Genetic variants and signatures of selective sweep of Hanwoo population (Korean native cattle)

BMB Reports

Volumn 46, Issue 7, 2013, Pages 346-351

  Lee, Taeheon ^a   Cho, Seoae ^b   Seo, Kang Seok ^c   Chang, Jongsoo ^d   Kim, Heebal ^a   Yoon, Duhak ^e  

^a Seoul National University   (South Korea)

^b C and K Genomics Inc   (South Korea)

^c Sunchon National University   (South Korea)

^d Korea National Open University   (South Korea)

^e Kyungpook National University   (South Korea)

Author keywords

Adaptation; Genetic variants; Hanwoo; Korean native cattle; Selective sweep

Indexed keywords

CALCIUM BINDING PROTEIN; G PROTEIN COUPLED RECEPTOR; MITOCHONDRIAL PROTEIN;

ANIMAL; ARTICLE; CATTLE; COPY NUMBER VARIATION; GENETIC VARIABILITY; GENETICS; GENOME; INDEL MUTATION; MALE; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTH KOREA;

ANIMALS; CALCIUM-BINDING PROTEINS; CATTLE; DNA COPY NUMBER VARIATIONS; GENETIC VARIATION; GENOME; INDEL MUTATION; MALE; MITOCHONDRIAL PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTORS, G-PROTEIN-COUPLED; REPUBLIC OF KOREA;

EID: 84881306743     PISSN: 19766696     EISSN: 1976670X     Source Type: Journal    
DOI: 10.5483/BMBRep.2013.46.7.211     Document Type: Article

References (41)

