Genome-wide association study identifies 22 new loci for body dimension and body weight traits in a White Duroc×Erhualian F2 intercross population

  • Ji, Jiuxiu (National Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University) ;
  • Zhou, Lisheng (National Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University) ;
  • Guo, Yuanmei (National Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University) ;
  • Huang, Lusheng (National Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University) ;
  • Ma, Junwu (National Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University)
  • Received : 2016.09.05
  • Accepted : 2017.01.08
  • Published : 2017.08.01


Objective: Growth-related traits are important economic traits in the swine industry. However, the genetic mechanism of growth-related traits is little known. The aim of this study was to screen the candidate genes and molecular markers associated with body dimension and body weight traits in pigs. Methods: A genome-wide association study (GWAS) on body dimension and body weight traits was performed in a White $Duroc{\times}Erhualian$ $F_2$ intercross by the illumina PorcineSNP60K Beadchip. A mixed linear model was used to assess the association between single nucleotide polymorphisms (SNPs) and the phenotypes. Results: In total, 611 and 79 SNPs were identified significantly associated with body dimension traits and body weight respectively. All SNPs but 62 were located into 23 genomic regions (quantitative trait loci, QTLs) on 14 autosomal and X chromosomes in Sus scrofa Build 10.2 assembly. Out of the 23 QTLs with the suggestive significance level ($5{\times}10^{-4}$), three QTLs exceeded the genome-wide significance threshold ($1.15{\times}10^{-6}$). Except the one on Sus scrofa chromosome (SSC) 7 which was reported previously all the QTLs are novel. In addition, we identified 5 promising candidate genes, including cell division cycle 7 for abdominal circumference, pleiomorphic adenoma gene 1 and neuropeptides B/W receptor 1 for both body weight and cannon bone circumference on SSC4, phosphoenolpyruvate carboxykinase 1, and bone morphogenetic protein 7 for hip circumference on SSC17. Conclusion: The results have not only demonstrated a number of potential genes/loci associated with the growth-related traits in pigs, but also laid a foundation for studying the genes' role and further identifying causative variants underlying these loci.


Supported by : National Nature Science Foundation of China


  1. McGlone J. The future of pork production in the world: towards sustainable, welfare-positive systems. Animals 2013;3:401-15.
  2. Johnson ZB, Nugent RA, 3rd. Heritability of body length and measures of body density and their relationship to backfat thickness and loin muscle area in swine. J Anim Sci 2003;81:1943-9.
  3. Rothschild MF, Plastow GS. Impact of genomics on animal agriculture and opportunities for animal health. Trends Biotechnol 2008; 26:21-5.
  4. Andersson L, Haley CS, Ellegren H, et al. Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science 1994;263:1771-4.
  5. Freking BA, Murphy SK, Wylie AA, et al. Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar overdominance in mammals. Genome Res 2002;12:1496-506.
  6. Van Laere AS, Nguyen M, Braunschweig M, et al. A regulatory mutation in IG$F_2$ causes a major QTL effect on muscle growth in the pig. Nature 2003;425:832-6.
  7. Qiao R, Gao J, Zhang Z, et al. Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations. Genet Sel Evol 2015;47:17.
  8. Ai H, Ren J, Zhang Z, et al. Detection of quantitative trait loci for growth- and fatness-related traits in a large-scale White Duroc x Erhualian intercross pig population. Anim Genet 2012;43:383-91.
  9. Ma J, Ren J, Guo Y, et al. Genome-wide identification of quantitative trait loci for carcass composition and meat quality in a large-scale White Duroc${\times}$Chinese Erhualian resource population. Anim Genet 2009;40:637-47.
  10. Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-75.
  11. Aulchenko YS, Ripke S, Isaacs A, van Duijn CM. GenABEL: an R library for genome-wide association analysis. Bioinformatics 2007;23: 1294-6.
  12. Yang Q, Cui J, Chazaro I, Cupples LA, Demissie S. Power and type I error rate of false discovery rate approaches in genome-wide association studies. BMC Genet 2005;6 Suppl 1:S134.
  13. Sanchez MP, Tribout T, Iannuccelli N, et al. A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality. Genet Sel Evol 2014;46:12.
  14. Pearson TA, Manolio TA. How to interpret a genome-wide association study. JAMA 2008;299:1335-44.
  15. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005;21:263-5.
  16. Okumura N, Matsumoto T, Hayashi T, et al. Genomic regions affecting backfat thickness and cannon bone circumference identified by genome-wide association study in a Duroc pig population. Anim Genet 2013;44:454-7.
  17. Uemoto Y, Nagamine Y, Kobayashi E, et al. Quantitative trait loci analysis on Sus scrofa chromosome 7 for meat production, meat quality, and carcass traits within a Duroc purebred population. J Anim Sci 2008;86:2833-9.
  18. Wang L, Zhang L, Yan H, et al. Genome-wide association studies identify the loci for 5 exterior traits in a Large White x Minzhu pig population. PLoS One 2014;9:e103766.
  19. Kim JM, Takemoto N, Arai K, Masai H. Hypomorphic mutation in an essential cell-cycle kinase causes growth retardation and impaired spermatogenesis. EMBO J 2003;22:5260-72.
  20. Karim L, Takeda H, Lin L, et al. Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nat Genet 2011;43:405-13.
  21. Rubin CJ, Megens HJ, Martinez Barrio A, et al. Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci USA 2012; 109:19529-36.
  22. Ishii M, Fei H, Friedman JM. Targeted disruption of GPR7, the endogenous receptor for neuropeptides B and W, leads to metabolic defects and adult-onset obesity. Proc Natl Acad Sci USA 2003;100:10540-5.
  23. Federico A, Forzati F, Esposito F, et al. Hmga1/Hmga2 double knockout mice display a "superpygmy" phenotype. Biol Open 2014;3:372-8.
  24. Iiritano S, Chiefari E, Ventura V, et al. The HMGA1-IGF-I/IGFBP system: a novel pathway for modulating glucose uptake. Mol Endocrinol 2012;26:1578-89.
  25. Zhang L-C, Li N, Liu X, et al. A genome-wide association study of limb bone length using a Large White${\times}$Minzhu intercross population. Genet Sel Evol:GSE 2014;46:56.
  26. Beale EG, Harvey BJ, Forest C. PCK1 and PCK2 as candidate diabetes and obesity genes. Cell Biochem Biophys 2007;48:89-95.
  27. Millward CA, Desantis D, Hsieh CW, et al. Phosphoenolpyruvate carboxykinase (Pck1) helps regulate the triglyceride/fatty acid cycle and development of insulin resistance in mice. J Lipid Res 2010;51: 1452-63.
  28. Beederman M, Lamplot JD, Nan G, et al. BMP signaling in mesenchymal stem cell differentiation and bone formation. J Biomed Sci Eng 2013;6:32-52.
  29. Huang J, Liu Y, Filas B, Gunhaga L, Beebe DC. Negative and positive auto-regulation of BMP expression in early eye development. Dev Biol 2015;407:256-64.
  30. Manson SR, Austin PF, Guo Q, Moore KH. BMP-7 signaling and its critical roles in kidney development, the responses to renal injury, and chronic kidney disease. Vitam Horm 2015;99:91-144.

Cited by

  1. A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland vol.19, pp.1, 2018,