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Title: Whole genome snp discovery and analysis of genetic diversity in turkey (meleagris gallopavo)

Author
item ASLAM, MUHAMMAD - University Of Wageningen
item BASTIAANSEN, JOHN - University Of Wageningen
item ELFERINK, MARTIN - University Of Wageningen
item MEGENS, HENDRICK JAN - University Of Wageningen
item CROOIJMAS, RICHARD - University Of Wageningen
item Blomberg, Le Ann
item FLEISCHER, ROBERT - Smithsonian Institute
item VAN TASSELL, CURTIS - US Department Of Agriculture (USDA)
item SONSTEGARD, TAD - US Department Of Agriculture (USDA)
item SCHROEDER, STEVEN - US Department Of Agriculture (USDA)
item GROENEN, MARTIEN - University Of Wageningen
item Long, Julie

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2012
Publication Date: 8/14/2012
Citation: Aslam, M.L., Bastiaansen, J.W., Elferink, M., Megens, H., Crooijmas, R.P., Blomberg, L., Fleischer, R.C., Van Tassell, C.P., Sonstegard, T.S., Schroeder, S.G., Groenen, M.A., Long, J.A. 2012. Whole genome snp discovery and analysis of genetic diversity in turkey (meleagris gallopavo). Biomed Central (BMC) Genomics. 13:391.

Interpretive Summary: The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. The goal of this project was to investigate turkey genome variation and to provide a resource for subsequent genomic work in the turkey. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome.

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 investigate turkey genome variation and to provide a resource for subsequent genomic work in the turkey and to cover a wide sampling of population for the development of a high-density SNP chip with minimal ascertainment bias. Eleven turkey populations were available for this study. Males from seven commercial lines, three heritage varieties and 113 year-old samples of wild turkeys from South Mexico were used for whole genome sequencing. The seven commercial lines were obtained from two different primary breeding companies. The three heritage varieties were the Beltsville Small White, the Royal Palm and the Narragansett. Tissue samples representing the wild population were obtained from the Bird Collection of the Smithsonian Institution’s National Museum of Natural History, and were originally collected in 1899 from Chihuahua, Mexico. These samples represent the progenitor subspecies, the South Mexican turkey. In total 32 individuals were selected for whole genome re-sequencing. Genome wide mapping density, or read depth distribution, and the nucleotide diversity across the whole genome were assessed for each individual of the 11 turkey populations. In total, 5.49 million putative SNPs were identified compared to the reference genome, and 4.76 million SNPs were segregating in at least one population. There were 223,264 SNPs segregating in at least 9 turkey populations, and these were used to calculate Nei’s pair wise genetic distances. The genetic diversity analysis among the 11 different turkey lines showed that the heritage varieties and the commercial populations are derived from the wild South Mexican population. The presence of different alleles/haplotypes in the South Mexican population highlights that specific haplotypes have been selected in the modern domesticated turkey.