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.
journal_name
Biochem Genetjournal_title
Biochemical geneticsauthors
Matsumoto T,Okumura N,Uenishi H,Hayashi T,Hamasima N,Awata Tdoi
10.1007/s10528-011-9486-9subject
Has Abstractpub_date
2012-06-01 00:00:00pages
428-39issue
5-6eissn
0006-2928issn
1573-4927journal_volume
50pub_type
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