab, IGEPP, Rennes, France. Genetics, clubroot, Brassica, Arabidopsis.

  • 2001-2002: Temporary position in Dr A.-M. Chèvre’s lab (IGEPP, Rennes, France): Introgression, blackleg, Brassica napus, cytogenetics, interspecific hybridization, gene flow.

  • 2001: Postdoctoral fellow (OECD) in Dr Pat Heslop-Harrison’s lab, Department of Biology, University of Leicester, Leicester/United Kingdom. Brassica, retrotransposons, organization, evolution.

  • 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

  • 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

  • Special adviser in the Director committee of GQE – Le Moulon, since 2020

  • Appointed Member for CNECA 5 - since 2018

  • Appointed member for CSS GVA, INRAE - since 2016

  • Appointed member for CCSU 64-69, Univ. Paris-Saclay - since 2015

  • 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).

Figure 1. The evolutionary genomics of allopolyploidy in oilseed rape. To characterize the genomic changes triggered by allopolyploidy, we analyse newly synthesized Brassica napus lines at different generations. Pictures by K . Alix.

Figure 1. The evolutionary genomics of allopolyploidy in oilseed rape. To characterize the genomic changes triggered by allopolyploidy, we analyse newly synthesized Brassica napus lines at different generations. Pictures by K . Alix.

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.

Figure 2. We analyse the contribution of TEs in modeling the genome of apple tree during domestication and adaptation. To help in exploiting genetic resources for plant breeding, we study the genomic determinants of the genetic barriers between crops and their wild relatives, using cabbage as one of the fourteen systems under survey. Pictures by K . Alix.

Figure 2. We analyse the contribution of TEs in modeling the genome of apple tree during domestication and adaptation. To help in exploiting genetic resources for plant breeding, we study the genomic determinants of the genetic barriers between crops and their wild relatives, using cabbage as one of the fourteen systems under survey. Pictures by K . Alix.

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

Teaching

For students at AgroParisTech, (cursus Ingénieurs)

First year

  • Population genetics

  • Stakes and challenges « the wild biodiversity and the cultivated biodiversity: the current situation »

Second year

  • Plant genetics and breeding

  • (i) What we can learn from genome exploration, (ii) Adaptation of plants to environment, (iii) The new challenges of plant breeding

Third year

  • Specialization in Production and Innovation in Plant Systems: Genomics, plant biotechnologies and seed biology; Genetics and plant breeding

  • 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);

  • Responsible for the common course - Course dedicated to genome evolution and organisation

  • 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

  • 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
  • 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
  • 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
  • Akakpo R., 2018-05-16 16/05/18, Étude de la domestication et de l’adaptation de l’igname (Dioscorea spp) en Afrique par des approches génomiques, PhD thesis, Université Paris-Saclay
  • 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
  • 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
  • Vitte C., Fustier MA., Alix K. , Tenaillon MI.. (2014) The bright side of transposons in crop evolution. Briefings in functional genomics, 4 (13) 276-95
  • 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
  • Becker A., Alix K. , Damerval C.. (2011) The evolution of flower development: current understanding and future challenges. Annals of botany, 9 (107) 1427-31
  • Sarilar V., Marmagne A., Brabant P., Joets J., Alix K. . (2011) BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space. Plant molecular biology, 1-2 (77) 59-75
  • Marmagne A., Brabant P., Thiellement H., Alix K. . (2010) Analysis of gene expression in resynthesized Brassica napus allotetraploids: transcriptional changes do not explain differential protein regulation. The New phytologist, 1 (186) 216-27
  • Parisod C., Alix K. , Just J., Petit M., Sarilar V., Mhiri C., Ainouche M., Chalhoub B., Grandbastien MA.. (2010) Impact of transposable elements on the organization and function of allopolyploid genomes. The New phytologist, 1 (186) 37-45
  • Zerjal T., Joets J., Alix K. , Grandbastien MA., Tenaillon MI.. (2009) Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome. Plant molecular biology, 1-2 (71) 99-114
  • Alix K. , Joets J., Ryder CD., Moore J., Barker GC., Bailey JP., King GJ., Pat Heslop-Harrison JS.. (2008) The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation. The Plant journal : for cell and molecular biology, 6 (56) 1030-44
  • Pouilly N., Delourme R., Alix K. , Jenczewski E.. (2008) Repetitive sequence-derived markers tag centromeres and telomeres and provide insights into chromosome evolution in Brassica napus. Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 5 (16) 683-700