Department of Biology
Annotated genes and non-annotated genomes: use of model organism gene annotation information for understanding the molecular basis of traits of ecological and evolutionary importance
Author(s): Primmer, CR, Papakostas, S, Leder, EH, Davis, MJ, Ragan, MA
Recent advances in molecular technologies have opened up unprecedented opportunities for evolutionary biologists and ecologists to better understand the molecular basis of traits of ecological and evolutionary importance in almost any organism. Nevertheless, reliable and systematic inference of functionally relevant information from these masses of data remains challenging. In my poster, I will highlight how the Gene Ontology (GO) database can be of use in meeting this challenge. The GO provides a largely species-neutral source of information on the molecular function, biological role and cellular location of tens of thousands of gene products. As it is designed to be species neutral, the GO is well suited for cross-species use i.e. functional annotation derived from model organisms can be transferred to inferred orthologs in newly sequenced species. In other words, the GO can provide gene annotation information for species with non-annotated genomes. I will highlight the both the strengths and the current weaknesses of using GO for enhancing the understanding of molecular function in ecologically relevant species and present some examples of its use for evolutionary contexts
Department of ecology and genetics
Genetic basis of leaf trichome density in natural populations of Arabidopsis thaliana
Author(s): Lundemo, S, Breed, MF, Ågren, J
Trichomes are hair-like epidermal structures on plant surfaces that may contribute to herbivore deterrence, UV protection, and tolerance to drought. In the annual plant Arabidopsis thaliana, leaf trichome density varies considerably among populations. We examined the genetic basis of differences in trichome density between two populations located close to the northern (Sweden) and southern (Italy) margin of the native range. We planted parental lines and 400 recombinant inbred lines (RILs) derived from a cross between the two populations at the sites of both source populations. Seedlings were planted at the time of natural seedling establishment in the autumn, and trichome density was scored on leaves before flowering in spring. We mapped QTL for trichome density using a linkage map based on 360 SNPs spaced at ca. 1 cM intervals. We asked how many QTL contribute to differences in trichome density and what is the magnitude of their effects? Do QTL for trichome density co-locate with candidate genes known to influence trichome density? Can QTL effects be linked to mutations in these genes? Preliminary analyses detected 11 QTL influencing trichome density. Of these, one QTL on chromosome 2 was consistently detected across years and at both study sites, and explained between 19% and 44% of the variation in RIL means. This QTL was located in a genomic region harbouring two genes known to influence trichome density: ETC2 and TCL1. Sequence differences between the two parental lines in these two candidate genes corresponded to four and one amino acid, respectively. We will present an analysis of the functional significance of the sequence differences detected and of their geographic distribution. In ongoing work, we explore the adaptive significance of trichome density by connecting variation in trichome density to variation in other putatively adaptive traits and to fitness in the field.
Department of Ecology and Evolution
Genetic exchange in a multigenomic fungus; Rhisophagus irregularis
Author(s): Rosikiewicz, P, Sanders, IR
Rhizophagus irregularis is a model species of an arbuscular mycorrhizal fungi (AMF). The AMF forms symbiotic relationship with roots of land plants, improving plant growth and protecting plants against parasites. R. irregularis is a particularly important species of AMF because it colonizes roots of most of crop plants such as rice, potato and wheat. However, different isolates of this fungus can affect plant phenotype differently. Moreover, it recently has been shown that two isolates of AMF can exchange genetic material, a process that can alter both, plant and fungal phenotypes. R. irregularis, is a coenocytic organism, which means that many nuclei coexist and can move in the common cytoplasm. The genetic exchange between two AMF isolates occurs via vegetative hyphal fusion. However, unlike in most fungi AMF produces multinucleate spores and it has been shown that each isolate of R. irregularis carries genetically different nuclei, which are maintained in successive AMF generations. What is unknown is the fate of parental nuclei after the genetic exchange, how many parental nuclei are exchanged and whether the mix of nuclei is random. In addition the nuclei are exchange with the surrounding cytoplasm. This lead to a question whether mitochondria from both parental isolates are transmitted to the offspring and how can it influence the fungal and plant phenotypes.
