INRAE and University of Angers 3-year PhD Position 2023

Deadline: 31 st July, 2023.

INRAE and University of Angers 3-year PhD Position 2023

Discipline: Genomics, Ecophysiology, Transcriptomics

Laboratory: Research Institute of Horticulture and Seeds (IRHS) of Angers, France

Host institution: INRAE and University of Angers

Doctoral school: VAAME (Plant, Animal, Food, Sea, Environment)

Financing: 50% University of Angers (acquired) and 50% Region Pays de la Loire (submitted)

Starting date: October 2023

Context and description:

Applications are invited for a 3-year PhD position to study the impact of pedo-climatic conditions on the anthocyanin content and overall red coloration of red-flesh apples. This position is opened in the VALEMA research team (Valorization of Epigenetic Marks in plAnts), at the IRHS institute ( This thesis will be conducted in interaction with IFO, a company specialized in the breeding and marketing of new pipfruit varieties, based in the Region Pays de la Loire.

The main subjects of the research team are:

(i) the study of plant adaptation to abiotic constrains in a context of climate warming and

(ii) the study of fruit qualities (particularly specialized metabolites such as anthocyanins) elaboration in a changing environment. Our model of study is apple (Malus domestica), which genome has been sequenced (

Objectives and scientific questions:

For several years, apple classical varieties are being replaced by new varieties responding to new environmental and consumer requirements. To meet these requirements, our partner IFO is currently involved in the breeding of new red-flesh varieties. These varieties, some of them at the commercial stage, are currently being tested in contrasted pedo-climatic environments. Preliminary observations have revealed major environmental effects on anthocyanin concentrations in the fruit flesh, therefore affecting overall flesh color and appeal. The objective of the proposed PhD project is to investigate the genetic x epigenetic x environment interactions regulating apple red flesh color.

In this study we will focus on the following scientific questions:

– What are the effects of pedo-climatic factors of red flesh color regulation?

– To what extend does the environment affect the epigenome of a variety?

– At which stages during fruit development do two key factors (light and drought stress) affect most the final red flesh phenotype, and what are the metabolic and transcriptomic mechanisms affected by modifications in these factors?

Main steps and approaches:

Firstly, a study of red flesh intensity variation will be conducted using varieties growing in contrasted environments. We will use a world-wide experimental set up designed by IFO and its partners to investigate the effects of various pedo-climatic factors. Secondly, the project will focus on two key factors (light and drought stress). The effects of these factors on flesh color will be investigated using an experimental design set up on site. Targeted metabolomic, transcriptomic and epigenomic analysis will allow the candidate to decipher the mechanisms driving fruit flesh pigmentation variation. Outputs of the projects will include:

(i) a better understanding of the mechanisms controlling anthocyanins production in response to various environmental constrains,

(ii) the design of ideotypes, and

(iii) to propose alternative agricultural practices allowing an increase in fruit flesh coloration.