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Genome-Wide Association Studies Using Haplotypes and Individual SNPs in Simmental Cattle

Author

Listed:
  • Yang Wu
  • Huizhong Fan
  • Yanhui Wang
  • Lupei Zhang
  • Xue Gao
  • Yan Chen
  • Junya Li
  • HongYan Ren
  • Huijiang Gao

Abstract

Recent advances in high-throughput genotyping technologies have provided the opportunity to map genes using associations between complex traits and markers. Genome-wide association studies (GWAS) based on either a single marker or haplotype have identified genetic variants and underlying genetic mechanisms of quantitative traits. Prompted by the achievements of studies examining economic traits in cattle and to verify the consistency of these two methods using real data, the current study was conducted to construct the haplotype structure in the bovine genome and to detect relevant genes genuinely affecting a carcass trait and a meat quality trait. Using the Illumina BovineHD BeadChip, 942 young bulls with genotyping data were introduced as a reference population to identify the genes in the beef cattle genome significantly associated with foreshank weight and triglyceride levels. In total, 92,553 haplotype blocks were detected in the genome. The regions of high linkage disequilibrium extended up to approximately 200 kb, and the size of haplotype blocks ranged from 22 bp to 199,266 bp. Additionally, the individual SNP analysis and the haplotype-based analysis detected similar regions and common SNPs for these two representative traits. A total of 12 and 7 SNPs in the bovine genome were significantly associated with foreshank weight and triglyceride levels, respectively. By comparison, 4 and 5 haplotype blocks containing the majority of significant SNPs were strongly associated with foreshank weight and triglyceride levels, respectively. In addition, 36 SNPs with high linkage disequilibrium were detected in the GNAQ gene, a potential hotspot that may play a crucial role for regulating carcass trait components.

Suggested Citation

  • Yang Wu & Huizhong Fan & Yanhui Wang & Lupei Zhang & Xue Gao & Yan Chen & Junya Li & HongYan Ren & Huijiang Gao, 2014. "Genome-Wide Association Studies Using Haplotypes and Individual SNPs in Simmental Cattle," PLOS ONE, Public Library of Science, vol. 9(10), pages 1-11, October.
    • Handle: RePEc:plo:pone00:0109330
    DOI: 10.1371/journal.pone.0109330
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    References listed on IDEAS

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    1. Haiyan Jiang & Andrew Orr & Duane L Guernsey & Johane Robitaille & Géraldine Asselin & Mark E Samuels & Marie-Pierre Dubé, 2009. "Application of Homozygosity Haplotype Analysis to Genetic Mapping with High-Density SNP Genotype Data," PLOS ONE, Public Library of Science, vol. 4(4), pages 1-13, April.
    2. Gregory S Barsh & Gregory P Copenhaver & Greg Gibson & Scott M Williams, 2012. "Guidelines for Genome-Wide Association Studies," PLOS Genetics, Public Library of Science, vol. 8(7), pages 1-2, July.
    3. Peter Donnelly, 2008. "Progress and challenges in genome-wide association studies in humans," Nature, Nature, vol. 456(7223), pages 728-731, December.
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