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Title: Genome-wide signatures of selection revealed through massive parallel sequencing of DNA across ten turkey populations

Author
item Aslam, Muhammad
item Bastiaansen, John
item Elferink, Martin
item Megens, Hendrik-jan
item Crooijmans, Richard Pma
item Blomberg, Le Ann
item Van Tassell, Curtis - Curt
item Sonstegard, Tad
item Schroeder, Steven - Steve
item Groenen, Martien Am
item Long, Julie

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/22/2014
Publication Date: 11/25/2014
Citation: Aslam, M.L., Bastiaansen, J.W., Elferink, M., Megens, H., Crooijmans, R., Blomberg, L., Van Tassell, C.P., Sonstegard, T.S., Schroeder, S.G., Groenen, M., Long, J.A. 2014. Genome-wide signatures of selection revealed through massive parallel sequencing of DNA across ten turkey populations. Biomed Central (BMC) Genomics. 15:117.

Interpretive Summary: The domestic turkey (Meleagris gallopavo) is an important agricultural species that is largely used as a meat-type bird. All domesticated turkeys descend from wild turkeys indigenous to North and South America. Intense selective breeding and population bottlenecks are expected to leave signatures in the genome of domesticated species, such as unusually similar regions of DNA sequence. These patterns of variation in selected populations are highly useful to not only understand the consequences of selective breeding and population dynamics, but also to provide insights into biological mechanisms affected by these physiological processes important to production.

Technical Abstract: The presence of genetic diversity in domestic livestock species is of great importance for sustained genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. The goal of this project was to find genomic regions where selection or domestication has changed the frequency of haplotypes or alleles for production towards fixation. The genomes of male turkeys from seven commercial lines and three heritage varieties were evaluated to discover signatures of selection. A total of 54 genomic regions on 14 different chromosomes showed significant (P < 0.05) signatures of selection in the heritage and commercial turkey populations. Areas with evidence of selective sweeps varied from 1.5 Mb to 13.8 Mb in length. Out of these 54 selective sweep regions, 23 were observed as overlapping regions in multiple populations, and these regions were distributed over 13 different chromosomes. Of the remaining 31 unique signatures, 26 were present in commercial populations. The commercial populations (L1-L7) averaged nearly four selective sweeps per population; whereas only 1.6 population-specific selection sweeps were observed per heritage population. Differences between commercial populations were considerable, with as many as eight sweep regions observed in population L3 and only one population-specific selective sweep region observed in population L6. The high number of sweep regions in commercial turkey populations compared to heritage varieties provides strong evidence of intense selection in these commercial lines.