Porcine single nucleotide polymorphism (SNP) development and population structure of pigs assessed by validated SNPs.

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 Genet

journal_title

Biochemical genetics

authors

Matsumoto T,Okumura N,Uenishi H,Hayashi T,Hamasima N,Awata T

doi

10.1007/s10528-011-9486-9

subject

Has Abstract

pub_date

2012-06-01 00:00:00

pages

428-39

issue

5-6

eissn

0006-2928

issn

1573-4927

journal_volume

50

pub_type

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