Genome-wide analysis of the genetic architecture of flowering time and fitness in wheat experimental populations
Author(s): Thépot, S, Goldringer, I, Mackay, I, Enjalbert, J
Flowering time is a major adaptive trait, as it allows plants to synchronize their vegetative cycle with optimal environmental conditions and thus to maximize their fitness. This trait has been studied over 20 generations in different experimental wheat populations, relying on three gene pools: two selfing pools obtained by pyramid crosses of two sets of 16 parents. The third is an outcrossing pool obtained by random crossing of 61 parents by the use of male sterility. These three pools have been dispatched over 12 sites in France, and then cultivated year after year in isolation, without migration or human selection. Fast evolution, both over time and in space, was noticed for flowering time. Using both shifts in allelic, or association genetics, these adaptations were in part explained by polymorphisms at key genes controlling vernalisation or photoperiod sensitivity (Rhoné et al. 2008, 2010). We recently developed an extended study of the outcrossing population, genotyping about 400 SSD lines with a 9k SNPs array (Chao et al. 2010), and performing an extended phenotyping of flowering time, under contrasted environmental conditions (variations in vernalization and photoperiod). With this highly recombinant and highly diverse population we describe the distribution of effects over detected QTNs, the major QTNs corresponding to previously described candidate genes. The detected QTNs x environment interactions highlight the genetics of local adaptation. Comparing major genes handled by plant breeders, and results obtained on wheat experimental populations, we will show how the genetic architecture of flowering time and its strong interaction with environment can explain the genetic architecture of fitness traits in natural populations.
Laboratoire Evolution, Génome et Spéciation
Single gene polymorphism alters the foraging activity of a pest Lepidoptera
Author(s): Chardonnet, F, Capdevielle-Dulac, C, Chouquet, B, Joly, N, Harry, M, Le Ru, B, Silvain, J, Kaiser, L
The extension of agriculture areas, needed to meet the food needs of a growing world population, subjects the environment to important anthropic pressures and rapid changes. However, some phytophagous insect species from the wild habitats have taken advantage of these abundant and nutritious cultivated hosts, where they establish and become pests. A representative of a major insect pest family, the Noctuidae, is Sesamia nonagrioides moth, well known for its economical losses on maize in African and Mediterranean countries. This species shows two populations distinct by their ecological preferences: one is a pest found in maize fields, while the other is exclusively found on wild herbaceous host-plants. The qualitative and quantitative differences between wild and cultivated resources should involve the expression and the selection of different foraging strategies. Because foraging (for) is a candidate gene and a major modulator of foraging strategies in a variety of invertebrate species, it could be involved in the adaptation of phytophagous insects to cultivated plants. Following an integrative approach, we compared the crop and the wild populations of S. nonagrioides. We found that they differ in their foraging activity by measuring their tendency to change of food patches. We identified two allelic variants of the for gene respectively associated with specific gene expression rates. One of the variant was harboured by the wild population and the other was predominant in the crop population. Activating the encoded cGMP-dependent PKG by a pharmacological compound increased the foraging activity of larvae, which suggests a causal link between for genotypes and the identified behavioural phenotypes. To understand if the evolution of the for gene would be a factor of the adaptation of S. nonagrioides to cultivated host-plant, analysis of neutral markers and for polymorphism over the geographic and ecological range of the species is in progress.
Department of Evolutionary Biology
The X Factor: the genomic distribution of eQTNs that regulate sexual dimorphism
Author(s): Dean, RF, Stocks, M, Rogell, B, Friberg, U
How can sex differences arise from a largely shared genome? Theory predicts sex chromosome linkage is crucial: by reducing the intersexual genetic correlation, sex chromosomes allow males and females to evolve separately and reach their phenotypic optima. However, studies on the role of sex chromosomes and sexual dimorphism find mixed results: whereas sex chromosomes tend to harbor sex biased genes, the association between sexually dimorphic phenotypes and sex chromosomes is more tentative. We approach this question from a different perspective by examining the role of the X chromosome in the regulation of sexually dimorphic gene expression.
Using the Drosophila Genetic Reference Panel we perform a genome-wide study to find SNPs that associate with variation in sexually dimorphic gene expression. First, we find the X chromosome is a hotspot for SNPs that associate with variation in sexually dimorphic expression, particularly when SNPs are located between genes. Furthermore, we show the far reach of the X chromosome - trans-regulating SNPs that associate with variation in sexual dimorphism are more common on the X chromosome. Finally, we look in fine detail at the genomic regions with dense dimorphism-associated SNPs to see whether we can identify individual SNPs as general regulators of sexual dimorphism.
