Source: UTAH STATE UNIVERSITY submitted to
THE ADDITION OF 60,000 SNPS TO THE OVINE GENOME MAP
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
NRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0217048
Grant No.
2009-35205-05272
Project No.
UTA00155
Proposal No.
2008-03923
Multistate No.
(N/A)
Program Code
43.0
Project Start Date
Feb 15, 2009
Project End Date
Feb 14, 2013
Grant Year
2009
Project Director
Cockett, N. E.
Recipient Organization
UTAH STATE UNIVERSITY
(N/A)
LOGAN,UT 84322
Performing Department
Animal Dairy & Veterinary Sciences
Non Technical Summary
The International Sheep Genomics Consortium (ISGC), which includes active participation of scientists from Australia, Canada, France, New Zealand, the UK and the USA, has collectively developed and distributed resources that advance research in sheep genomics. Most recently, funding from Australia's International Sciences Linkage Program, New Zealand's Ovita, and the UK's Genesis Faraday has generated at least 9.7 Gbp of genome sequence from six sheep of diverse types and another 3 Gbp from a pool of 60 sheep samples. These sequence data are being used to design an Illumnia iSelect Infinium II BeadChip containing 60,000 (60K) ovine SNPs. In this project, the newly developed 60K SNP array will be used to generate a high-density SNP map for sheep. Samples from the International Mapping Flock and the USU radiation hybrid panel will be analyzed with the chip, thereby integrating existing ovine linkage, radiation hybrid and physical maps, as well as available genome sequence, into a whole genome assembly for sheep. The resulting high resolution map will be anchored to the genomes of other species, including humans, mice and cattle. Data will also be generated on genome-wide linkage disequilibrium in Rambouillets, Suffolks and Gulf Coast Natives, which represent U.S. wool, meat and parasite resistant breeds, respectively. Genetic "selection sweeps" associated with traits of economically importance in sheep will be investigated, and the genotypes will be included in the international ovine HapMap project.
Animal Health Component
100%
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3043610108050%
3043610104050%
Knowledge Area
304 - Animal Genome;

Subject Of Investigation
3610 - Sheep, live animal;

Field Of Science
1080 - Genetics; 1040 - Molecular biology;
Goals / Objectives
The first objective of the project is to develop an integrated ovine genome map using data generated with the ovine 60K SNP array. Samples from the USUo5000RH panel and the IMF pedigree will be assayed with the ovine Illumina iSelect Infinium BeadChip. Data will be analyzed and incorporated into the existing RH and linkage maps, respectively. Aligning SNP content across several genome elements, including ovine sequence traces, will allow the development of a comprehensive, high-resolution whole genome assembly connected to genomes of other mammalian species. The second objective of the project is to determine genome-wide LD for US Rambouillet, Suffolk and Gulf Coast Native breeds using the ovine 60K SNP array. These three breeds represent populations selected for wool and maternal traits (Rambouillet), growth and muscling (Suffolk), and resistance to intestinal parasites (Gulf Coast Native). This collection of animal germplasm offers the opportunity to analyze SNP data for signatures of selection and to identify regions of the genome likely to harbor functional mutations. In addition, the pattern and extent of linkage disequilibrium will be assessed to draw conclusions about population history and genetic diversity, and to aid in whole genome association studies directed towards the identification of genes and genetic regions that impact phenotypic performance in sheep.
Project Methods
Under the first objective, samples from the USUo5000 RH panel will be typed on the ovine 60K Illumina iSelect Infinium BeadChip. Data from the SNP chip will be combined into the existing RH maps using the RH_TSP_map_3.0 software package. Two-point RH linkage groups will be constructed with a LOD threshold of 6.0. New markers will also be assigned to the existing linkage map using genotypes from the IMF pedigree. Chromosomal linkage groups will be generated using MultiMap. For best-position maps, additional markers will be placed in the most likely positions on the basis of likelihood data generated by MultiMap. The predicted order of the SNPs will be interpolated into the consolidated sheep genome assembly now referred to as the virtual sheep genome. Under the second objective, genome-wide LD will be determined for Rambouillet, Suffolk, and Gulf Coast Native breeds using samples collected across the US. Each breed will be represented by a minimum of 18 unrelated families that include a grand-sire, sire, and three or more half-sib offspring, and an additional 60 unrelated animals, for a minimum of 150 animals/breed. The samples will be collected from US producers and researchers who have previously provided samples for the first generation ovine HapMap project. Families will be "industry relevant" but unrelated so as to capture as many unique chromosomes as possible within each breed. High-quality DNA will be extracted from each animal using standard procedures and quantified. Small numbers of other species including Ovis dalli and Ovis canadensis will also be genotyped so as to infer the ancestral SNP allele. Based on the pedigrees and the genomic locations of the SNPs as determined above, a set of haplotypes for each chromosome will be predicted based on the most likely phase configuration (oGmx). Linkage disequilibrium will be estimated using the metric r2 for both syntenic and non-syntenic marker pairs. Values of r2 will be determined independently for the maternally and paternally inherited haplotypes. Loci which have undergone strong, recent selection will be identified by calculation of the extended haplotype homozygosity (EHH) statistic. This relies on the prediction that a favourable allele which has increased in frequency very quickly will be accompanied by an unusually long haplotype with low diversity (i.e. regions containing selective sweeps). Haplotypes generated on the US Rambouillet, Suffolk, and Gulf Coast Native samples will be incorporated into the ongoing ovine HapMap project (http://www.sheephapmap.org/).

