Practical capability of a DNA pool‐based genome‐wide association study using BovineSNP50 array in a cattle population |
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| Authors: | Yoshinobu UEMOTO Nanae SASAGO Tsuyoshi ABE Hideki OKADA Hitomi MARUOKA Hiroaki NAKAJIMA Noriaki SHOJI Shin MARUYAMA Naohiko KOBAYASHI Hideyuki MANNEN Eiji KOBAYASHI |
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| Institution: | 1. National Livestock Breeding Center, Nishigo;2. G&G Science Co. Ltd, Fukushima, Fukushima;3. Yamagata Prefectural Animal Industrial Institute, Agricultural Research Center, Shinjo, Yamagata;4. Gifu Prefectural Livestock Research Institute, Takayama, Gifu;5. Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan |
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| 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. |
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| Keywords: | allele frequency BovineSNP50 DNA pooling genome‐wide association study |
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