PhD opportunity

Title of the PhD thesis:
Improved knowledge and pan-genomic prediction of complex phenotypes using a multi-omic integrative approach in black poplar

Plants are fixed organisms, with continuous development, no pre-established germline, and highly varied life cycles ranging up to hundreds of years in trees. Thus, they are relevant biological models for studying the relationship between development and adaptation to the environment (Mladenov et al., 2021). The woody species Populus nigra, the black poplar, constitutes a reference model where so-called “omics” resources such as phenomics, transcriptomics, genomics and epigenomics have been accumulated for more than 20 years in collaboration between BioForA and the LBLGC.

Genome-wide evaluation is an innovation in the way genetic progress is managed and generated in breeding programs. However, like traditional genetic evaluation, it relies on very little consideration of the underlying genetic architecture of traits of interest. However, new resources from omics approaches are bridging the gap between the phenotypes studied and the DNA sequence, paving the way for systems approaches to integrative biology. Recently, systems biology approaches allow, through the integration of different types of data (genomic, transcriptomic), to better understand the interaction of functional factors that condition the expression of phenotypes (Chateigner et al 2020).

Epigenetics is involved in phenotypic plasticity (Maury et al., 2019), stress memory, and even transgenerational transmission and is of interest in plant breeding (Kakoulidou et al., 2021). Epigenomic data thus offer a new and innovative perspective for improving phenotypic predictions through the integration of information from heterogeneous omics data. The challenge will therefore be to decipher the complexity of quantitative traits of interest using explicit predictive models, while maintaining the predictive qualities necessary for operational selection.

This thesis project is thus placed at the interface between 2 teams (LBLGC and BioForA) for which it reinforces the synergies by developing an integrative and ambitious subject.

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B4EST Stakeholder Meeting: Research on Maritime Pine resilience and bioeconomy

The B4EST consortium, in collaboration with the IEFC, the INRAE and the FCBA, is organizing a symposium on latest studies on maritime pine resilience and bioeconomy, July 6, 2022 at the Institute of Agricultural Sciences in Gradignan (Bordeaux), France. Amphi C, 1st Floor, from 13:30 to 18:00.

This event aims to review and discuss the latest research on the resilience and the bioeconomy of maritime pine, focusing on the maritime pine improvement programme. It is organized as part of a series of international events supported by the B4EST project, “Breeding for adaptation: for productive, sustainable and resilient forests under climate change”. It is intended for all stakeholders in the maritime pine sector who wish to gain relevant information and interact with research experts to learn more about the work in progress. This symposium, in French, will also be an opportunity to get an overview of ongoing initiatives abroad, such as in Galicia with the selection of material resistant to pinewood nematode (PWN).

The working language will be in French.

To register please visit:


13h30 : Accueil

Session 1 – Programme d’amélioration génétique du Pin maritime et enjeux futurs

13h45 : Présentation de la filière du pin maritime (Sabrina Fuseliez, FIBOIS)

14h : L’amélioration génétique du pin maritime et le déploiement de variétés (Annie Raffin, INRAe)

14h15 : Enjeux pour le futur, résultats d’enquêtes auprès des professionnels : Enquête régionale et enquête B4EST (Christophe Orazio, IEFC)

14h30 : Pause

Session 2 – Travaux de recherche de B4EST

14h45 : Présentation du projet B4EST (Santiago Gonzalez-Martinez, INRAe)

15h15 : Stratégie d’amélioration à l’aide de marqueurs moléculaires (Laurent Bouffier, INRAe)

15h30 : Tests clonaux multi-provenances (Santiago Gonzalez-Martinez, INRAe)

15h45 : Variabilité de la résistance des pins maritimes à différents agents pathogènes et évolution de leur agressivité (Cyril Dutech & Jean-Paul Soularue, INRAe)

16h : Gain économique associé au gain génétique (Christophe Orazio, IEFC)

16h15 : Analyse coût bénéfice du coût de l’amélioration génétique (Stéphane Lemarié, INRAe)

16h30 Pause

Session 3 – Déploiement des variétés améliorées

16h45 : Santé des vergers à graines (Hervé Jactel, INRAe)

17h : Problématique autour de la sélection de matériel génétique résistant au nématode (Raquel Diaz Vazquez, XUNTA)

17h15 : Modélisation de l’impact climatique sur la production (Denis Loustau, INRAe)

17h30 : Bioéconomie du massif et amélioration génétique (Alain Bailly, FCBA)

18h : Clôture

Télécharger le programme et le plan d’accès

Image by Julia Casada, Pixabay

Training course “Phenotypic plasticity and norms of reaction modelling”

Course date: October 5-7, 2021

This is one of three B4EST training courses to deliver key scientific results and tools via hands-on training events, targeting researchers, Master and PhD students and post-doctorate fellows. The course is co-organized by the SLU Breeding Network and the SLU Industry Research School of Forest Genetics, Biotechnology, and Breeding.

The training course is organized into three consecutive days, including six lectures, plus several case studies about 75 minutes per lecture/case study (3.5-4 hours per day), using Zoom as a meeting format. Some lecturers will give their lecture from North America and hands-on demonstration with R will be included in some lectures.

The following course instructors will hold the course: Harry Wu/Zhiqiang Chen (SLU, Sweden), Tongli Wang (UBC, Canada), Tore Skrøppa/Arne Steffenrem (NIBIO, Norway), Laurent Bouffier (INRAE, France), Philippe Rozenberg (INRAE, France), Marie Denis (CIRAD, France), Jean-Marc Gion/Alexandre Bosc (CIRAD/INRAE, France), Maurizio Marchi (CNR, Italy).

