Mapping the zebra finch genome

点击翻译按钮获取中文摘要

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.