Novel coding genetic variants of the GBP1 gene in wild and domestic pigs (Sus scrofa)

Shanyuan Chen, Rui Gomes, Vânia Costa, Isabel Rocha, A. Zsolnai, István Anton, Rui Charneca, Pedro Santos, José Luis Nunes, József Buzgó, Gyula Varga, Ya ping Zhang, Albano Beja-Pereira

Research output: Contribution to journalArticle

Abstract

The interferon-induced guanylate-binding protein 1 gene (GBP1) plays an important role in host defense against viral, bacterial and protozoan infections. To explore novel genetic variants in this gene, we re-sequenced a 587-bp fragment spanning the exon 2 of the GBP1 gene in a sample panel consisting of 34 wild boars and 59 local domestic pigs from three geographic regions (China, Iberian Peninsula, and Central Europe) and 12 individuals of three commercial breeds (Pietrain, Landrace, and Large White). In a final 543-bp sequence fragment, there were 14 single nucleotide polymorphisms (SNPs), of which five were coding (three novel mutations). A total of 19 haplotypes were reconstructed and most haplotypes were shared by two or more sample groups. Those shared haplotypes revealed a clear signature of genetic introgression from Chinese domestic pigs into European domestic pigs. In addition, there were six haplotypes with frequencies below 1%, but none of them were present in the three commercial breeds (Pietrain, Landrace, and Large White). Although a limited number of individuals and breeds were analyzed, the absence of rare alleles (or haplotypes) in the commercial breeds is an indication that a significant proportion of genetic diversity in domestic species is not present in commercial breeds. This study demonstrated the potential to find sufficient genetic variation for population genetic analyses of demography versus selection, in functional candidate genes of domestic pigs and wild boars worldwide.

Original languageEnglish
Pages (from-to)1-4
Number of pages4
JournalLivestock Science
Volume146
Issue number1
DOIs
Publication statusPublished - Jun 2012

Fingerprint

Sus scrofa
binding proteins
haplotypes
Carrier Proteins
Haplotypes
breeds
swine
Pietrain
Genes
wild boars
Large White
genes
landraces
protozoal infections
genetic variation
Protozoan Infections
interferons
bacterial infections
demography
Iberian Peninsula

Keywords

  • Domestic pig
  • GBP1
  • Genetic variability
  • Rare alleles
  • SNP
  • Wild boar

ASJC Scopus subject areas

  • Animal Science and Zoology
  • veterinary(all)

Cite this

Novel coding genetic variants of the GBP1 gene in wild and domestic pigs (Sus scrofa). / Chen, Shanyuan; Gomes, Rui; Costa, Vânia; Rocha, Isabel; Zsolnai, A.; Anton, István; Charneca, Rui; Santos, Pedro; Nunes, José Luis; Buzgó, József; Varga, Gyula; Zhang, Ya ping; Beja-Pereira, Albano.

In: Livestock Science, Vol. 146, No. 1, 06.2012, p. 1-4.

Research output: Contribution to journalArticle

Chen, S, Gomes, R, Costa, V, Rocha, I, Zsolnai, A, Anton, I, Charneca, R, Santos, P, Nunes, JL, Buzgó, J, Varga, G, Zhang, YP & Beja-Pereira, A 2012, 'Novel coding genetic variants of the GBP1 gene in wild and domestic pigs (Sus scrofa)', Livestock Science, vol. 146, no. 1, pp. 1-4. https://doi.org/10.1016/j.livsci.2012.02.008
Chen, Shanyuan ; Gomes, Rui ; Costa, Vânia ; Rocha, Isabel ; Zsolnai, A. ; Anton, István ; Charneca, Rui ; Santos, Pedro ; Nunes, José Luis ; Buzgó, József ; Varga, Gyula ; Zhang, Ya ping ; Beja-Pereira, Albano. / Novel coding genetic variants of the GBP1 gene in wild and domestic pigs (Sus scrofa). In: Livestock Science. 2012 ; Vol. 146, No. 1. pp. 1-4.
@article{89c24e98cd64441285cd171d37af1428,
title = "Novel coding genetic variants of the GBP1 gene in wild and domestic pigs (Sus scrofa)",
abstract = "The interferon-induced guanylate-binding protein 1 gene (GBP1) plays an important role in host defense against viral, bacterial and protozoan infections. To explore novel genetic variants in this gene, we re-sequenced a 587-bp fragment spanning the exon 2 of the GBP1 gene in a sample panel consisting of 34 wild boars and 59 local domestic pigs from three geographic regions (China, Iberian Peninsula, and Central Europe) and 12 individuals of three commercial breeds (Pietrain, Landrace, and Large White). In a final 543-bp sequence fragment, there were 14 single nucleotide polymorphisms (SNPs), of which five were coding (three novel mutations). A total of 19 haplotypes were reconstructed and most haplotypes were shared by two or more sample groups. Those shared haplotypes revealed a clear signature of genetic introgression from Chinese domestic pigs into European domestic pigs. In addition, there were six haplotypes with frequencies below 1{\%}, but none of them were present in the three commercial breeds (Pietrain, Landrace, and Large White). Although a limited number of individuals and breeds were analyzed, the absence of rare alleles (or haplotypes) in the commercial breeds is an indication that a significant proportion of genetic diversity in domestic species is not present in commercial breeds. This study demonstrated the potential to find sufficient genetic variation for population genetic analyses of demography versus selection, in functional candidate genes of domestic pigs and wild boars worldwide.",
keywords = "Domestic pig, GBP1, Genetic variability, Rare alleles, SNP, Wild boar",
author = "Shanyuan Chen and Rui Gomes and V{\^a}nia Costa and Isabel Rocha and A. Zsolnai and Istv{\'a}n Anton and Rui Charneca and Pedro Santos and Nunes, {Jos{\'e} Luis} and J{\'o}zsef Buzg{\'o} and Gyula Varga and Zhang, {Ya ping} and Albano Beja-Pereira",
year = "2012",
month = "6",
doi = "10.1016/j.livsci.2012.02.008",
language = "English",
volume = "146",
pages = "1--4",
journal = "Livestock Science",
issn = "1871-1413",
publisher = "Elsevier",
number = "1",

