Analysis of extended haplotype in Korean cattle (Hanwoo) population

  • Lim, Dajeong ;
  • Choi, Bong Hwan ;
  • Cho, Yong Min ;
  • Chai, Han Ha ;
  • Jang, Gul Won ;
  • Gondro, Cedric ;
  • Jeoung, Yeoung Ho ;
  • Lee, Seung Hwan
  • Received : 2016.04.25
  • Accepted : 2016.07.27
  • Published : 2016.09.30


Korean cattle (Hanwoo) are categorized into three breeds based on color: brown, brindle, and black. Among these breeds, brown Hanwoo has been subjected to intensive selection to improve meat traits. To identify genetic traces driven by recent selection in brown Hanwoo, we scanned the genomes of brown and brindle Hanwoo using a bovine SNP chip. We identified 17 candidate selection signatures in brown Hanwoo and sequenced four candidate regions from 10 individuals each of brown and brindle Hanwoo. In particular, non-synonymous SNPs in the ADSL gene (K88M, L189H, and R302Q) might have had mutational effects on protein structure as a result of altering the purine pathway during nucleotide breakdown. The ADSL gene was previously reported to affect meat quality and yield in livestock. Meat quality and yield are main breeding goals for brown Hanwoo, and our results support a potential causal influence of non-synonymous SNPs in the ADSL gene.


ADSL;Brindle Hanwoo;Extendend haplotype;Hanwoo


  1. Seo K, Mohanty TR, Choi T and Hwang I (2007) Biology of epidermal and hair pigmentation in cattle: a minireview. Vet Dermatol 18, 392-400
  2. Choi TJ (2009) establishment of phylogenetic characteristics for korean traditional cattle breeds. Chonbuk National University.
  3. Qanbari S, Pimentel EC, Tetens J et al (2010) The pattern of linkage disequilibrium in German Holstein cattle. Anim Genet 41, 346-356
  4. Yoon D, Kwon Y, Lee K et al (2008) Discrimination of Korean Cattle (Hanwoo) Using DNA Markers Derived from SNPs in Bovine Mitochondrial and SRY Genes. Asian-Australas J Anim Sci 21, 25-28
  5. Kim H, Lee S, Cho Y et al (2011) Genomic Information and Its Application in Hanwoo (Korean Native Cattle) Breeding Program - A Mini Review. Ann Anim Resour Sci 22, 125-133
  6. Kim Y and Stephan W (2002) Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160, 765-777
  7. Schwarzenbacher H, Dolezal M, Flisikowski K et al (2012) Combining evidence of selection with association analysis increases power to detect regions influencing complex traits in dairy cattle. BMC Genomics 13, 48
  8. Gautier M and Naves M (2011) Footprints of selection in the ancestral admixture of a New World Creole cattle breed. Mol Ecol 20, 3128-3143
  9. MacEachern S, Hayes B, McEwan J and Goddard M (2009) An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle. BMC Genomics 10, 181
  10. Flori L, Fritz S, Jaffrezic F et al (2009) The genome response to artificial selection: a case study in dairy cattle. PLoS One 4, e6595
  11. Hayes B, Chamberlain A, Maceachern S et al (2009) A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle. Animal Genetics 40, 176-184
  12. Lee SH, Choi BH, Lim D et al (2013) Genome-wide association study identifies major loci for carcass weight on BTA14 in Hanwoo (Korean Cattle). PLoS One 8, e74677
  13. Gautier M, Flori L, Riebler A et al (2009) A whole genome Bayesian scan for adaptive genetic divergence in West African cattle. BMC Genomics 10, 550
  14. Liu J, Damon M, Guitton N et al (2009) Differentiallyexpressed genes in pig Longissimus muscles with contrasting levels of fat, as identified by combined transcriptomic, reverse transcription PCR, and proteomic analyses. J Agric Food Chem 57, 3808-3817
  15. Ye M, Chen J, Zhao G, Zheng M and Wen J (2010) Correlation between polymorphisms in ADSL and GARS-AIRS- GART genes with inosine 5'-monophosphate (IMP) contents in Beijing-you chickens. Br Poult Sic 51, 609-613
  16. Lee S, Van Der Werf J, Park E, Oh S, Gibson J and Thompson J (2010) Genetic polymorphisms of the bovine fatty acid binding protein 4 gene are significantly associated with marbling and carcass weight in Hanwoo (Korean Cattle). Animal Genetics 41, 442-444
  17. Tang K, Thornton KR and Stoneking M (2007) A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol 5, e171
  18. Li H and Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760
  19. Li H, Handsaker B, Wysoker A et al (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079
  20. McKenna A, Hanna M, Banks E et al (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20, 1297-1303
  21. Jorgensen JA, Zadravec D and Jacobsson A (2007) Norepinephrine and rosiglitazone synergistically induce Elovl3 expression in brown adipocytes. Am J Physiol Endocrinol Metab 293, E1159-1168
  22. Wang K, Li M and Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38, e164
  23. Taniguchi M, Guan LL, Basarab JA, Dodson MV and Moore SS (2008) Comparative analysis on gene expression profiles in cattle subcutaneous fat tissues. Comp Biochem Physiol Part D Genomics Proteomics 3, 251-256
  24. Mizoguchi Y, Hirano T, Itoh T et al (2010) Differentially expressed genes during bovine intramuscular adipocyte differentiation profiled by serial analysis of gene expression. Anim Genet 41, 436-441
  25. Reverter A, Hudson NJ, Wang Y et al (2006) A gene coexpression network for bovine skeletal muscle inferred from microarray data. Physiol Genomics 28, 76-83

Cited by

  1. Genetic diversity and divergence among Korean cattle breeds assessed using a BovineHD single-nucleotide polymorphism chip vol.31, pp.11, 2018,


Grant : BK21플러스

Supported by : 충남대학교