Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/11/2013
Publication Date: 1/11/2013
Citation: Long, J.A., Blomberg, L., Groenen, M. 2013. Poultry germplasm preservation: modulating membrane lipids for successful cryopreservation of semen from valuable genetic stocks. Meeting Abstract.
Technical Abstract: 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 (120 base-pair read length; PE; 6X coverage per bird). The average individual sequence depth, based on the turkey’s genome size of 1 billion bases, was 4.3X with 12.8X coverage per line/breed. Alignment of sequencing data of 32 individual turkeys from different populations 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. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/kilobase (Kb), while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. 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 haplotypes have been selected in the modern domesticated turkey.