Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection |
Choi, Jung-Woo
(Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration)
Choi, Bong-Hwan (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration) Lee, Seung-Hwan (Division of Animal and Dairy Science, Chung Nam National University) Lee, Seung-Soo (Animal Genetic and Breeding Division, National Institute of Animal Science) Kim, Hyeong-Cheol (Hanwoo Experiment Station, National Institute of Animal Science, RDA) Yu, Dayeong (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration) Chung, Won-Hyong (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration) Lee, Kyung-Tai (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration) Chai, Han-Ha (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration) Cho, Yong-Min (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration) Lim, Dajeong (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration) |
1 | Cheng, P. (1984). Livestock breeds of China. FAO Animal Production and Health Paper 46. |
2 | Choi, J.W., Chung, W.H., Lee, K.T., Lee, J.W., Jung, K.S., Cho, Y., Kim, N., and Kim, T.H. (2013a). Whole genome resequencing of Heugu (Korean Black Cattle) for the genome-wide SNP discovery. Korean J. Food Sci. An. 33, 715-722. DOI ScienceOn |
3 | Choi, J.W., Liao, X., Park, S., Jeon, H.J., Chung, W.H., Stothard, P., Park, Y.S., Lee, J.K., Lee, K.T., Kim, S.H., et al. (2013b). Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels. Mol. Cells 36, 203-211. DOI |
4 | Choi, J.W., Liao, X., Stothard, P., Chung, W.H., Jeon, H.J., Miller, S.P., Choi, S.Y., Lee, J.K., Yang, B., Lee, K.T., et al. (2014). Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing. PLoS One 9, e101127. DOI ScienceOn |
5 | Cingolani, P., Platts, A., Wang le, L., 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. DOI |
6 | Dadi, H., Lee, S.H., Lee, S.S., Park, C., and Kim, K.S. (2014). Interand intra-population genetic divergence of East Asian cattle populations: focusing on Korean cattle. Genes Genom. 36, 261-265. DOI ScienceOn |
7 | Daetwyler, H.D., Capitan, A., Pausch, H., Stothard, P., van Binsbergen, R., Brondum, R.F., Liao, X., Djari, A., Rodriguez, S.C., Grohs, C., et al. (2014). Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat. Genet. 46, 858-865. DOI ScienceOn |
8 | Eck, S.H., Benet-Pages, A., Flisikowski, K., Meitinger, T., Fries, R., and Strom, T.M. (2009). Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery. Genome Biol. 10, R82. DOI ScienceOn |
9 | Elsik, C.G., Tellam, R.L., Worley, K.C., Gibbs, R.A., Muzny, D.M., Weinstock, G.M., Adelson, D.L., Eichler, E.E., et al. (2009). The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324, 522-528. DOI ScienceOn |
10 | Food and Agriculture Organization (FAO). (2014). Domestic Animal Diversity Information Service (DAD-IS). http://dad.fao.org/, Accessed September 5, 2014. |
11 | Ito, M., Nakano, T., Erdodi, F., and Hartshorne, D.J. (2004). Myosin phosphatase: structure, regulation and function. Mol. Cell. Biochem. 259, 197-209. DOI |
12 | Fujimoto, A., Nakagawa, H., Hosono, N., Nakano, K., Abe, T., Boroevich, K.A., Nagasaki, M., Yamaguchi, R., Shibuya, T., Kubo, M., et al. (2010). Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat. Genet. 42, 931-936. DOI ScienceOn |
13 | Hu, Z.L., Park, C.A., Wu, X.L., and Reecy, J.M. (2013). Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Res. 41, D871-879. DOI |
14 | Huang da, W., Sherman, B.T., and Lempicki, R.A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57. DOI |
15 | Kawahara-Miki, R., Tsuda, K., Shiwa, Y., Arai-Kichise, Y., Matsumoto, T., Kanesaki, Y., Oda, S., Ebihara, S., Yajima, S., Yoshikawa, H., et al. (2011). Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi. BMC Genomics 12, 103. DOI ScienceOn |
16 | Kim, B.J., Kim, Y.H., Cho, W.H., Bok, K.K., Kim, B.J., and Kang, C.M. (1981). Yanbian Cattle. Yanbian People Publishing House, 1-5. |
17 | Kozova, M., Kalac, P., and Pelikanova, T. (2009). Changes in the content of biologically active polyamines during beef loin storage and cooking. Meat Sci. 81, 607-611. DOI ScienceOn |
18 | Lee, K.T., Chung, W.H., Lee, S.Y., Choi, J.W., Kim, J., Lim, D., Lee, S., Jang, G.W., Kim, B., Choy, Y.H., et al. (2013). Wholegenome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity. BMC Genomics 14, 519. DOI ScienceOn |
19 | Li, H., and Durbin, R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595. DOI ScienceOn |
20 | Lee, S.H., Park, B.H., Sharma, A., Dang, C.G., Lee, S.S., Choi, T.J., Choy, Y.H., Kim, H.C., Jeon, K.J., Kim, S.D., et al. (2014). Hanwoo cattle: origin, domestication, breeding strategies and genomic selection. J. Anim. Sci. Technol. 56. |
21 | Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and Genome Project Data Processing, S. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079. DOI ScienceOn |
