Progress 10/01/12 to 09/30/13
Outputs
Progress Report 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. 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.
Impacts
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Publications
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report 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. 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.
Impacts
(N/A)
Publications
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Progress 10/01/10 to 09/30/11
Outputs
Progress Report 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. 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. We expect to generate a minimum of 500,000 SNPs that are uniformly distributed across the turkey genome, using the recently sequenced turkey genome (version 2.01) as the reference genome. 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 2 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 bp 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. To date, 4 million SNPs have been discovered from 3 elite commercial, 1 heritage and the Beltville Small White lines. The total number of SNPs and number of segregated SNPs for each of the 5 lines was similar (1,751,036 SNP and 1,012,966, respectively); however, the Beltsville Small White had a higher number of fixed SNP (1,049,800) than the other 4 lines (mean SNP = 660,135). Individual male Beltsville Small White had higher numbers of homozygous SNP (1,053,216) than males from the other 4 lines (range, 583,191-795,330). The number of heterozygous SNP of individual males from all lines ranged from 206,285 to 579,232.
Impacts
(N/A)
Publications
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report 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. 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 SNP chip for use by the commercial turkey industry similar to the highly successful Illumina BovineSNP50 SNP chip. We expect to generate a minimum of 500,000 SNPs that are uniformly distributed across the turkey genome. Progress to date includes obtaining representative blood samples from the eight relevant populations (four commercial pure lines, Beltsville Small White, two Heritage breeds, wild turkey) for DNA extraction and cDNA library construction. The ADODR has organized four conference calls with collaborating partners to facilitate sample transfer to BARC. Additionally, email communication with Co- Investigators at Wageningen University has been used to develop and modify timelines for project goals. Finally, in-house meetings with ARS Co-Investigators have been held to develop timelines for library construction and sequencing.
Impacts
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