GWAS for Meat and Carcass Traits Using Imputed Sequence Level Genotypes in Pooled F2-Designs in Pigs.
Genome wide association study
Imputation
Meat
Variant calling
Whole genome sequencing
and production traits
carcass
Journal
G3 (Bethesda, Md.)
ISSN: 2160-1836
Titre abrégé: G3 (Bethesda)
Pays: England
ID NLM: 101566598
Informations de publication
Date de publication:
04 09 2019
04 09 2019
Historique:
pubmed:
13
7
2019
medline:
15
2
2020
entrez:
13
7
2019
Statut:
epublish
Résumé
In order to gain insight into the genetic architecture of economically important traits in pigs and to derive suitable genetic markers to improve these traits in breeding programs, many studies have been conducted to map quantitative trait loci. Shortcomings of these studies were low mapping resolution, large confidence intervals for quantitative trait loci-positions and large linkage disequilibrium blocks. Here, we overcome these shortcomings by pooling four large F2 designs to produce smaller linkage disequilibrium blocks and by resequencing the founder generation at high coverage and the F1 generation at low coverage for subsequent imputation of the F2 generation to whole genome sequencing marker density. This lead to the discovery of more than 32 million variants, 8 million of which have not been previously reported. The pooling of the four F2 designs enabled us to perform a joint genome-wide association study, which lead to the identification of numerous significantly associated variant clusters on chromosomes 1, 2, 4, 7, 17 and 18 for the growth and carcass traits average daily gain, back fat thickness, meat fat ratio, and carcass length. We could not only confirm previously reported, but also discovered new quantitative trait loci. As a result, several new candidate genes are discussed, among them
Identifiants
pubmed: 31296617
pii: g3.119.400452
doi: 10.1534/g3.119.400452
pmc: PMC6723123
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2823-2834Informations de copyright
Copyright © 2019 Falker-Gieske et al.
Références
Science. 1988 Dec 16;242(4885):1528-34
pubmed: 3201241
PLoS One. 2009 Aug 05;4(8):e6524
pubmed: 19654876
Mol Genet Genomics. 2016 Aug;291(4):1715-25
pubmed: 27174137
Nat Genet. 1999 Feb;21(2):155-6
pubmed: 9988262
Dev Biol. 1999 Jun 15;210(2):367-80
pubmed: 10357897
Genet Sel Evol. 2016 Nov 4;48(1):83
pubmed: 27809758
Am J Hum Genet. 2007 Nov;81(5):1084-97
pubmed: 17924348
Med Sci Monit. 2016 Dec 01;22:4699-4706
pubmed: 27906902
Nucleic Acids Res. 2003 Jul 1;31(13):3812-4
pubmed: 12824425
Diabetes. 2015 Feb;64(2):604-17
pubmed: 25187368
BMC Dev Biol. 2008 Oct 01;8:94
pubmed: 18826651
Nat Protoc. 2009;4(1):44-57
pubmed: 19131956
PLoS One. 2012;7(12):e51954
pubmed: 23251661
Genetica. 2009 Jun;136(2):341-9
pubmed: 18704695
Am J Hum Genet. 2018 Sep 6;103(3):338-348
pubmed: 30100085
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Nucleic Acids Res. 2019 Jan 8;47(D1):D701-D710
pubmed: 30407520
Anim Genet. 2018 Oct;49(5):403-412
pubmed: 29978910
Philos Trans R Soc Lond B Biol Sci. 2005 Jul 29;360(1459):1435-42
pubmed: 16048786
Gigascience. 2015 Feb 25;4:7
pubmed: 25722852
BMC Genet. 2015 Oct 30;16:129
pubmed: 26518887
Genet Sel Evol. 2001 May-Jun;33(3):209-29
pubmed: 11403745
Genes Chromosomes Cancer. 2018 Sep;57(9):446-451
pubmed: 29700887
PLoS One. 2015 Nov 03;10(11):e0140301
pubmed: 26528553
PLoS One. 2015 May 07;10(5):e0126880
pubmed: 25950439
Science. 1991 Jul 26;253(5018):448-51
pubmed: 1862346
Am J Med Genet. 1977;1(1):21-9
pubmed: 610423
PLoS One. 2018 Oct 11;13(10):e0205576
pubmed: 30308042
Genet Sel Evol. 2015 Nov 02;47:84
pubmed: 26525050
Am J Hum Genet. 2011 Jan 7;88(1):76-82
pubmed: 21167468
Sci Rep. 2017 May 17;7(1):2053
pubmed: 28515432
J Dairy Sci. 2015 Jun;98(6):4107-16
pubmed: 25892697
Int J Obes (Lond). 2013 Oct;37(10):1399-406
pubmed: 23381556
Int J Biol Sci. 2014 Feb 07;10(3):236-44
pubmed: 24644423
Genetics. 2003 Jun;164(2):629-35
pubmed: 12807783
PLoS One. 2013 Apr 24;8(4):e62534
pubmed: 23638110
J Thorac Dis. 2016 Oct;8(10):2911-2923
pubmed: 27867568
Sci Rep. 2018 Jul 30;8(1):11421
pubmed: 30061673
Int J Oncol. 2013 Oct;43(4):1095-102
pubmed: 23900689
BMC Bioinformatics. 2019 Jan 11;20(1):22
pubmed: 30634901
Genes Chromosomes Cancer. 2004 Feb;39(2):126-37
pubmed: 14695992
J Biol Chem. 2008 Jun 6;283(23):15740-6
pubmed: 18387954
Oncogene. 2017 Feb 2;36(5):593-605
pubmed: 27375028
Genet Sel Evol. 2013 Jul 29;45:28
pubmed: 23895218
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
BMC Genet. 2018 Apr 3;19(1):22
pubmed: 29614956
Genome Biol. 2007;8(9):R183
pubmed: 17784955
Genome Res. 2005 Jul;15(7):936-44
pubmed: 15998908
Dev Biol. 2007 Jan 1;301(1):70-81
pubmed: 17150207
Cancer Res. 2007 Oct 1;67(19):9528-34
pubmed: 17909063
BMC Genomics. 2012 Nov 15;13:584
pubmed: 23153364
Int J Oncol. 2015 Apr;46(4):1498-506
pubmed: 25625960
Eur Rev Med Pharmacol Sci. 2015 Nov;19(21):4139-45
pubmed: 26592840
Int J Biol Sci. 2007 Feb 10;3(3):192-7
pubmed: 17384738
BMC Genet. 2010 Apr 23;11:26
pubmed: 20416077
Mol Genet Genomics. 2018 Oct;293(5):1205-1216
pubmed: 29948331
Genet Sel Evol. 2010 Nov 01;42:40
pubmed: 21040563
Database (Oxford). 2017 Jan 1;2017:
pubmed: 29220438