Browse > Article
http://dx.doi.org/10.14348/molcells.2016.0148

Evolutionary Analyses of Hanwoo (Korean Cattle)-Specific Single-Nucleotide Polymorphisms and Genes Using Whole-Genome Resequencing Data of a Hanwoo Population  

Lee, Daehwan (Department of Stem Cell and Regenerative Biology, Konkuk University)
Cho, Minah (Department of Stem Cell and Regenerative Biology, Konkuk University)
Hong, Woon-young (Department of Stem Cell and Regenerative Biology, Konkuk University)
Lim, Dajeong (National Institute of Animal Science)
Kim, Hyung-Chul (National Institute of Animal Science)
Cho, Yong-Min (National Institute of Animal Science)
Jeong, Jin-Young (National Institute of Animal Science)
Choi, Bong-Hwan (National Institute of Animal Science)
Ko, Younhee (Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine)
Kim, Jaebum (Department of Stem Cell and Regenerative Biology, Konkuk University)
Publication Information
Molecules and Cells / v.39, no.9, 2016 , pp. 692-698 More about this Journal
Abstract
Advances in next generation sequencing (NGS) technologies have enabled population-level studies for many animals to unravel the relationships between genotypic differences and traits of specific populations. The objective of this study was to perform evolutionary analysis of single nucleotide polymorphisms (SNP) in genes of Korean native cattle Hanwoo in comparison to SNP data from four other cattle breeds (Jersey, Simmental, Angus, and Holstein) and four related species (pig, horse, human, and mouse) obtained from public databases through NGS-based resequencing. We analyzed population structures and differentiation levels for the five cattle breeds and estimated species-specific SNPs with their origins and phylogenetic relationships among species. In addition, we identified Hanwoo-specific genes and proteins, and determined distinct changes in protein-protein interactions among five species (cattle, pig, horse, human, mouse) in the STRING network database by additionally considering indirect protein interactions. We found that the Hanwoo population was clearly different from the other four cattle populations. There were Hanwoo-specific genes related to its meat trait. Protein interaction rewiring analysis also confirmed that there were Hanwoo-specific protein-protein interactions that might have contributed to its unique meat quality.
Keywords
evolutionary analyses; Hanwoo; interaction network; single nucleotide polymorphism; resequencing;
Citations & Related Records
Times Cited By KSCI : 3  (Citation Analysis)
연도 인용수 순위
1 Ai, H., Fang, X., Yang, B., Huang, Z., Chen, H., Mao, L., Zhang, F., Zhang, L., Cui, L., He, W., et al. (2015). Adaptation and possible ancient interspecies introgression in pigs identified by wholegenome sequencing. Nat. Genet. 47, 217-225.   DOI
2 Alexander, D.H., Novembre, J., and Lange, K. (2009). Fast modelbased estimation of ancestry in unrelated individuals. Genome Res. 19, 1655-1664.   DOI
3 Begun, D.J., Holloway, A.K., Stevens, K., Hillier, L.W., Poh, Y.P., Hahn, M.W., Nista, P.M., Jones, C.D., Kern, A.D., Dewey, C.N., et al. (2007). Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol. 5, e310.   DOI
4 Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M.F., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J.F., et al. (2012). Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res. 22, 778-790.   DOI
5 Cho, M., Lee, D., Hong, W.Y., Lee, J., and Kim, J. (2015). evoSNPI:a pipeline for the evolutionary analysis of the origin of single nucleotide polymorphisms and the change of protein interactions. In Proceedings of the 6th Computational Systems-Biology and Bioinformatics (CSBio2015) (Bankok, Tailand), pp. 17-21.
6 Choi, J.W., Lee, K.T., Liao, X., Stothard, P., An, H.S., Ahn, S., Lee, S., Lee, S.Y., Moore, S.S., and Kim, T.H. (2013). Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle. Mamm Genome 24, 151-163.   DOI
7 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
8 Choi, J.W., Choi, B.H., Lee, S.H., Lee, S.S., Kim, H.C., Yu, D., Chung, W.H., Lee, K.T., Chai, H.H., Cho, Y.M., et al. (2015). Whole-genome resequencing analysis of Hanwoo and Yanbian cattle to identify genome-wide SNPs and signatures of selection. Mol. Cells 38, 466-473.   DOI
9 Choi, J.W., Chung, W.H., Lim, K.S., Lim, W.J., Choi, B.H., Lee, S.H., Kim, H.C., Lee, S.S., Cho, E.S., Lee, K.T., et al. (2016). Copy number variations in Hanwoo and Yanbian cattle genomes using the massively parallel sequencing data. Gene 589, 36-42.   DOI
10 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 (Austin) 6, 80-92.   DOI
11 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
12 Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., et al. (2011). The variant call format and VCFtools. Bioinformatics 27, 2156-2158.   DOI
13 Decker, J.E., Pires, J.C., Conant, G.C., McKay, S.D., Heaton, M.P., Chen, K., Cooper, A., Vilkki, J., Seabury, C.M., Caetano, A.R., et al. (2009). Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc. Natl. Acad. Sci. USA 106, 18644-18649.   DOI
14 Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., De Moor, B., Brazma, A., and Huber, W. (2005). BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21, 3439-3440.   DOI
15 Genomes Project, C., Abecasis, G.R., Altshuler, D., Auton, A., Brooks, L.D., Durbin, R.M., Gibbs, R.A., Hurles, M.E., and McVean, G.A. (2010). A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073.   DOI
16 Gou, X., Wang, Z., Li, N., Qiu, F., Xu, Z., Yan, D., Yang, S., Jia, J., Kong, X., Wei, Z., et al. (2014). Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to highaltitude hypoxia. Genome Res. 24, 1308-1315.   DOI
17 International HapMap, C. (2003). The international HapMap project. Nature 426, 789-796.   DOI
18 Hayes, B. (2012). 1000 bull genomes consortium project. In Plant and Animal Genome XX Conference (January 14-18, 2012) (Plant and Animal Genome).
