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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

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Published on: May 6, 2010

High-resolution haplotype block structure in the cattle genome.

Rafael Villa-Angulo1, Lakshmi K Matukumalli, Clare A Gill

  • 1Department of Bioinformatics and Computational Biology, George Mason University, VA, USA. rvillaan@gmu.edu

BMC Genetics
|April 28, 2009
PubMed
Summary

Cattle and humans share similar linkage disequilibrium (LD) and haplotype block structures. Unexpected similarities between dairy and beef breeds were found, suggesting a need for ~30,000 SNPs for a complete cattle genome LD map.

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Published on: December 10, 2012

Area of Science:

  • Genomics
  • Population Genetics
  • Animal Breeding

Background:

  • The Bovine HapMap Consortium generated SNP assay panels for 501 animals across 19 breeds.
  • Focused on 101 high-density regions to analyze linkage disequilibrium (LD) and haplotype block structure.

Purpose of the Study:

  • To conduct the first high-resolution analysis of haplotype block structure in worldwide cattle.
  • To compare cattle and human genetic structures.
  • To investigate genetic similarities between different cattle breeds.

Main Methods:

  • Genotyping of ~30,000 single nucleotide polymorphisms (SNPs) in targeted high-density regions.
  • Analysis of linkage disequilibrium (LD) and haplotype block structure.
  • Estimation of effective population sizes over the last 10,000 generations.
  • Clustering techniques to group breeds based on genetic structure.

Main Results:

  • High similarity in LD and haplotype block structure (1-100 kb scale) between cattle and humans.
  • Regions of high LD extended up to ~100 kb, with average haplotype block size of 10.3 kb.
  • Unexpected genetic similarities found between some beef and dairy breeds, rendering them non-differentiable.
  • Effective population size estimations align with cattle domestication and recent bottlenecks.
  • Clustering revealed distinct breed groupings based on genetic similarities.

Conclusions:

  • Cattle and humans exhibit significant similarities in LD and haplotype block structure.
  • Dairy and beef breeds show indistinguishable haplotype block structures.
  • Approximately 30,000 uniformly distributed SNPs are needed for a complete Bos taurus genome LD map.
  • Characterizing the complete cattle genome's haplotype block structure requires ~580,000 SNPs.