Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip.
Animals
Animals, Domestic
/ genetics
Breeding
/ methods
Genetic Variation
/ genetics
Genetics, Population
/ methods
Genome
Genomics
/ methods
Genotype
Linkage Disequilibrium
/ genetics
Oligonucleotide Array Sequence Analysis
/ methods
Phenotype
Polymorphism, Single Nucleotide
/ genetics
Population Density
Principal Component Analysis
/ methods
Swine
/ genetics
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
19 09 2019
19 09 2019
Historique:
received:
06
03
2019
accepted:
30
08
2019
entrez:
21
9
2019
pubmed:
21
9
2019
medline:
28
10
2020
Statut:
epublish
Résumé
Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on F
Identifiants
pubmed: 31537860
doi: 10.1038/s41598-019-49830-6
pii: 10.1038/s41598-019-49830-6
pmc: PMC6753209
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
13546Références
PLoS One. 2009 Aug 05;4(8):e6524
pubmed: 19654876
Mol Biol Rep. 2011 Jan;38(1):319-25
pubmed: 20358298
Acta Physiol Scand. 1990 Aug;139(4):591-6
pubmed: 1701068
J Anim Breed Genet. 2016 Apr;133(2):145-54
pubmed: 26059912
J Anim Breed Genet. 2014 Dec;131(6):473-82
pubmed: 25047461
Nat Genet. 2001 Oct;29(2):229-32
pubmed: 11586305
Genet Sel Evol. 2000 Mar-Apr;32(2):187-203
pubmed: 14736401
Anim Genet. 2010 May;41 Suppl 1:6-31
pubmed: 20500753
J Anim Sci. 2006 Dec;84(12):3346-55
pubmed: 17093227
Genet Sel Evol. 2008 Jan-Feb;40(1):103-28
pubmed: 18096118
Anim Genet. 2019 Apr;50(2):166-171
pubmed: 30741434
Anim Genet. 2002 Dec;33(6):422-7
pubmed: 12464016
Theor Popul Biol. 1971 Jun;2(2):125-41
pubmed: 5170716
Nat Commun. 2015 Dec 11;6:10162
pubmed: 26657010
Mol Phylogenet Evol. 2010 Mar;54(3):680-6
pubmed: 19900568
Anim Biotechnol. 2019 Jul;30(3):242-251
pubmed: 29938587
PLoS One. 2011 Apr 04;6(4):e14782
pubmed: 21483733
Genetics. 1931 Mar;16(2):97-159
pubmed: 17246615
PLoS One. 2018 Nov 20;13(11):e0207475
pubmed: 30458028
Genome Res. 2003 Apr;13(4):635-43
pubmed: 12654718
J Anim Sci. 2014 Apr;92(4):1385-94
pubmed: 24663154
Nat Rev Genet. 2002 Apr;3(4):299-309
pubmed: 11967554
BMC Genomics. 2014 Jul 16;15:601
pubmed: 25030608
Mitochondrial DNA A DNA Mapp Seq Anal. 2016;27(1):747-52
pubmed: 24810064
BMC Genomics. 2016 Aug 26;17:685
pubmed: 27566279
BMC Genomics. 2012 Nov 15;13:583
pubmed: 23153328
Heredity (Edinb). 2014 Dec;113(6):471-84
pubmed: 25074569
Mamm Genome. 2004 Jul;15(7):552-9
pubmed: 15366375
PLoS One. 2013;8(2):e56001
pubmed: 23409110
Genetics. 2008 May;179(1):569-79
pubmed: 18493072
Anim Genet. 2012 Oct;43(5):620-3
pubmed: 22497205
Trends Genet. 2002 Feb;18(2):83-90
pubmed: 11818140
Theor Appl Genet. 1968 Jun;38(6):226-31
pubmed: 24442307
Biochimie. 2005 Jan;87(1):99-109
pubmed: 15733744
BMC Genet. 2013 Oct 30;14:106
pubmed: 24172017
BMC Genomics. 2014 May 31;15:413
pubmed: 24885501
Front Genet. 2012 Jan 05;2:101
pubmed: 22303395
BMC Genomics. 2009 Jan 14;10:22
pubmed: 19144180
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
Nature. 2012 Nov 15;491(7424):393-8
pubmed: 23151582
Mamm Genome. 2003 Sep;14(9):650-6
pubmed: 14629115
Anim Genet. 2018 Aug;49(4):321-325
pubmed: 29672877
Curr Genomics. 2011 Apr;12(2):138-46
pubmed: 21966252
PLoS Genet. 2009 Jan;5(1):e1000341
pubmed: 19148282
Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19529-36
pubmed: 23151514
Am J Hum Genet. 2007 Sep;81(3):559-75
pubmed: 17701901
PLoS Genet. 2013 Apr;9(4):e1003453
pubmed: 23637623
BMC Genomics. 2015 Nov 11;16:922
pubmed: 26559809
Genet Sel Evol. 2009 Jun 11;41:35
pubmed: 19519896
Science. 1994 Mar 25;263(5154):1771-4
pubmed: 8134840
Genet Sel Evol. 2012 Mar 01;44:5
pubmed: 22376364
BMC Genet. 2007 Jul 12;8:48
pubmed: 17626638
Asian-Australas J Anim Sci. 2014 Sep;27(9):1263-9
pubmed: 25178369
Genome Res. 2000 Feb;10(2):220-7
pubmed: 10673279
Bioinformatics. 2004 Jan 22;20(2):289-90
pubmed: 14734327
BMC Genomics. 2012 Nov 15;13:584
pubmed: 23153364
Genome Res. 2007 Apr;17(4):520-6
pubmed: 17351134
BMC Genomics. 2014 Dec 03;15:1057
pubmed: 25471201