Taken together, these results suggest the X chromosome is a master regulator of sexual dimorphism and give more general insights into the genomic basis of complex phenotypes.
Animal & Plant Sciences
The genetic architecture of a reproductive trait in a wild bird population
Author(s): Armstrong, JC
The timing of egg-laying (lay date) in wild birds is a key determinant of overall reproductive success, with some species timing their breeding events to coincide with peaks in the abundances of key prey species. Mistimed breeding events can result in trophic mismatches and subsequently lower chick survival and fledging success. A phenotypic shift to earlier laying has been observed in a population of great tits (Parus major) in response to the earlier emergence of their winter moth larvae prey, itself the result of climate warming. Lay date has been found to have a small but significant heritable component. This study combines several genetic analysis tools, including QTL mapping and Genome Wide Association Study (GWAS) techniques, to describe the genetic architecture of lay date. Variation in this trait appears to have a polygenic basis.
The genetic architecture of skin prickling and body shape in hybridizing sculpins (Cottus)
Author(s): Cheng, J, Nolte, AW
European freshwater sculpins, Cottus rhenanus and Cottus perifretum, have formed hybrid lineages (invasive Cottus) in the Lower River Rhine. The hybrid Cottus particularly resembles one of its ancestral species, C. perifretum, in phenotypic features. This contrasts with the expectation of hybrid intermediacy, which is suggested by the fact that the invasive genome is thoroughly admixed. Among these traits, the scale-like skin prickling and body shape represent a common source of variation among a number of Cottus species. The Ectodysplasin (EDA) signaling pathway provides promising candidates to investigate the genetic basis of prickling because it is known to affect the development of dermal bones and scales in fishes. We identified and mapped Cottus EDA signaling pathway components and performed quantitative trait loci (QTL) mapping for prickling and body shape in Cottus. A single highly significant QTL that affects prickling in all F2 mapping families was detected in an interval that contains the EDA receptor (Edar) with the maximum LOD score on Cottus linkage group 3 but none of the other EDA pathway genes. The same QTL region also shows effects on body shape. An investigation of gene structure from 6 individuals suggests that the genomic architecture of the Edar gene makes it a more likely contributor to evolutionary changes than other components in this pathway. An analysis of ancestral allele frequencies within EDA pathway gene regions in the invasive gene pool shows that Edar genomic ancestry is biased towards C. perifretum (85%-96%), which is correlated with the phenotypic similarity of invasive Cottus with that species. The Edar carrying QTL is currently the best candidate that strongly determines phenotypic variation of hybrid Cottus in the River Rhine. EDA signaling constitutes a key adaptive trait in stickleback and our results suggest that the same pathway may contribute to conspicuous phenotypic variation in Cottus as well.
Department of Plant Ecology and Evolution
The genomic architecture of adaptive differentiation in seed dormancy and germination timing between two natural populations of Arabidopsis thaliana
Author(s): Postma, FM, Ågren, J
Timing of germination is expected to influence plant fitness strongly, because it determines not only the environmental conditions for the emerging seedling but also sets the context for all subsequent life stages. We studied the genomic architecture and adaptive significance of differentiation in seed dormancy and germination timing between two natural populations of the annual herb Arabidopsis thaliana located close to the geographic limits of the native range (northern Sweden and central Italy). With recombinant inbred lines (RILs) derived from a cross between the two focal populations, we mapped QTL for germination traits. First, seed dormancy was estimated for more than 400 RILs and the two parental lines using seeds that had matured in the greenhouse. Second, the timing of germination at the Swedish field site and seedling establishment at both field sites were documented for 220 RILs and the two parental lines using seeds matured at the respective field site and planted at the time of seed dispersal in spring. The Italian genotype produced seeds with a markedly stronger dormancy and germinated later at the Swedish field site than did the Swedish genotype. At both field sites, the local genotype outperformed the non-local genotype in terms of seedling establishment. In Italy, seed dormancy was positively correlated with RIL establishment success, while in Sweden this relationship was negative. Of the 11 QTL identified, one affected all three germination traits (dormancy, timing, establishment). This QTL had a huge effect size compared to the other detected QTL, and co-locates with the known dormancy gene DOG1. The results demonstrate that genetically based differences in seed dormancy are associated with differences in timing of germination and successful seedling establishment at the sites of the source populations, and thereby contribute to adaptive differentiation among natural populations of A. thaliana.