1. Qanbari, S., Gianola, D., Hayes, B., Schenkel, F., Miller, S., Moore, S., Thaller, G. and Simianer, H. (2011) Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics 12, 318.
2. Larkin, D. M., Daetwyler, H. D., Hernandez, A. G., Wright, C. L., Hetrick, L. A., Boucek, L., Bachman, S. L., Band, M. R., Akraiko, T. V. and Cohen-Zinder, M. (2012) Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. Proc. Natl. Acad. Sci. U.S.A. 109, 7693-7698.
3. Xia, Q., Guo, Y., Zhang, Z., Li, D., Xuan, Z., Li, Z., Dai, F., Li, Y., Cheng, D. and Li, R. (2009) Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326, 433-436.
4. Rubin, C. J., Zody, M. C., Eriksson, J., Meadows, J. R. S., Sherwood, E., Webster, M. T., Jiang, L., Ingman, M., Sharpe, T. and Ka, S. (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464, 587-591.
5. Kim, J., Park, S. and Yeo, J. (2003) Linkage mapping and QTL on chromosome 6 in Hanwoo (Korean Cattle). Asian-Aust. J. Anim. Sci. 16, 1402-1405.
6. Lee, Y., Lee, J., Lee, J., Kim, J., Park, H. and Yeo, J. (2008) Identification of candidate SNP (single nucleotide polymorphism) for growth and carcass traits related to QTL on chromosome 6 in Hanwoo (Korean cattle). Asian-Aust. J. Anim. Sci. 21, 1703-1709.
7. Lee, S. H., Gondro, C., van der Werf, J., Kim, N. K., Lim, D., Park, E. W., Oh, S. J., Gibson, J. and Thompson, J. (2010) Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo (Korean Cattle). BMC Genomics 11, 623.
8. 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). Anim. Genet. 41, 442-444.
9. Lim, D., Lee, S. H., Cho, Y. M., Yoon, D., Shin, Y., Kim, K. W., Park, H. S. and Kim, H. (2010) Transcript profiling of expressed sequence tags from intramuscular fat, longissimus dorsi muscle and liver in Korean cattle (Hanwoo). BMB Rep. 43, 151-121.
10. Lee, S. H., Park, E. W., Cho, Y. M., Kim, S. K., Lee, J. H., Jeon, J. T., Lee, C. S., Im, S. K., Oh, S. J. and Thompson, J. (2007) Identification of differentially expressed genes related to intramuscular fat development in the early and late fattening stages of hanwoo steers. J. Biochemical. Mol. Biol. 40, 757-764.
11. Yang, B. C., Hwang, S. S., Im, G. S., Lee, D. K., Jeon, I. S. and Park, S. B. (2012) Phenotypic characterization of Hanwoo (native Korean cattle) cloned from somatic cells of a single adult. BMB Rep. 45, 38-43.
12. Barrett, R. D. H. and Schluter, D. (2008) Adaptation from standing genetic variation. Trends Ecol. Evol. 23, 38-44.
13. Eizaguirre, C., Lenz, T. L., Kalbe, M. and Milinski, M. (2012) Rapid and adaptive evolution of MHC genes under parasite selection in experimental vertebrate populations. Nat. Commun. 3, 621.
14. Barrett, R. D. H., Paccard, A., Healy, T. M., Bergek, S., Schulte, P. M., Schluter, D. and Rogers, S. M. (2011) Rapid evolution of cold tolerance in stickleback. P. Roy. Soc. B-Biol Sci. 278, 233-238.
15. Hermisson, J. and Pennings, P. S. (2005) Soft sweeps molecular population genetics of adaptation from standing genetic variation. Genetics 169, 2335-2352.
16. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M. and DePristo, M. A. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303.
17. Quinlan, A. R. and Hall, I. M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842.
18. Handsaker, R. E., Korn, J. M., Nemesh, J. and McCarroll, S. A. (2011) Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat. Genet. 43, 269-276.
19. Zhan, B., Fadista, J., Thomsen, B., Hedegaard, J., Panitz, F. and Bendixen, C. (2011) Global assessment of genomic variation in cattle by genome resequencing and highthroughput genotyping. BMC Genomics. 12, 557.
20. Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T. and Sherry, S. T. (2011) The variant call format and VCFtools. Bioinformatics 27, 2156-2158.
21. Feulner, P. G. D., Chain, F. J. J., Panchal, M., Eizaguirre, C., Kalbe, M., Lenz, T. L., Mundry, M., Samonte, I. E., Stoll, M. and Milinski, M. (2012) Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks. Mol. Ecol. 22, 635-649.
22. Jarrell, V. L., Lewin, H. A., Da, Y. and Wheeler, M. B. (1995) Gene-centromere mapping of bovine DYA, DRB3, and PRL using secondary oocytes and first polar bodies: evidence for four-strand double crossovers between DYA and DRB3. Genomics 27, 33-39.
23. Andersson, L., Lundén, A., Sigurdardottir, S., Davies, C. J. and Rask, L. (1988) Linkage relationships in the bovine MHC region. High recombination frequency between class II subregions. Immunogenetics 27, 273-280.
24. Park, C., Russ, I., Da, Y. and Lewin, H. A. (1995) Genetic mapping of F13A to BTA23 by sperm typing: difference in recombination rate between bulls in the DYA-PRL interval. Genomics 27, 113-118.
25. Paape, T., Zhou, P., Branca, A., Briskine, R., Young, N. and Tiffin, P. (2012) Fine-scale population recombination rates, hotspots, and correlates of recombination in the medicago truncatula genome. Genome Biol. Evol. 4, 726-737.
26. Hedrick, P. W. (2002) Pathogen resistance and genetic variation at MHC loci. Evolution 56, 1902-1908.
27. Zimin, A. V., Kelley, D. R., Roberts, M., Marçais, G., Salzberg, S. L. and Yorke, J. A. (2012) Mis-assembled "segmental duplications" in two versions of the bos taurus genome. PloS One 7, e42680.
28. Partipilo, G., D'Addabbo, P., Lacalandra, G. M., Liu, G. E. and Rocchi, M. (2011) Refinement of Bos taurus sequence assembly based on BAC-FISH experiments. BMC Genomics 12, 639.
29. Alachiotis, N., Stamatakis, A. and Pavlidis, P. (2012) OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets. Bioinformatics 28, 2274-2275.
30. Kim, Y. and Nielsen, R. (2004) Linkage disequilibrium as a signature of selective sweeps. Genetics 167, 1513-1524.
31. Nielsen, R., Williamson, S., Kim, Y., Hubisz, M. J., Clark, A. G. and Bustamante, C. (2005) Genomic scans for selective sweeps using SNP data. Genome Res. 15, 1566-1575.
32. Chen, J. J., Reid, C. E., Band, V. and Androphy, E. J. (1995) Interaction of papillomavirus E6 oncoproteins with a putative calcium-binding protein. Science 269, 529-531.
33. De Groot, N. G., Otting, N., Doxiadis, G. G. M., Balla-Jhagjhoorsingh, S. S., Heeney, J. L., Van Rood, J. J., Gagneux, P. and Bontrop, R. E. (2002) Evidence for an ancient selective sweep in the MHC class I gene repertoire of chimpanzees. Proc. Natl. Acad. Sci. U.S.A. 99, 11748-11753.
34. Bae, Y., Lee, C., Kang, M., Yoon, S., Park, J. and Jean, Y. (2005) Bovine papillomavirus detection from bovine teats using immunohistochemistry and electronmicroscopy. Korean J. Vet. Res. 45, 233-238.
35. Langmead, B. and Salzberg, S. L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods. 9, 357-359.
36. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. and 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079.
37. Browning, S. R. and Browning, B. L. (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Gen. 81, 1084-1097.
38. Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S. and Fitzgerald, S. (2012) Ensembl 2012. Nucl Acids Res. 40, D84-D90.
39. Cingolani, P., Platts, A., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X. and Ruden, D. M. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80-92.
40. Smit, A., Hubley, R. and Green, P. (1996) Repeat Masker Open-3.0. http://www.repeatmasker.org.
41. Friendly, M. (2002) Corrgrams. Am. Stat. 56, 316-324.