Mots-Clés

RNA-seq transcriptomic differential expression field phenotyping agroecology

Description

Context Conventional agriculture has been accompanied by a dramatic increase in yield at the cost of negative environmental consequences due to the heavy use of pesticides and fertilizers. A major lever of the agroecological transition consists in diversifying the stands, notably through inter-specific mixtures. Previous work has documented the ecological and ecophysiological processes involved in species mixtures whether they are related to niche complementarity or facilitation (Fréville et al. 2022). While these mechanisms have been documented from an agronomy perspective, current knowledge on the genetic and molecular basis of plant-plant interactions in crops remains very limited (Becker et al. 2022). Furthermore, the few studies that have been conducted use controlled conditions, and therefore fail to account for the dynamics of species interactions under realistic agronomic conditions.

Objectives We propose to compare molecular profiles of plants grown in pure and mixed stands, as assessed by gene transcription (transcriptomics with RNA-seq), and to relate their differences to phenotypes (traits related to canopy, yield and disease). Our experiments were performed in the field under agronomic realistic conditions in two cereal-legume intercropping systems: wheat-pea and maize-bean. Both associate one cereal and one N-fixing legume. The goal of this internship will first to identify (i) differentially expressed genes between the stand types (pure and mixed), and (ii) co-expression clusters between stand types. Pure vs mixed differences in plant phenotypes will be used to guide the interpretations.

Plant material For both systems, two cereal cultivars were associated to two legume cultivars, hence resulting in four mixtures. Field trials In each trial, performed on the Saclay plateau, all pure and mixed stands were replicated three times. Trait phenotyping Traits were phenotyped along the crop cycle as well as at harvest, in relation to phenology, competition, disease and yield. Similar phenotyping will be done for the 2nd season of wheat-pea/maize-bean, to which the student will be able to participate. Leaf sampling For both systems, leaves were sampled at three dates along the crop cycle. A total of 216 samples were collected. Similar leaf sampling will be done for the 2nd season of wheat-pea/maize-bean, to which the student will be able to participate. Molecular profiling RNA sequencing is underway at the POPS platform this Autumn to provide a total of 12 millions reads of 150 nt each.

First, the student will pre-process the data: quality control of sequencing reads, alignment on reference genomes and read counting per annotated gene. Second, he/she will identify differentially expressed genes and co-expression clusters between pure vs mixed stands using the DiCoExpress software (Lambert et al 2020). Enrichment studies will be performed to annotate the groups of genes. Third, the student will analyze the phenotypic data, and use them to interpret the results coming from the RNA-seq analyzes.

Supervision Timothée Flutre (INRAE) and Maud Tenaillon (CNRS)

Lab https://moulon.inrae.fr/