Comparative population genomics in wild and crop plants: a genome-wide phylogenic approach

Rationale

Domestication strongly impacted phenotypic and genomic evolution in crop species. Crop species typically exhibit lower genetic diversity than their wild ancestors, and may show dramatic phenotypic changes in their morphology, phenology and metabolism (Doebley et al. 2006). Understanding the domestication process is thus a key to crop breeding but also a unique opportunity to study rapid evolutionary processes on a short time scale. Differences among genomic patterns are still not adequately explained. For instance, in many crops, how many genes - and which - are involved in domestication and artificial selection is still not clear. Comparing the domestication process in a range of species, varying from ancient domesticated species (Vitis, Sorghum ) to more recently cultivated species (Coffea ) should provide key information on the dynamics of adaptation and the correlated evolution of polymorphism patterns.

It is also especially important to compare molecular evolutionary patterns among species with contrasted life-history or ecological traits. Life-history or ecological traits may influence genome evolution through their effect on key population genetic parameters (effective size, recombination rates, and mutation rates). Genomic patterns may also vary among phylogenetically distant species because of specific molecular mechanisms such as recombination and repair mechanisms.

Knowing the molecular functions that are targeted by selection is also of interest to increase our understanding of adaptation. Thus, studying the evolution of gene families and relating it to expression data across lineages may help to identify which molecular functions play a key role in adaptation

Today, a comparative population genomic approach among many species is both indispensable and possible thanks to massive sequencing technologies.

Objectives and general methodology

Main objectives

First, we aim to conduct comparative analyses of the effect of domestication on genome evolution in different crop species to:

• quantify the loss/recovery of diversity associated with domestication;
• identify the genes selectively involved in the domestication process;
• investigate variations in domestication patterns among crop species based on their life history, domestication depth, or phylogenetic position.

Second, we aim to investigate the genomic selective patterns among angiosperm species and possible causes of variation using a comparative approach, taking into account the life-history traits and the genomic environment (GC-content, BGC) of the species to:

• quantify the whole genome level of selective constraints and the proportion of adaptive substitutions;
• test the predictions of the effects of life-history traits (breeding systems, life span) on polymorphism within species and divergence among species;
• investigate the phylogenetic distribution of the BGC process in angiosperms, and how it affects selective patterns.

Third, we aim to investigate in more detail how genes functionally evolve in the different species to:

• identify general tendencies, in terms of gene or gene family content, along the angiosperm phylogeny and lineage-specific families, subfamilies or clades;
• compare selective constraints between genes from different functional categories, and genes belonging to subfamilies with different expansion dynamics;
• quantify selective constraints in gene families involved in specific metabolic networks.

General approach

We will study quadruplets of species comprising a crop species, its wild ancestor (for which sequence polymorphism data will be acquired), and two outgroup species, used for phylogenetic analyses (Figure 1).

Figure 1: Species sampling design

We will compare 11 quadruplets of diploid species with contrasted life-history traits, across the angiosperm phylogeny (Table 1). 

Table 1. List of studied crops

For each quadruplet, the domestication process will be investigated by comparing polymorphism patterns between the wild and the domesticated species. Selective constraints, adaptive evolution, and GC-content evolution will be investigated using classical frameworks, and both polymorphism and divergence data. The emblematic species Amborella trichopoda  will be added, which may not be a crop, but which is the most basal extant Angiosperm, endemic to New Caledonia. It is worth noting that model species that still have numerous genomic resources will also be used in the comparison.
To address these questions it is still neither possible nor reasonable to sequence full genomes. Instead, we propose to focus on the expressed portion of the genome to obtain information on the maximum possible number of genes and hence to draw a general and comparable picture between different species. We thus aim to gather large amounts of polymorphism and divergence data by sequencing the transcriptome of each species, using 454 Roche GsFlex technology.

Actions planned

WP 1: Data acquisition

Task 1.1: Collection and conservation of DNA samples
Task 1.2: Sequencing

WP 2: Sequence pre-treatment and database (see Bioinformatics  project)

WP 3: Comparative population genomics of the domestication process

Task 3.1: Loss and gain of genetic diversity following domestication
Task 3.2: Investigation of demographic scenarios
Task 3.3: Identification of domestication genes
Task 3.4: Investigation of the effect of domestication history and life-history traits on the domestication process

WP4: Life history traits and genome evolution

Task 4.1: Characterization of polymorphism and divergence patterns at the quadruplet scale
Task 4.2: Investigation of the effect of life-history traits and taxonomy: comparison between quadruplets

WP 5: Comparative functional genomics

Task 5.1 Comparative analyses of gene content and organisation of gene families
Task 5.2 Analysis of selective constraints affecting the genes and comparison of molecular function, expression level and family organisation.
Task 5.3: Focus on specific metabolic networks

Project team

Project leaders and responsible staff for the work packages