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From  Tlistmaster May 25 12:06:54 2023
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From: "Tatiana Zerjal" <>
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To: Members of AnGenMap <>
Subject: PhD position at INRAE, France: Genetic and
       epigenetic spatial population structure of local
       chicken breeds
Date: Thu, 25 May 2023 12:06:54 -0500

Genetic diversity is crucial for populations to adapt to various
environments. These adaptive capacities are of major importance in the
light of the ongoing climate change that will drastically affect the
environmental conditions, influencing biotic (feed, diseases and
pathogens distribution) and abiotic components (temperature, rainfall???).
Local chicken breeds represent a large reservoir of genetic diversity
valuable for adaptation, particularly in local breeds raised in harsh
production environments over a long period of time and presenting
characteristics that enable them to cope with these conditions. The study
of their genetic diversity and its links with environmental conditions
can give some clues for the future challenges that breeding should meet
to cope with climate change and set the necessary agroecological

In this context, we propose to study the spatial genetic and epigenetic
structure of a large range of European local chicken breeds and the
determinants of their adaptation to various environments. The final goal
is to improve the understanding about how the environment shapes both
genetic and epigenetic diversity and how these interact with each other.
We will focus on both, 1) very localized breeds (i.e. found in a single
restricted area) along a large environmental gradient in terms of
climatic conditions raised in free-range conditions, and 2) more
cosmopolitan breeds raised in contrasted conditions (raised free-range
but bred in-house vs full free-range). This study is innovative since it
will both consider the genetic and the epigenetic features of adaptation
to understand the link between the environment, the genetic composition
of the breed and the methylation profile. Links between all compartments
will be investigated using classical landscape genetics tools and
tailored multivariate approaches.

The PhD candidate will be responsible for:
- data processing
- phenotype, genotype and epigenotype analysis
- conducting genetic and epigenetic diversity analyses
- communication of results in congress and through scientific
  publications in peer review journals

Training and skills requirements

The PhD candidate must hold a master???s degree in genetics, population
genetics,  bioinformatics or any background relevant for this project.
This thesis is targeted towards students who have a keen interest in
investigating high-throughput genome/epigenome-wide data. The thesis
project will require the use of scripts and bioinformatic (i.e.  linux)
and statistical programs (such as R), a minimum of interest for this type
of analysis is essential.

Proficiency in English, including the ability to comprehend and produce
scientific publications and effectively communicate orally in
international conferences and with collaborators, is a prerequisite for
this position. Fluency in French is not mandatory for the application;
however, having a basic knowledge or a willingness to learn the language
can be advantageous for day-to-day interactions


INRAE, Universit?? Paris-Saclay, AgroParisTech
GABI lab (Animal Genetics and Integrative Biology)
GiBBS team (Genomics, Biodiversity, Bioinformatics and Statistics),
Domaine de Vilvert, 78350 Jouy-en-Josas, FRANCE


Please send an application letter and a CV to the three following

If your application is retained to the next step, you will be contacted
for interviews planned in June.

Starting date: Between September and December 2023

Duration: 36 months


French National Association for Research and Technology
Geronimo European H2020 project -
This thesis will be conducted in collaboration between INRAE (French
National Institute for Research on Agriculture and Environment) and
SYSAAF (French National Association for Aviculture and Aquaculture).



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