Progress 02/15/09 to 02/14/13

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? The Illumina Ovine SNP50 BeadChip is commercially available for purchase. In addition, genetic testing laboratories offer genotyping of sheep samples with the BeadChip if the researcher does not have the expertise or equipment necessary for running the BeadChip. Information about the SNP array has been disseminated through a list-serve maintained by the International Sheep Genomics Consortium (ISGC), which includes investigators from across the world who are engaged in research on livestock genomics. In addition, updates on the chip, as well as presentations on results using the chip, have been made primarily at the annual Plant and Animal Genome (PAG) meeting and the bi-annual meetings of the International Society of Animal Genetics (ISAG). A refereed journal article describing the construction of the SNP BeadChip and its application to the ovine HapMap project was published in 2012. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The availability of a high density SNP array for the sheep, referred to as the Illumina Ovine SNP50 BeadChip, has been a significant milestone for researchers investigating the sheep genome. This SNP array, funded in part by a USDA/AFRI Tools and Resources grant and developed by the International Sheep Genomics Consortium, was first released in January, 2009 followed by a second release in September, 2011. Researchers can now obtain genotypes for over 50,000 SNPs for hundreds of animals in a single analysis. The identification of SNPs on the BeadChip was done through a large, international sequencing effort. The first source of sequence data (9.7 Gbp) used for SNP mining was generated from six sheep (Romney, Texel, Merino, Dorset, Rambouillet and Suffolk) while the second source of sequence data (3 Gbp) was generated from a pool of DNA comprised of 60 genetically divergent animals. All sequences were compared to identify single nucleotide differences (i.e. SNPs) that differed in at least 5% of the sequenced animals. This approach assured that the SNPs were actual genetic differences rather than sequencing anomalies. To date, at least 40,000 sheep have been genotyped with the SNP50 chip and analyses of the genotypes are ongoing in a myriad of research projects. For example, SNP genotypes of 2,810 sheep from 74 breeds have been combined with genotype data from seven species of wild sheep and nine outgroup species such as bighorn sheep and Mouflons as part of the world-wide ovine HapMap project. Results from the HapMap analysis indicate that domestic breeds diverged from their wild ancestors about 11,000 years ago and modern breeds started to differentiate around 200 years ago. Analysis of the SNP50 data also indicated that American breeds are most closely related to Europe and Middle East breeds than to Asian or African breeds. The SNP50 BeadChip was also typed across the USU and INRA ovine radiation hybrid panels and the International Mapping Flock (IMF) and the resulting RH and linkage maps were then used to refine the ovine whole genome reference sequence. Other populations of sheep across the world are being genotyped with the SNP chip and published results from these studies are now appearing in the literature, with more than 30 publications to date. The impact of this genomic resource, funded in part by USDA/AFRI, is truly astounding.