For more information and registration, visit

Tentative Schedule

Each day will start at 9:00 and finish around 17:30 Central Europe Time (CET).

Day 1 (5th, October)

Lecture 1: From genotype by environment interactions to norm of reactions (Wu) (9:00-10:30)

Lecture 2: Climate modelling (Marchi) (10:45-12:15)

Lecture 3: Response functions – norm of reactions (Wang) (16:00-17:30)

Day 2 (6th, October)

Case study 1: Norway spruce (Skrøppa & Chen) (10:45-12:15)

Chen: Local adaptation and plasticity of Norway spruce tree height

Lecture 4: Bayesian varying coefficient model with selection: An application to functional mapping (Denis) (14:15-15:45)

Lecture 5: Integration of genetic and environmental effects into a linear mixed model or a universal response function (URF) (Wang) (16:00-17:30)

Day 3 (7th, October)

Case study 2: New modeling method on plasticity and norm of reaction for Larch and Douglas-fir (Rozenberg) (9:00-10:30)

Case study 3: Norm of reaction and genomic selection for Maritime pine (Bouffier & Papin) (10:45-12:15)

Case study 4: Reaction norms related to tree water status: a case study in eucalyptus and maritime pine (Bosc & Gion) (13:15-14:45)

A training report will be produced for the funding organization after the training course is completed. A certificate of training completion will be issued to each participant who completes the course.

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 773383.

Web Conference on Genetic Basis of Quantitative Traits and Multitrait Association.

*Please note, this training course is postponed until early 2022*

The B4EST consortium, through the University of UPPSALA, INRAE, University of OULU and Consiglio Nazionale delle Ricerche, in collaboration with EVOLTREE, is hosting a web course from September 21-24, 2021. The course will present the latest extensions of Fisher’s infinitesimal model, in particular the omnigenic model and discuss their implications for breeding, association studies and evolutionary inferences.

The course will cater to PhD students and postfoctoral fellows with background in population genetics and/or quantitative genetics.

The conference will take place via zoom To register please send an email to Martin Lascoux If you have problems with this address, please contact communications @

General course plan: Each day we shall have 2 hours lecture in the morning and 2-3 hours tutorial in the afternoon. A detailed schedule will be sent to participants later on.

Panel of Experts (preliminary list): Santiago C. González-Martínez, Juliette Archambeau, Kalle Leppälä, Tanja Pyhäjärvi, Alina Niskanen, G. Giuseppe Vendramin, Antoine Kremer, Martin Lascoux


• Day 1: From the infinitesimal to the omnigenic model

• Day 2: The omnigenic model and evolution of quantitative traits architecture

• Day 3: Consequences of the omnigenic model for genomewide, multi-traits association: what we already know and what needs to be known

• Day 4: Estimating the genome-wide contribution of selection to temporal allele frequency change: principle and an application to forest trees

First EVOLTREE Conference 2021: Genomics and Adaptation in Forest Ecosystems

The first EVOLTREE Conference, hosted by WSL Birmensdorf (Switzerland) from 14-17 September, 2021, focuses on the genomics and adaptation of trees and interacting species from evolutionary, demographic, and ecological perspectives.

Contributions that apply innovative approaches and consider the relevance of their research in the context of biodiversity conservation through natural dynamics or silvicultural interference are welcome.

Registration and abstract submission is now open!

EVOLTREE is a European network of research institutions and universities engaged in studying the evolution and functioning of forest ecosystems, in particular trees as the foundation species in forest stands. A prime topic in the face of ongoing climate change is to elucidate how trees, together with their associated organisms such as mycorrhizal fungi, respond to rapid environmental changes.

For more details, visit our conference website:

Please note that due to the COVID-19 pandemic, for now you can register only for the online conference. In early June 2021, decisions will be made if and how many attendees can participate on-site (subject to government travel restrictions that may change at short notice). You will then be able to acquire an additional on-site package.

Image by Lukasz Szmigiel from Pixabay

EVOLTREE Second series of online Seminars: Adaptation to climate change

EVOLTREE is organizing a second series of virtual events featuring leading experts in research on climate change adaptation – both in forest trees and other organisms. The series is an opportunity to hear the latest from relevant scientists in the field, exchange ideas and discuss potential collaborations and projects.

You can participate in the discussions that follow the presentations by registering through the links below or follow the seminars on the EVOLTREE YouTube channel


14 April 2021, 11:00-12.30 CEST: “Building genetic resilience in a rapidly changing world” Ary Hoffmann, Melbourne University, Australia

21 April 2021, 16:30-18.00 CEST: “Integrating niche evolution with life history theory can help us better understand the consequences of climate change” Ophélie Ronce, University of Montpellier, France

5 May 2021, 16:30-18.00 CEST: “Locally-adaptive mutations and their relevance for climate change ecology” Moisés Expósito-Alonso, Carnegie Institute for Science & Stanford University, California

More information

The seats in the live sessions are limited to 150. All seminars will be streamed on the EVOLTREE YouTube channel and recorded to be available afterwards.

Please register for each webinar separately here

Image: Enrique Lopez Garre, Pixabay

Summer school on scientific writing, reviewing and publishing & forest genetic monitoring knowledge transfer into practice

LIFE project LIFESySTEMiC, EVOLTREE and COST Action(s), in collaboration with the Slovenian Forestry Institute, is organising its 8th summer school on scientific writing, reviewing and publishing & forest genetic monitoring knowledge transfer into practice this coming August 9 to 14.

The summer school aims to provide Ph.d students, as well as junior and senior researchers training sessions on the production, the submission and the reviewing process of scientific publications.

For more information please visit Evoltree

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