P3-14: Dissecting Intraspecific Variation in Compound Eye Size in Drosophila Melanogaster via Integration of Genome, Transcriptome and Phenotype Data

PhD Student: Amel Chtioui
Supervisor: Prof. Dr. Henner Semianer
Group: Animal Breeding and Genetics

Project Description:
One major aim of biological research is to describe the diversity of life forms on earth and to understand the processes involved in its origin. Adult morphology is defined during embryonic and postembryonic development and therefore diversification is the result of changes in developmental programs [1]. The emerging "micro-evo-devo" [2, 3] approach allows to identify the nucleotide changes that led to differences in the body form of extant taxa. In the last decade a growing amount of data has been accumulated identifying the genes underlying morphological evolution among populations of one species and between closely related species [4-11].

The development of complex organs relies on the action of gene regulatory networks (GRN) that act through transcriptional activation, maintenance and repression of interconnected genes, which code for transcription factors or signaling proteins [12]. Although these networks are highly complex, it has been shown that variation in similar traits in different lineages seem to be based on changes in the same nodes of the respective GNR [13, 14], suggesting that developmental constraints like pleiotropy and epistasis might reduce the number of nodes within the GRNs that can evolve [15, 16]. On the other hand, for other traits it has been shown that the same qualitative change is the result of changes in different genes between lineages [17-19]. It is therefore still unclear, whether similar morphological traits evolve through changes in the same nodes within the underlying GRN or if different genes are involved in different lineages.

The Drosophila melanogaster Genetic Reference Panel (DGRP) represents an excellent community resource to address these questions in detail. The DGRP consists of more than 200 inbred lines obtained from one natural population. For all of these lines, genome sequences and recombination maps are available to allow for a rapid identification of the genetic basis of variation in quantitative traits [20, 21]. It has been shown that sequence data allow reasonably accurate predictions of complex phenotypes with additive [22] and epistatic models [23].

While the evolution of rather simple morphological traits like the loss or gain of a given structure is well-understood, our knowledge about how the size and shape of complex organs evolves is still limited. In recent years it has been shown that compound eye size and the head morphology are highly variable complex traits in various insect species including Drosophila melanogaster and closely related Drosophila species [24-26].

The successful candidate will study eye size variation in various DGRP fly lines and determine the genetic basis for these differences. For representative strains, developmental transcriptome data using RNAseq will be generated to be integrated with the obtained mapping data. Similar data will be generated for artificial selection experiments based on a subset of the DGRP fly lines. The analysis will aim at identifying the decisive elements for phenotypic and developmental diversification in complex biological networks using statistical approaches across the different scales (genome, transcriptome, phenotype). Methods to be used will encompass complex modelling approaches such as structural equation models [27] and network-based kernel methods [28]. Part of the work will be conducted during an extended research stay in the group of one of the international collaborators overseas.