title: Genome-wide association studies identify the loci for 5 exterior traits in a Large White × Minzhu pig population.
abstract: As one of the main breeding selection criteria, external appearance has special economic importance in the hog industry. In this study, an Illumina Porcine SNP60 BeadChip was used to conduct a genome-wide association study (GWAS) in 605 pigs of the F2 generation derived from a Large White × Minzhu intercross. Traits under study were abdominal circumference (AC), body height (BH), body length (BL), cannon bone circumference (CBC), chest depth (CD), chest width (CW), rump circumference (RC), rump width (RW), scapula width (SW), and waist width (WW). A total of 138 SNPs (the most significant being MARC0033464) on chromosome 7 were found to be associated with BH, BL, CBC, and RC (P-value= 4.15E-6). One SNP on chromosome 1 was found to be associated with CD at genome-wide significance levels. The percentage phenotypic variance of these significant SNPs ranged from 0.1-25.48%. Moreover, a conditional analysis revealed that the significant SNPs were derived from a single quantitative trait locus (QTL) and indicated additional chromosome-wide significant association for 25 SNPs on SSC4 (BL, CBC) and 9 SNPs on SSC7 (RC). Linkage analysis revealed two complete linkage disequilibrium haplotype blocks that contained seven and four SNPs, respectively. In block 1, the most significant SNP, MARC0033464, was present. Annotations from pig reference genome suggested six genes (GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1) in block 1 (495 kb), and one gene (SCUBE3) in block 3 (124 kb). Functional analysis indicated that HMGA1 and SCUBE3 genes are the potential genes controlling BH, BL, and RC in pigs, with an application in breeding programs. We screened several candidate intervals and genes based on SNP location and gene function, and predicted their function using bioinformatics analyses.
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Ligang
authors.initials: L
authors.lastname: Wang
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Longchao
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Yan
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China; Jilin Academy of Agricultural Sciences, Changchun, China.
authors.forename: Na
authors.initials: N
authors.lastname: Li
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Liang
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Pu
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Yuebo
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Huibi
authors.initials: H
authors.lastname: Shi
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Kebin
authors.initials: K
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Lixian
authors.initials: L
authors.lastname: Wang
mesh_terms: D000818:Animals; D001827:Body Height / Q000235:genetics; D019295:Computational Biology; D003433:Crosses, Genetic; D005260:Female; D055106:Genome-Wide Association Study; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics; D008297:Male; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D019655:Quantitative Trait, Heritable; D034421:Sus scrofa / Q000033:anatomy & histology / Q000235:genetics*
references.citation: Genet Epidemiol. 2008 May;32(4):341-9
references.pmid: 18271028
references.citation: Med Hypotheses. 2013 Nov;81(5):948-53
references.pmid: 24084593
references.citation: Bioinformatics. 2007 Oct 1;23(19):2633-5
references.pmid: 17586829
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D355-60
references.pmid: 19880382
references.citation: J Anim Sci. 2003 Aug;81(8):1943-9
references.pmid: 12926776
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D871-9
references.pmid: 23180796
references.citation: Genomics. 2000 Nov 15;70(1):74-81
references.pmid: 11087664
references.citation: Anim Genet. 2009 Oct;40(5):637-47
references.pmid: 19397518
references.citation: Bioinformatics. 2005 Jan 15;21(2):263-5
references.pmid: 15297300
references.citation: Poult Sci. 2006 Dec;85(12):2061-78
references.pmid: 17135660
references.citation: Nature. 2010 Oct 14;467(7317):832-8
references.pmid: 20881960
references.citation: J Anim Sci. 2008 Nov;86(11):2833-9
references.pmid: 18567733
references.citation: Nat Rev Genet. 2004 Mar;5(3):202-12
references.pmid: 14970822
references.citation: Int J Biol Sci. 2012;8(6):870-81
references.pmid: 22745577
references.citation: Mol Cell Biol. 2001 Apr;21(7):2485-95
references.pmid: 11259597
references.citation: Am J Hum Genet. 2002 Feb;70(2):425-34
references.pmid: 11791212
references.citation: Int J Biol Sci. 2012;8(4):580-95
references.pmid: 22532790
references.citation: Int J Oncol. 2008 Feb;32(2):289-305
references.pmid: 18202751
references.citation: Anim Genet. 2013 Aug;44(4):454-7
references.pmid: 23777416
references.citation: Oncogene. 1996 Dec 5;13(11):2439-46
references.pmid: 8957086
references.citation: PLoS One. 2011 Feb 24;6(2):e14726
references.pmid: 21383979
references.citation: Nat Protoc. 2009;4(1):44-57
references.pmid: 19131956
references.citation: Nat Genet. 2010 Nov;42(11):937-48
references.pmid: 20935630
references.citation: Genetics. 2007 Sep;177(1):577-85
references.pmid: 17660554
references.citation: Mod Pathol. 2010 Jan;23(1):98-104
references.pmid: 19820691
references.citation: J Anim Sci. 2011 Mar;89(3):601-8
references.pmid: 21097684
references.citation: J Biol Chem. 2004 Sep 3;279(36):37485-90
references.pmid: 15234972
references.citation: Genet Epidemiol. 2008 May;32(4):361-9
references.pmid: 18271029
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Genet Sel Evol. 2005 Nov-Dec;37(6):677-98
references.pmid: 16277974
references.citation: Nat Genet. 2013 May;45(5):501-12
references.pmid: 23563607
references.citation: BMC Genomics. 2010 Dec 09;11:699
references.pmid: 21143916
references.citation: Science. 2007 Apr 6;316(5821):112-5
references.pmid: 17412960
references.citation: BMC Genomics. 2011 Jul 13;12:362
references.pmid: 21752240
references.citation: PLoS One. 2007 Dec 05;2(12):e1274
references.pmid: 18060068
references.citation: J Anim Sci. 2011 Mar;89(3):680-92
references.pmid: 21346135
references.citation: J Anim Sci. 2005 Sep;83(9):1979-87
references.pmid: 16100052
references.citation: BMC Genet. 2011 Apr 20;12:35
references.pmid: 21507230
references.citation: BMC Genet. 2010 May 20;11:42
references.pmid: 20487517
references.citation: Mol Ecol. 1998 May;7(5):639-55
references.pmid: 9633105