4.7 Article

Developing a 670k genotyping array to tag ∼2M SNPs across 24 horse breeds

期刊

BMC GENOMICS
卷 18, 期 -, 页码 -

出版社

BMC
DOI: 10.1186/s12864-017-3943-8

关键词

Equine genomics; Whole genome sequence; SNP-tagging; SNP chip; Variant recalibration; SNP discovery; SNP informativeness; SNP validation; Linkage disequilibrium

资金

  1. USDA NIFA project [2012-67,015-19,432]
  2. Minnesota Agricultural Experiment Station Multistate project [MIN-62-090]
  3. National Animal Genome Project (NRSP8)
  4. Danish Council for Independent Research, Natural Sciences [4002-00152B]
  5. Danish National Research Foundation [DNRF94]
  6. Initiative d'Excellence Chaires d'attractivite, Universite de Toulouse (OURASI)
  7. European Research Council [ERC-CoG-2015-681,605]
  8. Bavarian Ministry State Ministry for Food and Agriculture, and Forestry [A/13/39]
  9. Israel Science Foundation (ISF) [1365/10]
  10. Swedish Research Council Formas [221-2013-1661]
  11. Swedish Research Council VR [621-2012-4666]

向作者/读者索取更多资源

Background: To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array. Results: Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of similar to 5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of similar to 2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of similar to 670 thousand SNPs (MNEc670k), was designed for genotype imputation. Conclusions: Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

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