Genome-wide candidate regions for selective sweeps revealed through massive parallel sequencing of DNA across ten turkey populations

Abstract

Background: The domestic turkey (Meleagris gallopavo) is an important agricultural species that is largely used as ameat-type bird. Characterizing genetic variation in populations of domesticated species and associating thesevariation patterns with the evolution, domestication, and selective breeding is critical for understanding the dynamics ofgenomic change in these species. Intense selective breeding and population bottlenecks are expected to leave signaturesin the genome of domesticated species, such as unusually low nucleotide diversity or the presence of exceptionallyextended haplotype homozygosity. These patterns of variation in selected populations are highly useful to not onlyunderstand the consequences of selective breeding and population dynamics, but also to provide insights into biologicalmechanisms that may affect physiological processes important to bring changes in phenotype of interest.Results: We observed 54 genomic regions in heritage and commercial turkey populations on 14 different chromosomesthat showed statistically significant (P<0.05) reduction in genomic variation indicating candidate selective sweeps. Areaswith evidence of selective sweeps varied from 1.5 Mb to 13.8 Mb in length. Out of these 54 sweeps, 23 overlapped atleast partially between two or more populations. Overlapping sweeps were found on 13 different chromosomes. Theremaining 31 sweeps were population-specific and were observed on 12 different chromosomes, with 26 of these regionspresent only in commercial populations. Genes that are known to affect growth were enriched in the sweep regions.Conclusion: The turkey genome showed large sweep regions. The relatively high number of sweep regions incommercial turkey populations compared to heritage varieties and the enrichment of genes important to growth inthese regions, suggest that these sweeps are the result of intense selection in these commercial lines, moving specifichaplotypes towards fixation.