}

TY - JOUR

T1 - Novel coding genetic variants of the GBP1 gene in wild and domestic pigs (Sus scrofa)

AU - Chen, Shanyuan

AU - Gomes, Rui

AU - Costa, Vânia

AU - Rocha, Isabel

AU - Zsolnai, A.

AU - Anton, István

AU - Charneca, Rui

AU - Santos, Pedro

AU - Nunes, José Luis

AU - Buzgó, József

AU - Varga, Gyula

AU - Zhang, Ya ping

AU - Beja-Pereira, Albano

PY - 2012/6

Y1 - 2012/6

N2 - The interferon-induced guanylate-binding protein 1 gene (GBP1) plays an important role in host defense against viral, bacterial and protozoan infections. To explore novel genetic variants in this gene, we re-sequenced a 587-bp fragment spanning the exon 2 of the GBP1 gene in a sample panel consisting of 34 wild boars and 59 local domestic pigs from three geographic regions (China, Iberian Peninsula, and Central Europe) and 12 individuals of three commercial breeds (Pietrain, Landrace, and Large White). In a final 543-bp sequence fragment, there were 14 single nucleotide polymorphisms (SNPs), of which five were coding (three novel mutations). A total of 19 haplotypes were reconstructed and most haplotypes were shared by two or more sample groups. Those shared haplotypes revealed a clear signature of genetic introgression from Chinese domestic pigs into European domestic pigs. In addition, there were six haplotypes with frequencies below 1%, but none of them were present in the three commercial breeds (Pietrain, Landrace, and Large White). Although a limited number of individuals and breeds were analyzed, the absence of rare alleles (or haplotypes) in the commercial breeds is an indication that a significant proportion of genetic diversity in domestic species is not present in commercial breeds. This study demonstrated the potential to find sufficient genetic variation for population genetic analyses of demography versus selection, in functional candidate genes of domestic pigs and wild boars worldwide.

AB - The interferon-induced guanylate-binding protein 1 gene (GBP1) plays an important role in host defense against viral, bacterial and protozoan infections. To explore novel genetic variants in this gene, we re-sequenced a 587-bp fragment spanning the exon 2 of the GBP1 gene in a sample panel consisting of 34 wild boars and 59 local domestic pigs from three geographic regions (China, Iberian Peninsula, and Central Europe) and 12 individuals of three commercial breeds (Pietrain, Landrace, and Large White). In a final 543-bp sequence fragment, there were 14 single nucleotide polymorphisms (SNPs), of which five were coding (three novel mutations). A total of 19 haplotypes were reconstructed and most haplotypes were shared by two or more sample groups. Those shared haplotypes revealed a clear signature of genetic introgression from Chinese domestic pigs into European domestic pigs. In addition, there were six haplotypes with frequencies below 1%, but none of them were present in the three commercial breeds (Pietrain, Landrace, and Large White). Although a limited number of individuals and breeds were analyzed, the absence of rare alleles (or haplotypes) in the commercial breeds is an indication that a significant proportion of genetic diversity in domestic species is not present in commercial breeds. This study demonstrated the potential to find sufficient genetic variation for population genetic analyses of demography versus selection, in functional candidate genes of domestic pigs and wild boars worldwide.

KW - Domestic pig

KW - GBP1

KW - Genetic variability

KW - Rare alleles

KW - SNP

KW - Wild boar

UR - http://www.scopus.com/inward/record.url?scp=84862814598&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84862814598&partnerID=8YFLogxK

U2 - 10.1016/j.livsci.2012.02.008

DO - 10.1016/j.livsci.2012.02.008

M3 - Article

AN - SCOPUS:84862814598

VL - 146

SP - 1

EP - 4

JO - Livestock Science

JF - Livestock Science

SN - 1871-1413

IS - 1

ER -