2013 Annual Report
1a.Objectives (from AD-416):
Specific Aim 1. Use broad species diversity to identify and select new SNPs that are uniformly distributed across the turkey genome;
Specific Aim 2. Validate and characterize SNPs in relevant commercial populations.
1b.Approach (from AD-416):
For the emerging turkey genome sequence to successfully be applied to gene discovery, there is a need to improve the process of SNP discovery and create high-density SNP genotyping assays. Advances in DNA sequencing technology have increased the capacity to the extent that the reduced representation library model is not the only approach for SNP discovery. Furthermore, aligning contigs containing putative SNPs against a reference genome sequence will enable the detection of contigs that map to a single, unique region of the genome, which increases the chance of obtaining a reliable genotype five times. We hypothesize that deep, shotgun sequencing (24-30X) of turkeys from a broad pedigree range (commercial, historical, heritage and ancestral populations) can be used to rapidly identify and characterize SNPs for creating a high-density (60K) SNP genotyping platform for use by the commercial industry and research communities. This Tools and Resources proposal represents an innovative, integrated approach to rapidly and cost effectively identify and validate SNPs and incorporates second generation sequencing technology to ensure broad genome coverage and the depth to uncover highly probable SNPs, clusters of segregating SNPs based on lines as well as SNPs lost through domestication.
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 facilitating rapid adaptation to changes in breeding programs. The goal of this project was to investigate turkey genome variation and to provide a resource for subsequent genomic work in the turkey by a wide sampling of populations for the development of a high-density single nucleotide polymorphism (SNP) chip with minimal ascertainment bias. Males from seven commercial lines, three heritage varieties and historical samples of wild turkeys from South Mexico, for a total of 11 turkey populations, were used for whole genome sequencing. After aligning against the turkey reference genome, 5.49 million SNPs were identified, which subsequently were used for the analysis of genetic diversity among the different populations. All commercial populations appear to share a common origin. The inclusion of 1 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 ancestral and derived allelic states; derived alleles arise from a random DNA mutation event to produce a new allele that is different from the "original" or ancestral allele and, with selective breeding for desired traits, have been preferentially selected in domesticated animal populations. Domesticated populations showed the derived allelic state, while the wild populations showed the ancestral allelic state within these regions. The low level of genetic variation within those six regions, as well as the distinctness of the alleles in domesticated from wild populations, indicates the selection of specific allele combinations closely linked together on the same chromosome that tend to be inherited together in domesticated populations. These data demonstrate the feasibility and potential utility of a turkey SNP chip. Both primary turkey breeders provided DNA from additional birds and lines for further sequencing and SNP validation. ARS scientists are currently constructing the DNA libraries from these additional birds.