Sequence-based Analysis of Selection during Domestication and Improvement of Chicken
Final Report Abstract
The research of the present project focused on genetic make-up of wild vs., domestic chicken populations and aimed to provide insights into the evolutionary forces that have shaped the genome of chicken during domestication and subsequent genetic improvement. In part 1, we used whole genome sequence data from 50 hens of commercial white and brown egg layers and compared it to the pool sequences of three broiler populations to explore evidences of differentiation, suggestive of selection during recent improvement of chicken. With the availability of more sequence data, in part 2 we conducted a systematic comparison of genomic sequence variation from multiple populations of broilers and layers, versus each other and versus Red Jungle Fowl– the progenitor of domestic chicken – to investigate major switches that took place during domestication and the later specialization of domestic chicken into egg and meat producing lines. We further scanned the genome to identify genes underwent selection. In part 3, we sougth to dissect the extent and structure of linkage disequilibriom (LD) more precisely and constructing an upgraded recombination map of chicken genome by employing resequencing data. Overall, the novelties presented in this research were sixfolds. First, we re-sequenced 125 wild and commercial birds that represents the largest data set ever used to study genetic make-up and recent evolution of domestic chicken. Second, we reported the discovery and characterization of over 20 million SNPs, 31% of which were not previously reported. Third, analysis of selection provided a comprehensive list of candidate loci underlying adaptation to the domestication and/ or production-relevant traits. Fourth, we reported a highly significant deficiency in the proportion of highly diverged amino-acid altering mutations in comparison of wild vs., commercial birds. This implies that commercial birds have undergone rigorous purifying selection that likely reflects human involvement in purging genetic variants contributing to phenotypic diversity during the establishment of commercial breeds. Fifth, on the basis of full sequencing data we demonstrated that LD in chicken decays at a much faster rate than previously thought. Sixth, we built up the recombination maps with an up to 3 folds higher resolution compared to the maps available so far. These studies overall demonstrate the value and impact of next generation sequencing data in exploring domestication and decipher human influence in shaping genome of commercial chicken.
Publications
- Parallel selection revealed by population sequencing in chicken. Genome Biol Evol. 2015
Qanbari S, Seidel M, Strom TM, Mayer KF, Preisinger R, Simianer H
(See online at https://doi.org/10.1093/gbe/evv222) - Patterns of recombination and parallel selection revealed by population sequencing in chicken. Proceedings of the 9th European Symposium on Poultry Genetics. 16.-18. June 2015, Tuusula, Finland
Qanbari S., M. Seidel, G. Mészáros, T.M. Strom, R. Preisinger and H. Simianer
- Sequence-based map reveal similar recombination rate between macro- and microchromosomoes in chicken. Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science. 31 August – 4 September 2016, Warsaw-Poland
Qanbari S., M. Seidel, G. Mészáros, T.M. Strom, R. Preisinger and H. Simianer
(See online at https://doi.org/10.3920/978-90-8686-859-9) - Massive sequencing reveals strong purifying selection in commercial chicken. Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science. 28 August – 1 September 2017, Tallinn-Estonia
Qanbari S., C.J. Rubin, S. Weigend, A. Weigend, R. Fries, R. Preisinger, H. Simianer and L. Andersson