22 | Liu, M., Nauta, A., Francke, C., and Siezen, R.J. (2008). Comparative genomics of enzymes in flavor-forming pathways from amino acids in lactic acid bacteria. Appl. Environ. Microbiol. 74, 4590-4600. DOI ScienceOn |
23 | Liu, Y., Qin, X., Song, X.Z., Jiang, H., Shen, Y., Durbin, K.J., Lien, S., Kent, M.P., Sodeland, M., Ren, Y., et al. (2009). Bos taurus genome assembly. BMC Genomics 10, 180. DOI ScienceOn |
24 | Lu, D., Miller, S., Sargolzaei, M., Kelly, M., Vander Voort, G., Caldwell, T., Wang, Z., Plastow, G., and Moore, S. (2013). Genome-wide association analyses for growth and feed efficiency traits in beef cattle. J. Anim. Sci. 91, 3612-3633. DOI ScienceOn |
25 | Matsumura, F., and Hartshorne, D.J. (2008). Myosin phosphatase target subunit: Many roles in cell function. Biochem. Biophys. Res. Commun. 369, 149-156. DOI ScienceOn |
26 | Mishra, C., Palai, T.K., Sarangi, L.N., Prusty, B.R. and Maharana, B.R. (2013). Candidate gene markers for sperm quality and fertility in bulls. Veterinary World 6, 905-910. DOI |
27 | McClure, M.C., Morsci, N.S., Schnabel, R.D., Kim, J.W., Yao, P., Rolf, M.M., McKay, S.D., Gregg, S.J., Chapple, R.H., Northcutt, S.L., et al. (2010). A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle. Anim. Genet. 41, 597-607. DOI ScienceOn |
28 | McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010). The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303. DOI ScienceOn |
29 | Merico, D., Isserlin, R., Stueker, O., Emili, A., and Bader, G.D. (2010). Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One 5, e13984. DOI ScienceOn |
30 | Nalaila, S.M., Stothard, P., Moore, S.S., Li, C., and Wang, Z. (2012). Whole-genome QTL scan for ultrasound and carcass merit traits in beef cattle using Bayesian shrinkage method. J. Anim. Breed. Genet. 129, 107-119. DOI ScienceOn |
31 | Norman, H., Powell, R., Wright, J., and Sattler, C. (2003). Timeliness and effectiveness of progeny testing through artificial insemination. J. Dairy Sci. 86, 1513-1525. DOI ScienceOn |
32 | Ostermeier, G.C., Sargeant, G.A., Yandell, B.S., Evenson, D.P., and Parrish, J.J. (2001). Relationship of bull fertility to sperm nuclear shape. J. Androl. 22, 595-603. |
33 | Rubin, C.J., Zody, M.C., Eriksson, J., Meadows, J.R., Sherwood, E., Webster, M.T., Jiang, L., Ingman, M., Sharpe, T., Ka, S., et al. (2010). Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464, 587-591. DOI ScienceOn |
34 | Peters, S.O., Kizilkaya, K., Garrick, D.J., Fernando, R.L., Reecy, J.M., Weaber, R.L., Silver, G.A., and Thomas, M.G. (2012). Bayesian genome-wide association analysis of growth and yearling ultrasound measures of carcass traits in Brangus heifers. J. Anim. Sci. 90, 3398-3409. DOI |
35 | Qanbari, S., Pausch, H., Jansen, S., Somel, M., Strom, T.M., Fries, R., Nielsen, R., and Simianer, H. (2014). Classic selective sweeps revealed by massive sequencing in cattle. PLoS Genet. 10, e1004148. DOI |
36 | Quang, N., and Zarkadas, C.G. (1989). Comparison of the amino acid composition and connective tissue protein contents of selected bovine skeletal muscles. J. Agric. Food Chem. 37, 1279-1286. DOI |
37 | Rubin, C.J., Megens, H.J., Martinez Barrio, A., Maqbool, K., Sayyab, S., Schwochow, D., Wang, C., Carlborg, O., Jern, P., Jorgensen, C.B., et al. (2012). Strong signatures of selection in the domestic pig genome. Proc. Nati. Acad. Sci. USA 109, 19529-19536. DOI ScienceOn |
38 | Stothard, P., Choi, J.W., Basu, U., Sumner-Thomson, J.M., Meng, Y., Liao, X., and Moore, S.S. (2011). Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12, 559. DOI |
39 | Sun, W.X., Wang, H.H., Jiang, B.C., Zhao, Y.Y., Xie, Z.R., Xiong, K., and Chen, J. (2013). Global comparison of gene expression between subcutaneous and intramuscular adipose tissue of mature Erhualian pig. Genet. Mol. Res. 12, 5085-5101. DOI ScienceOn |
40 | Utsunomiya, Y.T., O'Brien, A.M.P., Sonstegard, T.S., Van Tassell, C.P., do Carmo, A.S., Meszaros, G., Soelkner, J., and Garcia, J.F. (2013). Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods. PLoS One 8, e64280. DOI |
41 | Wasseriwan, A. (1979) Symposium on meat flavor chemial basis for meat flavor:A Review. J. Food Sci. 44, 6-11. DOI |
42 | Zhang, X., Ma, D., Caruso, M., Lewis, M., Qi, Y., and Yi, Z. (2014). Quantitative phosphoproteomics reveals novel phosphorylation events in insulin signaling regulated by protein phosphatase 1 regulatory subunit 12A. J. Proteomics 109, 63-75. DOI ScienceOn |
43 | Zimin, A.V., Delcher, A.L., Florea, L., Kelley, D.R., Schatz, M.C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C.P., Sonstegard, T.S., et al. (2009). A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 10, R42. DOI ScienceOn |