Mapping the zebra finch genome

Zebra finches (Taeniopygia guttata) are a passerine or songbird. Passerines are widely studied in a broad range of biological disciplines, both as laboratory model organisms, and in the wild. In the laboratory they are used to understand how song is developed, controlled and learned, and are a model system for understanding vocalisation in other species. Studies of wild passerine populations have advanced our understanding of natural selection, sexual selection, the effects of inbreeding, mechanisms of speciation, the causes of evolutionary stasis, and the genetic architecture of fitness-related traits. Enormous progress on many of these questions has been made in recent years by quantitative genetic analyses of pedigreed populations. Frustratingly, genomics resources are less well-developed for passerines than many other vertebrate taxa. As a result it is currently almost impossible to carry out gene mapping studies in passerines, a direction that many biologists feel is the next logical extension of previous work. However, an opportunity has now arisen to address this problem because the zebra finch genome is currently being sequenced. This will be the first genome sequence for a passerine species, and only the second of any bird; a first draft chicken genome assembly was released in 2004, but Galliforms (the group that includes chickens) and passerines diverged ~100 million years ago. In this project we will build a genetic linkage map of the zebra finch genome, using birds from a long-term study population maintained in Sheffield. The project is made possible by three things: (i) the availability of the zebra finch genome sequence, which will enable us to rapidly find genetic markers to put on the map, (ii) our multigenerational zebra finch population and (iii) new high-throughput genotyping platforms that can produce data on a scale that was not previously possible. Compared to older methods the new platforms produce data at 5-10 times lower cost and at least 5-10 times more rapidly. The zebra finch linkage map will serve several purposes. First, it will be used to help 'assemble' the zebra finch genome sequence. Sequencing programs typically produce large, overlapping sequences, but placing them in the correct order and on the correct chromosomes is very difficult. The task is made much simpler if reference can be made to a linkage map, where markers are ordered along the chromosomes. Second, we will use the map to test a number of population genetic hypotheses, particularly those relating to the evolution of chromosomal rearrangements and meiotic recombination rates. Third, the map represents a resource which can be used to identify the genes that are responsible for variation in a number of important phenotypes including sperm motility and morphology, body condition, plumage intensity and song performance. Finally, the map can be used to start building similar maps in other passerine species, especially those where gene mapping is an attractive future direction, such as those that have been the subject of long-term ecological studies in the wild. Good examples include the great tit population at Wytham Woods, Oxford and the collared flycatchers on the Swedish island of Gotland.

The overall aim of this proposal is to identify and map >2000 genetic markers to the zebra finch genome. The linkage map will be the first genome-wide map for any passerine species, and will establish the zebra finch as the model organism for passerine gene mapping. The work will be carried out in a 500-bird 'International Mapping Flock' created from our long-term study population. Birds from our population are currently being used to create cDNA libraries, which will then be sequenced at the University of Washington Genome Sequencing Centre. Many thousands of SNPs will be discovered in silico, and we will type ~2000 of them in the mapping flock. Genotyping will be performed on the Sequenom MassArray system in just 6-12 weeks. A further 200 microsatellite markers which we have already mined from existing zebra finch EST libraries will be added to the map. The microsatellites serve two main purposes. First they are more variable than SNPs and so can be used to 'anchor' the map during linkage map construction. Second, because they are exonic they are highly conserved across other species, making them an excellent comparative genomics resource. We will use the map to address a number of fundamental population genetic questions. We will identify the chromosomal rearrangements that occurred during avian evolution, and construct an ancestral avian karyotype. We will compare genetic recombination rates between a domesticated (chicken) and undomesticated (zebra finch) species, to test whether domestication may have caused the chicken to have a low recombination rate. We will compare recombination rates between microchromosomes and macrochromosomes, to further understand the evolutionary consequences of a functionally-important gene being located on a microchromosome. Finally we will estimate linkage disequilibrium (LD) between all pairs of markers, because an understanding of LD is central to many questions in population genetics, as well as in gene mapping.