Genome-wide association study for carcass quality traits and growth in purebred and crossbred pigs1.
breeding
genetics
heritability
swine
Journal
Journal of animal science
ISSN: 1525-3163
Titre abrégé: J Anim Sci
Pays: United States
ID NLM: 8003002
Informations de publication
Date de publication:
01 Jan 2020
01 Jan 2020
Historique:
received:
15
07
2019
accepted:
25
11
2019
pubmed:
27
11
2019
medline:
9
4
2020
entrez:
27
11
2019
Statut:
ppublish
Résumé
Carcass quality traits such as back fat (BF), loin depth (LD), and ADG are of extreme economic importance for the swine industry. This study aimed to (i) estimate the genetic parameters for such traits and (ii) conduct a single-step genome-wide association study (ssGWAS) to identify genomic regions that affect carcass quality and growth traits in purebred (PB) and three-way crossbred (CB) pigs. A total of 28,497 PBs and 135,768 CBs pigs were phenotyped for BF, LD, and ADG. Of these, 4,857 and 3,532 were genotyped using the Illumina PorcineSNP60K Beadchip. After quality control, 36,328 SNPs were available and were used to perform an ssGWAS. A bootstrap analysis (n = 1,000) and a signal enrichment analysis were performed to declare SNP significance. Genome regions were based on the variance explained by significant 10-SNP sliding windows. Estimates of PB heritability (SE) were 0.42 (0.019) for BF, 0.39 (0.020) for LD, and 0.35 (0.021) for ADG. Estimates of CB heritability were 0.49 (0.042) for BF, 0.27 (0.029) for LD, and 0.12 (0.021) for ADG. Genetic correlations (SE) across the two populations were 0.81 (0.02), 0.79 (0.04), and 0.56 (0.05), for BF, LD, and ADG, respectively. The variance explained by significant regions for each trait in PBs ranged from 1.51% to 1.35% for BF, from 4.02% to 3.18% for LD, and from 2.26% to 1.45% for ADG. In CBs, the variance explained by significant regions ranged from 1.88% to 1.37% for BF, from 1.29% to 1.23% for LD, and from 1.54% to 1.32% for ADG. In this study, we have described regions of the genome that determine carcass quality and growth traits of PB and CB pigs. These results provide evidence that there are overlapping and nonoverlapping regions in the genome influencing carcass quality and growth traits in PBs and three-way CB pigs.
Identifiants
pubmed: 31768540
pii: 5643613
doi: 10.1093/jas/skz360
pmc: PMC6978898
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Références
BMC Genet. 2015 May 30;16:59
pubmed: 26024912
PLoS One. 2015 Sep 29;10(9):e0139207
pubmed: 26418247
BMC Genomics. 2012 Nov 15;13:583
pubmed: 23153328
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Genetics. 2003 Jun;164(2):637-44
pubmed: 12807784
Commun Biol. 2019 Mar 14;2:100
pubmed: 30886909
Asian-Australas J Anim Sci. 2015 Aug;28(8):1061-5
pubmed: 26104512
J Anim Sci. 2014 Jul;92(7):2846-60
pubmed: 24962532
J Anim Sci. 2008 Feb;86(2):241-53
pubmed: 17965327
J Dairy Sci. 2008 Nov;91(11):4414-23
pubmed: 18946147
PLoS One. 2014 Oct 28;9(10):e110105
pubmed: 25350845
Anim Genet. 2018 Apr;49(2):127-131
pubmed: 29411893
Asian-Australas J Anim Sci. 2017 Apr;30(4):462-469
pubmed: 27809465
J Anim Sci. 2008 Feb;86(2):254-66
pubmed: 17965326
J Anim Sci. 2005 Sep;83(9):2058-65
pubmed: 16100060
Anim Genet. 2011 Dec;42(6):600-12
pubmed: 22035001
Anim Biotechnol. 2001 Nov;12(2):155-65
pubmed: 11808631
J Dairy Sci. 2018 Dec;101(12):11004-11019
pubmed: 30243637
J Anim Sci. 2017 Aug;95(8):3370-3380
pubmed: 28805927
Physiol Genomics. 2019 Jul 1;51(7):261-266
pubmed: 31100035
Nat Protoc. 2009;4(1):44-57
pubmed: 19131956
Genet Sel Evol. 2017 Feb 14;49(1):21
pubmed: 28196480
Front Genet. 2014 May 20;5:134
pubmed: 24904635
Genet Sel Evol. 2014 Feb 14;46:12
pubmed: 24528607
Genet Sel Evol. 2019 Jun 20;51(1):28
pubmed: 31221101
Genet Sel Evol. 2017 Jun 26;49(1):51
pubmed: 28651536
J Anim Sci. 2007 Apr;85(4):901-8
pubmed: 17178815
Animal. 2019 May;13(5):924-932
pubmed: 30152309
PLoS One. 2011 Feb 08;6(2):e16766
pubmed: 21346809
Anim Genet. 2006 Dec;37(6):543-53
pubmed: 17121599
PLoS One. 2015 Feb 06;10(2):e0114919
pubmed: 25658712
J Dairy Sci. 2010 Feb;93(2):743-52
pubmed: 20105546
Meat Sci. 2008 Apr;78(4):455-60
pubmed: 22062465
J Anim Sci. 2018 Apr 3;96(3):817-829
pubmed: 29378008
J Anim Sci. 2017 Aug;95(8):3467-3478
pubmed: 28805893
J Anim Sci. 2001 Dec;79(12):3002-7
pubmed: 11811453
Sci Rep. 2018 Feb 1;8(1):2045
pubmed: 29391556
Genet Res (Camb). 2012 Apr;94(2):73-83
pubmed: 22624567
J Anim Sci. 2005 Feb;83(2):324-33
pubmed: 15644503
Nucleic Acids Res. 2013 Jan;41(Database issue):D48-55
pubmed: 23203987
Genet Sel Evol. 2015 Mar 14;47:17
pubmed: 25885760
Am J Hum Genet. 2003 Sep;73(3):516-23
pubmed: 12900793
J Dairy Sci. 2009 Sep;92(9):4656-63
pubmed: 19700729
PLoS One. 2007 Dec 05;2(12):e1274
pubmed: 18060068
BMC Genomics. 2018 Oct 11;19(1):740
pubmed: 30305017
Genet Sel Evol. 2010 Jan 27;42:2
pubmed: 20105297
J Anim Sci. 2008 Dec;86(12):3300-14
pubmed: 18708606