Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire Pigs

  • Lee, Young-Sup (Department of Animal Biotechnology, Chonbuk National University) ;
  • Shin, Donghyun (Department of Animal Biotechnology, Chonbuk National University)
  • Received : 2018.05.17
  • Accepted : 2018.07.12
  • Published : 2018.09.30
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Abstract

Although pork quality traits are important commercially, genome-wide association studies (GWASs) have not well considered Landrace and Yorkshire pigs worldwide. Landrace and Yorkshire pigs are important pork-providing breeds. Although quantitative trait loci of pigs are well-developed, significant genes in GWASs of pigs in Korea must be studied. Through a GWAS using the PLINK program, study of the significant genes in Korean pigs was performed. We conducted a GWAS and surveyed the gene ontology (GO) terms associated with the backfat thickness (BF) trait of these pigs. We included the breed information (Yorkshire and Landrace pigs) as a covariate. The significant genes after false discovery rate (<0.01) correction were AFG1L, SCAI, RIMS1, and SPDEF. The major GO terms for the top 5% of genes were related to neuronal genes, cell morphogenesis and actin cytoskeleton organization. The neuronal genes were previously reported as being associated with backfat thickness. However, the genes in our results were novel, and they included ZNF280D, BAIAP2, LRTM2, GABRA5, PCDH15, HERC1, DTNBP1, SLIT2, TRAPPC9, NGFR, APBB2, RBPJ, and ABL2. These novel genes might have roles in important cellular and physiological functions related to BF accumulation. The genes related to cell morphogenesis were NOX4, MKLN1, ZNF280D, BAIAP2, DNAAF1, LRTM2, PCDH15, NGFR, RBPJ, MYH9, APBB2, DTNBP1, TRIM62, and SLIT2. The genes that belonged to actin cytoskeleton organization were MKLN1, BAIAP2, PCDH15, BCAS3, MYH9, DTNBP1, ABL2, ADD2, and SLIT2.

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References

  1. Rohrer GA, Thallman RM, Shackelford S, Wheeler T, Koohmaraie M. A genome scan for loci affecting pork quality in a Duroc-Landrace F population. Anim Genet 2006;37:17-27. https://doi.org/10.1111/j.1365-2052.2005.01368.x
  2. Okumura N, Matsumoto T, Hayashi T, Hirose K, Fukawa K, Itou 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: 454-457. https://doi.org/10.1111/age.12018
  3. Muslin AJ. MAPK signalling in cardiovascular health and disease: molecular mechanisms and therapeutic targets. Clin Sci (Lond) 2008;115:203-218. https://doi.org/10.1042/CS20070430
  4. Lee KT, Byun MJ, Kang KS, Park EW, Lee SH, Cho S, et al. Neuronal genes for subcutaneous fat thickness in human and pig are identified by local genomic sequencing and combined SNP association study. PLoS One 2011;6:e16356. https://doi.org/10.1371/journal.pone.0016356
  5. Subramaniam S, Ozdener MH, Abdoul-Azize S, Saito K, Malik B, Maquart G, et al. ERK1/2 activation in human taste bud cells regulates fatty acid signaling and gustatory perception of fat in mice and humans. FASEB J 2016;30:3489-3500. https://doi.org/10.1096/fj.201600422R
  6. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-575. https://doi.org/10.1086/519795
  7. Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, et al. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res 2007;35:W169-W175.
  8. Moisa SJ, Shike DW, Shoup L, Loor JJ. Maternal plane of nutrition during late-gestation and weaning age alter steer calf longissimus muscle adipogenic microRNA and target gene expression. Lipids 2016;51:123-138. https://doi.org/10.1007/s11745-015-4092-y
  9. Zong S, Zeng X, Liu T, Wan F, Luo P, Xiao H. Association of polymorphisms in heat shock protein 70 genes with the susceptibility to noise-induced hearing loss: a meta-analysis. PLoS One 2017;12:e0188195. https://doi.org/10.1371/journal.pone.0188195
  10. Jayne T, Newman M, Verdile G, Sutherland G, Munch G, Musgrave I, et al. Evidence for and against a pathogenic role of reduced gamma-secretase activity in familial Alzheimer's disease. J Alzheimers Dis 2016;52:781-799. https://doi.org/10.3233/JAD-151186
  11. Sacchetti E, Scassellati C, Minelli A, Valsecchi P, Bonvicini C, Pasqualetti P, et al. Schizophrenia susceptibility and NMDA-receptor mediated signalling: an association study involving 32 tagSNPs of DAO, DAOA, PPP3CC, and DTNBP1 genes. BMC Med Genet 2013;14:33.
  12. Mori K, Kanemura Y, Fujikawa H, Nakano A, Ikemoto H, Ozaki I, et al. Brain-specific angiogenesis inhibitor 1 (BAI1) is expressed in human cerebral neuronal cells. Neurosci Res 2002;43:69-74. https://doi.org/10.1016/S0168-0102(02)00018-4