Abstract
In this study, we identified porcine single nucleotide polymorphisms (SNPs) by aligning eight sequences generated with two approaches: amplification of 665 intronic regions using one sample from each of eight breeds, including three East Asian pigs, and amplification of 289 3′-UTR regions using two samples from each of four major commercial breeds. The 1,760 and 599 SNPs were validated using two 384-sample DNA panels by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The phylogenetic tree and Structure analyses classified the pigs into two large clusters: Euro-American and East Asian populations. The membership proportions, however, differed between inferred clusters for K = 2 generated by the two approaches. With intronic SNPs, Euro-American breeds constituted about 100% of the Euro-American cluster, but with 3′-UTR SNPs, about 17% of the East Asian cluster comprised five Euro-American breeds. The differences in the SNP discovery panels may affect population structure found in study panels of large samples.
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Acknowledgments
The authors are greatly indebted to Ikuyo Nakamori (STAFF Institute) for her technical assistance. The authors are also grateful to Taro Obata (STAFF Institute) for administration of the project. This study was supported by the Ministry of Agriculture, Fisheries and Forestry of Japan (Grant number II-304), the Japan Racing Association, and the Livestock Promotion Foundation.
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Matsumoto, T., Okumura, N., Uenishi, H. et al. Porcine Single Nucleotide Polymorphism (SNP) Development and Population Structure of Pigs Assessed by Validated SNPs. Biochem Genet 50, 428–439 (2012). https://doi.org/10.1007/s10528-011-9486-9
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DOI: https://doi.org/10.1007/s10528-011-9486-9