2012 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 goal of this project is to provide the content for development of a single nucleotide polymorphism (SNP) chip for use by the commercial turkey industry to interrogate genetic differences (single nucleotide variations in the genome’s DNA) and potentially enable the selection for preferred traits or genetic merit in turkey, particularly reproductive traits with low heritibility. Blood or tissue samples were obtained from male turkeys representing 11 relevant lines (n=3 males/line) for DNA extraction and cDNA library construction. Seven of the lines were elite pedigree lines provided by two turkey primary breeder companies. Two heritage breeds were sampled, the Narragansett and Royal Palm, as well as the Beltsville Small White, a specialty breed. Historic tissue samples (circa 1899) were obtained from the South Mexican turkey, believed to be the wild ancestral species of the modern commercial bird. The genomic DNA of all birds was sequenced individually using the Illumina Genome Analyzer II and, based on the turkey’s genome size of 1 billion bases, the average DNA sequence coverage per turkey line or breed was 12.8X. Alignment of sequencing data of the 32 individual turkeys (representing 11 populations) to the reference turkey genome was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/kilobase. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that were different than the wild turkeys. The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the South Mexican population highlights that specific traits have been selectively increased in the modern domesticated turkey.