Final Report Summary - AVIANEGG (Evolutionary genetics in a ‘classical’ avian study system by high throughput transcriptome sequencing and SNP genotyping)
Long-term studies of free-living vertebrate populations have proved a rich resource for understanding evolutionary and ecological processes, because individuals’ life histories can be measured by tracking them from birth/hatching through to death. In recent years analytical approaches from quantitative genetics have been employed with some success in such populations, leading to important advances in our understanding of the evolutionary dynamics of quantitative traits in variable environments. Unfortunately, these approaches have one major drawback – they cannot identify the actual genes responsible for genetic variation. Therefore, it is impossible to link these evolutionary studies to molecular genetic variation, which greatly restricts our understanding of the processes involved, and limits our ability to develop this understanding in the genomics era.
Many of the best long-term studies have been conducted in passerine birds, because they are easy to mark, have short generation times, and are sensitive to environmental change. Unfortunately, when the project began, genomics resources were lacking for wild bird species, being only available for two laboratory model species. In this project we filled this gap by exploiting recent advances in genomics technology to sequence the transcriptome (the part of the genome that encodes proteins) in individuals from one of the longest running studies of wild birds – the great tit population in Wytham Woods, Oxford. Having identified most of the sequence variation in the great tit transcriptome, we then, in collaboration with a group in the Netherlands, created a high density chip for genotyping great tits at 10,000 single nucleotide polymorphism (SNP) genetic markers. Almost 3000 birds for whom phenotype records and life history records were available were typed with this chip, resulting in one of the largest phenotype-genotype datasets of any free-living vertebrate population. By following the inheritance patterns of the SNP markers through the family tree or ‘pedigree’ of the study population we then constructed a genetic linkage map of the great tit genome. This map was used to provide insight into the evolution of bird karyotypes. We showed that bird genomes are highly conserved, that recombination is distributed non-randomly across the genome, and that subtle sex-differences in recombination are conserved across different populations (and are therefore real characteristics rather than ‘noise’).
Armed with the map, we were ready to proceed to the next phase of the program. We demonstrated that the genetic architecture of quantitative traits in our population was made up of many (undetectable) genes of small effect, rather than a handful of (detectable) genes of large effect. We also showed that previous studies claiming major genes in natural populations were likely to be biased and to have overstated the evidence for major genes. We developed a framework which combined linkage mapping, genomewide association studies and a new approach called ‘chromosome partitioning’, for exploring the genetic basis of continuous traits. We also showed how the amount of linkage disequilibrium (a statistical association) between linked genes was lower in great tits than in captive birds or in other intensively studied wild vertebrates. Therefore, genomewide association studies are likely to require many more markers. With this in mind we created a new SNP chip with 500,000 segregating SNP markers, and typed birds from the study population and across the species range. This dataset will underpin future research into this emerging ecological genomics model organism. Finally, we participated in a great tit genome project with our Netherlands collaborators to develop, assemble and annotate a high quality genome sequence with 100x coverage.
Many of the best long-term studies have been conducted in passerine birds, because they are easy to mark, have short generation times, and are sensitive to environmental change. Unfortunately, when the project began, genomics resources were lacking for wild bird species, being only available for two laboratory model species. In this project we filled this gap by exploiting recent advances in genomics technology to sequence the transcriptome (the part of the genome that encodes proteins) in individuals from one of the longest running studies of wild birds – the great tit population in Wytham Woods, Oxford. Having identified most of the sequence variation in the great tit transcriptome, we then, in collaboration with a group in the Netherlands, created a high density chip for genotyping great tits at 10,000 single nucleotide polymorphism (SNP) genetic markers. Almost 3000 birds for whom phenotype records and life history records were available were typed with this chip, resulting in one of the largest phenotype-genotype datasets of any free-living vertebrate population. By following the inheritance patterns of the SNP markers through the family tree or ‘pedigree’ of the study population we then constructed a genetic linkage map of the great tit genome. This map was used to provide insight into the evolution of bird karyotypes. We showed that bird genomes are highly conserved, that recombination is distributed non-randomly across the genome, and that subtle sex-differences in recombination are conserved across different populations (and are therefore real characteristics rather than ‘noise’).
Armed with the map, we were ready to proceed to the next phase of the program. We demonstrated that the genetic architecture of quantitative traits in our population was made up of many (undetectable) genes of small effect, rather than a handful of (detectable) genes of large effect. We also showed that previous studies claiming major genes in natural populations were likely to be biased and to have overstated the evidence for major genes. We developed a framework which combined linkage mapping, genomewide association studies and a new approach called ‘chromosome partitioning’, for exploring the genetic basis of continuous traits. We also showed how the amount of linkage disequilibrium (a statistical association) between linked genes was lower in great tits than in captive birds or in other intensively studied wild vertebrates. Therefore, genomewide association studies are likely to require many more markers. With this in mind we created a new SNP chip with 500,000 segregating SNP markers, and typed birds from the study population and across the species range. This dataset will underpin future research into this emerging ecological genomics model organism. Finally, we participated in a great tit genome project with our Netherlands collaborators to develop, assemble and annotate a high quality genome sequence with 100x coverage.