Publications


    Progress 02/15/12 to 02/14/13

    Outputs
    Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? The Illumina Ovine SNP50 BeadChip is commercially available for purchase. In addition, genetic testing laboratories offer genotyping of sheep samples with the BeadChip if the researcher does not have the expertise or equipment necessary for running the BeadChip. Information about the SNP array has been disseminated through a list-serve maintained by the International Sheep Genomics Consortium (ISGC), which includes investigators from across the world who are engaged in research on livestock genomics. In addition, updates on the chip, as well as presentations on results using the chip, have been made primarily at the annual Plant and Animal Genome (PAG) meeting and the bi-annual meetings of the International Society of Animal Genetics (ISAG). A refereed journal article describing the construction of the SNP BeadChip and its application to the ovine HapMap project was published in 2012. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

    Impacts
    What was accomplished under these goals? The availability of a high density SNP array for the sheep, referred to as the Illumina Ovine SNP50 BeadChip, has been a significant milestone for researchers investigating the sheep genome. This SNP array, funded in part by a USDA/AFRI Tools and Resources grant and developed by the International Sheep Genomics Consortium, was first released in January, 2009 followed by a second release in September, 2011. Researchers can now obtain genotypes for over 50,000 SNPs for hundreds of animals in a single analysis. The identification of SNPs on the BeadChip was done through a large, international sequencing effort. The first source of sequence data (9.7 Gbp) used for SNP mining was generated from six sheep (Romney, Texel, Merino, Dorset, Rambouillet and Suffolk) while the second source of sequence data (3 Gbp) was generated from a pool of DNA comprised of 60 genetically divergent animals. All sequences were compared to identify single nucleotide differences (i.e. SNPs) that differed in at least 5% of the sequenced animals. This approach assured that the SNPs were actual genetic differences rather than sequencing anomalies. To date, at least 40,000 sheep have been genotyped with the SNP50 chip and analyses of the genotypes are ongoing in a myriad of research projects. For example, SNP genotypes of 2,810 sheep from 74 breeds have been combined with genotype data from seven species of wild sheep and nine outgroup species such as bighorn sheep and Mouflons as part of the world-wide ovine HapMap project. Results from the HapMap analysis indicate that domestic breeds diverged from their wild ancestors about 11,000 years ago and modern breeds started to differentiate around 200 years ago. Analysis of the SNP50 data also indicated that American breeds are most closely related to Europe and Middle East breeds than to Asian or African breeds. The SNP50 BeadChip was also typed across the USU and INRA ovine radiation hybrid panels and the International Mapping Flock (IMF) and the resulting RH and linkage maps were then used to refine the ovine whole genome reference sequence. Other populations of sheep across the world are being genotyped with the SNP chip and published results from these studies are now appearing in the literature, with more than 30 publications to date. The impact of this genomic resource, funded in part by USDA/AFRI, is truly astounding.

    Publications


      Progress 02/15/11 to 02/14/12

      Outputs
      OUTPUTS: In order to search for genetic signatures of selection, the International Sheep Genomics Consortium (ISGC) assembled and genotyped over 3400 sheep from 74 diverse breeds using the SNP50 BeadChip. Initial testing of the SNP50 BeadChip revealed 91% of 59454 loci formatted for analysis displayed assay signal following genotyping. Of these, a further 5207 were removed using a series of quality control filters. Allele frequency data from the remaining 49034 loci was used to search for signatures of selection using multiple methods. PARTICIPANTS: CSIRO Livestock Industries, Louisianna State University, The International Sheep Genomics Consortium TARGET AUDIENCES: Researchers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

      Impacts
      Clear signals, in the form of outlier SNP, were detected surrounding both the Myostatin and Horns (Ho) locus. Further, breeds were partitioned to capture extremes for a variety of traits including highly complex examples such as parasite resistance.

