Practical capability of a DNA pool-based genome-wide association study using BovineSNP50 array in a cattle population

Yoshinobu Uemoto, Nanae Sasago, Tsuyoshi Abe, Hideki Okada, Hitomi Maruoka, Hiroaki Nakajima, Noriaki Shoji, Shin Maruyama, Naohiko Kobayashi, Hideyuki Mannen, Eiji Kobayashi

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)

Abstract

Genome-wide association mapping for complex traits in cattle populations is a powerful, but expensive, selection tool. The DNA pooling technique can potentially reduce the cost of genome-wide association studies. However, in DNA pooling design, the additional variance generated by pooling-specific errors must be taken into account. Therefore, this study aimed to investigate factors such as: (i) the accuracy of allele frequency estimation; (ii) the magnitude of errors in pooling construction and in the array; and (iii) the effect of the number of replicate arrays on P-values estimated by a genome-wide association study. Results showed that the Illumina correction method is the most effective method to correct the allele frequency estimation; pooling errors, especially array variance, should be taken into account in DNA pooling design; and the risk of a type I error can be reduced by using at least two replicate arrays. These results indicate the practical capability and cost-effectiveness of pool-based genome-wide association studies using the BovineSNP50 array in a cattle population.

Original languageEnglish
Pages (from-to)719-726
Number of pages8
JournalAnimal Science Journal
Volume83
Issue number11
DOIs
Publication statusPublished - 2012 Nov
Externally publishedYes

Keywords

  • Allele frequency
  • BovineSNP50
  • DNA pooling
  • Genome-wide association study

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

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