Crop adaptation to climate change: genetic and evolutionary processes involved in phenological responses

Rationale

Understanding the genetic and evolutionary mechanisms involved in adaptation linked to spatial or temporal heterogeneity under selection pressure is an important issue in evolutionary and conservation biology. This requires knowledge about the role of evolutionary processes such as mutation and recombination. For instance, the relative importance of ‘standing genetic variation’ (i.e. allelic variation that is currently segregating within a population or a species) as opposed to new mutations as a source of beneficial alleles is still unknown. It is also important to understand the role of selection in the adaptation process, as it shapes the evolution of genes involved in adaptive traits as well as their surrounding genetic diversity. Although the evolution of adaptive traits has received much attention from a theoretical point of view, data that allows such theoretical predictions to be tested are still rare and many important questions about the genetic basis of adaptation remain open. It is consequently important to obtain empirical data on adaptation routes and genetic mechanisms in both self-fertilizing and outcrossing species.

In the current context, it is crucial to understand the adaptation processes of crop plants and their wild relatives as there is mounting evidence that climate change affects biological and ecological processes. Climate change thus puts strong selective pressure on natural populations and raises two important questions regarding the conservation and use of plant genetic resources: (i) how will climate change affect the phenotypic and genetic diversity of crop species and (ii) what type of material should we produce to withstand the new climatic regime. These questions are particularly important in developing countries where human populations mainly rely on traditional rainfed cropping systems

The expansion of genomics paves the way to tackle these challenges. For an increasing number of plant species, new sequencing and high-throughput genotyping technologies allow the study of genetic variation patterns at hundreds of genome-wide loci. Such data enable us to make inferences about population structure and demographic processes (genetic drift, migration, frequency of recombination) and to provide a multilocus null distribution of variation across the genome that can be used to reliably detect footprints of selection in candidate genes.

Objectives

The aim of this project is to explore the genetics and evolutionary mechanisms involved in local adaptation to spatial and temporal heterogeneity of climatic conditions:

• Which genes/alleles are involved in the adaptation of a plant to climate variation?
• What is the role of standing genetic variation versus  new mutations in the generation of genotypes adapted to new climatic conditions?
• What are the roles of evolutionary mechanisms like migration and recombination in the evolution of a population/species under rapid climate change?

To address these questions, we will perform high throughput genome scan analyses (i ) on populations collected along climatic gradients (spatial contrast) and (ii ) on populations represented by repeated sampling at the same site at different times (temporal contrast). Climatic gradient analyses will allow the identification of sets of candidate genes underlying responses to climate-mediated selection, while monitoring the temporal evolution of populations during the past 20-30 years will provide evidence that evolution has occurred (or not) and insights into the demographic and selective trajectories of populations undergoing climatic variation. Both types of studies will rely on large datasets capturing genome-wide analyses of patterns of genetic variation, and methods for the detection of selection will be developed and used to pinpoint genes or genomic regions exhibiting a distinct diversity signature. Although these analyses will certainly lead to diverse sets of genes involved in different functions, our primary target will be candidate genes for flowering time.

Two crop species (rice, Oryza  sp and pearl millet, Pennisetum glaucum ) and one model species (Medicago truncatula ) will be studied as they exhibit different characteristics concerning their breeding system, domestication history and ecogeographic distribution.

Actions planned

WP1:  Analyses and development of methods for detecting allelic variation associated with geographic/ temporal climatic variation

Task 1.1 Comparison of current methodologies
Task 1.2. Development of a frequentist-based method adapted to environmental structure
Task 1.3. Development of an individual-based method.
Task 1.4. Identification of temporal genetic variation and footprints of selection.

WP 2: Spatial contrasts

Task 2.1: Production of datasets for the application of the methods developed in WP1.
Task 2.2. Assessing the role of the genes identified in genotype/phenotype association studies.

WP 3: Temporal contrasts

Task 3.1. Detection of selection footprints through genome scan analyses.
Task 3.2. Analysis of the potential role of identified genes or genotypes in the response to climate change.
Task 3.3. Inferring the role of phenotypic plasticity in population responses to climate change. 

Project team

Project leaders and responsible staff for the work packages