      Publications

      • No publications reported this period


      Progress 02/15/10 to 02/14/11

      Outputs
      OUTPUTS: A high-density ovine SNP array was released in January, 2009, as the Illumina Ovine SNP50 BeadChip. Samples from the USUo5000RH radiation hybrid panel and the International Mapping Flock (IMF) pedigree have been assayed with the ovine BeadChip. Data have been analyzed and incorporated into the existing RH and linkage maps, respectively, as well as the ovine whole genome assembly. The BeadChip was also genotyped across 3064 sheep from 64 breeds and strains, seven species of wild sheep and nine outgroup species, as part of the ovine HapMap project. The data were used to estimate the pattern and extent of linkage disequilibrium, origins of domestication, and genetic diversity. Aligning SNP content across several genome elements, including the ovine reference genome sequence, has led to the development of a comprehensive, high-resolution whole genome assembly connected to genomes of other mammalian species. This assembly will be used by researchers who are interested in identifying genetic regions controlling economically and/or biologically important traits in sheep. PARTICIPANTS: Utah State University (USA), CSIRO Livestock Industries (Australia), AgResearch (New Zealand), University of Melbourne (Australia), University of Sydney (Australia), University of New England (Australia), The Roslin Institute (UK), and Baylor College of Medicine-Human Genome Sequencing Center (USA). TARGET AUDIENCES: Researchers, sheep producers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

      Impacts
      Aligning SNP content across several genome elements, including the ovine reference genome sequence, has led to the development of a comprehensive, high-resolution whole genome assembly connected to genomes of other mammalian species. This assembly will be used by researchers who are interested in identifying genetic regions controlling economically and/or biologically important traits in sheep.

      Publications

      • No publications reported this period


      Progress 02/15/09 to 02/14/10

      Outputs
      OUTPUTS: The construction of a high-density ovine SNP array containing 50,000 informative SNPs is now completed. The array has been released to the public in January, 2009, as the Illumina Ovine SNP50 BeadChip (http://www.illumina.com/pages.ilmnID=319). SNPs for the chip were mined from 260,000 high-confidence SNPs identified from two sources of sequence data. The first source was generated using funding from the International Science Linkage Program (Australia) and Ovita (New Zealand). Genomic DNA from six sheep (Romney, Texel, Merino, Dorset, Rambouillet and Suffolk) was whole-genome shotgun sequenced to 0.5X coverage each (3X coverage total) using the Roche 454 FLX system at Baylor College of Medicine-Human Genome Sequence Center (BCM-HGSC, Texas USA) and the University of Otago (New Zealand). A total of 9.7 Gbp of sequence was generated. High quality SNPs were identified using AgResearch software that included read-specific animal sequence information. The second source of sequence data used for SNP mining was generated on a Solexa Genome Analyzer at Illumina (http://www.illumina.com/) using a reduced representation approach (Van Tassell et al. 2008). Approximately 3 Gbp of sequence was derived from a pool of DNA comprised of 60 genetically divergent animals. PARTICIPANTS: Utah State University (USA), Louisiana State University (USA), CSIRO Livestock Industries (Australia), AgResearch (New Zealand), University of Melbourne (Australia), University of Sydney (Australia), University of New England (Australia), The Roslin Institute (UK), and Baylor College of Medicine-Human Genome Sequencing Center (USA). TARGET AUDIENCES: Researchers, sheep producers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

      Impacts
      The availability of a high-density ovine SNP array will accelerate searches for genetic regions and genes influencing phenotypes in sheep. The SNP array will also serve as a genomic resource for researchers using sheep as a biomedical research model.

      Publications

      • No publications reported this period