How immunogenetically different are domestic pigs from wild boars: a perspective from single-nucleotide polymorphisms of 19 immunity-related candidate genes

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	How immunogenetically different are domestic pigs from wild boars: a perspective from single-nucleotide polymorphisms of 19 immunity-related candidate genes
	Chen SY 1; Gomes R 1; Costa V 1; Santos P 2; Charneca R 2; Zhang YP 3,4; Liu XH 5; Wang SQ 5; Bento P 6; Nunes JL 2
刊名	IMMUNOGENETICS
	2013
卷号	65 期号:10 页码:737-748
关键词	Wild boar Domestic pig Single nucleotide polymorphism Positive selection Balancing selection
通讯作者	albanobp@fc.up.pt
合作状况	其它
英文摘要	The coexistence of wild boars and domestic pigs across Eurasia makes it feasible to conduct comparative genetic or genomic analyses for addressing how genetically different a domestic species is from its wild ancestor. To test whether there are differences in patterns of genetic variability between wild and domestic pigs at immunity-related genes and to detect outlier loci putatively under selection that may underlie differences in immune responses, here we analyzed 54 single-nucleotide polymorphisms (SNPs) of 19 immunity-related candidate genes on 11 autosomes in three pairs of wild boar and domestic pig populations from China, Iberian Peninsula, and Hungary. Our results showed no statistically significant differences in allele frequency and heterozygosity across SNPs between three pairs of wild and domestic populations. This observation was more likely due to the widespread and long-lasting gene flow between wild boars and domestic pigs across Eurasia. In addition, we detected eight coding SNPs from six genes as outliers being under selection consistently by three outlier tests (BayeScan2.1, FDIST2, and Arlequin3.5). Among four non-synonymous outlier SNPs, one from TLR4 gene was identified as being subject to positive (diversifying) selection and three each from CD36, IFNW1, and IL1B genes were suggested as under balancing selection. All of these four non-synonymous variants were predicted as being benign by PolyPhen-2. Our results were supported by other independent lines of evidence for positive selection or balancing selection acting on these four immune genes (CD36, IFNW1, IL1B, and TLR4). Our study showed an example applying a candidate gene approach to identify functionally important mutations (i.e., outlier loci) in wild and domestic pigs for subsequent functional experiments.
收录类别	SCI
资助信息	This work was financially supported by Fundação para a Ciência e Tecnologia (FCT) projects PTDC/CVT/ 68907/2006 (ABP) and PTDC/CVT/099782/2008 (SC). SC is support- ed by FCT individual grant SFRH/BPD/46082/2008.
语种	英语
WOS记录号	WOS:000324386100004
公开日期	2013-10-08
内容类型	期刊论文
源URL	[http://159.226.149.42:8088/handle/152453/7692]
专题	昆明动物研究所_分子进化基因组学昆明动物研究所_遗传资源与进化国家重点实验室
作者单位	1.Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto (CIBIO/UP), Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal 2.ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Herdade da Mitra, 7002-554 Évora, Portugal 3.State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China 4.Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China 5.Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China 6.Associação Nacional de Criadores de Porco Alentejano (ANCPA), 7350 Elvas, Portugal 7.SEFAG Forest Management and Wood Industry Share Company, Kaposvár, Hungary 8.Research Institute for Animal Breeding and Nutrition, 2053 Herceghalom, Hungary 9.University of Kaposvár, 7400 Kaposvár, Hungary
推荐引用方式 GB/T 7714	Chen SY,Gomes R,Costa V,et al. How immunogenetically different are domestic pigs from wild boars: a perspective from single-nucleotide polymorphisms of 19 immunity-related candidate genes[J]. IMMUNOGENETICS,2013,65(10):737-748.
APA	Chen SY.,Gomes R.,Costa V.,Santos P.,Charneca R.,...&Beja-Pereira A[*].(2013).How immunogenetically different are domestic pigs from wild boars: a perspective from single-nucleotide polymorphisms of 19 immunity-related candidate genes.IMMUNOGENETICS,65(10),737-748.
MLA	Chen SY,et al."How immunogenetically different are domestic pigs from wild boars: a perspective from single-nucleotide polymorphisms of 19 immunity-related candidate genes".IMMUNOGENETICS 65.10(2013):737-748.