W587 Selective Sweep Analysis in Turkey Using Whole Genome Sequence Data

Date: Sunday, January 15, 2012
Time: 8:00 AM
Room: Sunset
Muhammad Luqman Aslam , Wageningen University, Animal Breeding and Genomics Centre, Wageningen, Netherlands
John Bastiaansen , Wageningen University, Animal Breeding and Genomics Centre, Wageningen, Netherlands
Martin Elferink , Wageningen University, Animal Breeding and Genomics Centre, Wageningen, Netherlands
Steven G. Schroeder , BFGL, ARS-USDA, Beltsville, MD
Richard Crooijmans , Wageningen University, Animal Breeding and Genomics Centre, Wageningen, Netherlands
Hendrik-Jan Megens , Wageningen University, Animal Breeding and Genomics Centre, Wageningen, Netherlands
Tad Sonstegard , BFGL, ARS-USDA, Beltsville, MD
Robert C. Fleischer , National Zoological Park, Smithsonian Institution, Washington, DC
LeAnn Blomberg , ABBL, ARS-USDA, Beltsville, MD
Curtis Van Tassell , BFGL, ARS-USDA, Beltsville, MD
Martien Groenen , Wageningen University, Animal Breeding and Genomics Centre, Wageningen, Netherlands
Julie Long , USDA BARC, Beltsville, MD
We sequenced the complete genome of 32 individual turkeys from 11 different populations at an average depth of 5x. The populations used included 7 commercial lines, three heritage varieties and one wild population. After aligning against the turkey reference genome and variant calling 5.49 million SNPs were identified of which 4.76 million were segregating in at least one population. Out of all the discovered SNPs, 75,254 were located in exonic regions, of which 23,795 were non-synonymous, 52,506 were synonymous, 377 were stop gain and 8 were stop loss variants. The turkey genome is much less diverse with a relatively low frequency of heterozygous SNP as compared to other livestock species like chicken and pig. The average frequency of heterozygous SNPs in the sequenced individuals was around 1 SNP every 1000 bp. All commercial populations appear to share a common origin. The inclusion of one wild turkey population allowed for the identification of the ancestral alleles for most of the SNPs. Six regions on five different turkey chromosomes (3, 4, 9, 14, and 22) showed differences between the wild and the domesticated populations with respect to the occurrence of ancestral and the derived allelic states respectively. Domesticated populations showed the derived allelic state while the wild populations showed the ancestral allelic state within these regions. The low heterozygosity as well as the presence of different alleles/haplotypes in domesticated vs. wild populations indicates selection for specific haplotypes in domesticated populations at these regions.