19 Heberle, H., Meirelles, G.V., da Silva, F.R., Telles, G.P., and Minghim, R. (2015). InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics 16, 169.   DOI
20 Hedges, S.B., Marin, J., Suleski, M., Paymer, M., and Kumar, S. (2015). Tree of life reveals clock-like speciation and diversification. Mol. Biol. Evol. 32, 835-845.   DOI
21 Jeremiah, L.E., Dugan, M.E.R., Aalhus, J.L., and Gibson, L.L. (2003). Assessment of the relationship between chemical components and palatability of major beef muscles and muscle groups. Meat Sci. 65, 1013-1019.   DOI
22 Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J., et al. (2003). The UCSC Genome Browser Database. Nucleic Acids Res. 31, 51-54.   DOI
23 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
24 Kim, T.H., Lee, K.M., and Lee, S.U.(2008). Generative image segmentation using randon walks with estart. In 10th European Conference on Computer vision, P.T. David Forsyth, Andrew Zisserman, ed. (Marseille, France, Springer Berlin Heidelberg), pp. 264-275.
25 Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359.   DOI
26 Kinsella, R.J., Kahari, A., Haider, S., Zamora, J., Proctor, G., Spudich, G., Almeida-King, J., Staines, D., Derwent, P., Kerhornou, A., et al. (2011). Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford) 2011, bar030.
27 Kopelman, N.M., Mayzel, J., Jakobsson, M., Rosenberg, N.A., and Mayrose, I. (2015). Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol. Ecol. Resour. 15, 1179-1191.   DOI
28 Kriventseva, E.V., Tegenfeldt, F., Petty, T.J., Waterhouse, R.M., Simao, F.A., Pozdnyakov, I.A., Ioannidis, P., and Zdobnov, E.M. (2015). OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. Nucleic Acids Res. 43, D250-256.   DOI
29 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). Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity. BMC Genomics 14, 519.   DOI
30 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, 2.   DOI
31 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
32 Li, Z., Yang, C., Jin, B., Yu, M., Liu, K., Sun, M., and Zhan, M. (2015). Enabling big geoscience data analytics with a cloudbased, MapReduce-enabled and service-oriented workflow framework. PLoS One 10, e0116781.   DOI
33 Metzker, M.L. (2010). Sequencing technologies - the next generation. Nat. Rev. Genet. 11, 31-46.   DOI
34 Liao, X., Peng, F., Forni, S., McLaren, D., Plastow, G., and Stothard, P. (2013). Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection. Genome / National Research Council Canada = Genome / Conseil national de recherches Canada 56, 592-598.   DOI
35 Lim, D., Chai, H.H., Lee, S.H., Cho, Y.M., Choi, J.W., and Kim, N.K. (2015). Gene expression patterns associated with peroxisome proliferator-activated receptor (PPAR) signaling in the longissimus dorsi of Hanwoo (Korean Cattle). Asian-Australas J. Anim. Sci. 28, 1075-1083.   DOI
36 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
37 Mi, H., Lazareva-Ulitsky, B., Loo, R., Kejariwal, A., Vandergriff, J., Rabkin, S., Guo, N., Muruganujan, A., Doremieux, O., Campbell, M.J., et al. (2005). The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 33, D284-288.   DOI
38 Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A., Bender, D., Maller, J., Sklar, P., de Bakker, P.I., Daly, M.J., et al. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575.   DOI
39 Ramey, H.R., Decker, J.E., McKay, S.D., Rolf, M.M., Schnabel, R.D., and Taylor, J.F. (2013). Detection of selective sweeps in cattle using genome-wide SNP data. BMC Genomics 14, 1-18.   DOI
40 Sherry, S.T., Ward, M.-H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M., and Sirotkin, K. (2001). dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308-311.   DOI
41 Wang, K., Li, M., and Hakonarson, H. (2010). ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164.   DOI
42 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
43 Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K.P., et al. (2014). STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43, D447-D452.
44 Takahashi, K., and Nei, M. (2000). Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol. Biol. Evol. 17, 1251-1258.   DOI
45 Waterhouse, R.M., Tegenfeldt, F., Li, J., Zdobnov, E.M., and Kriventseva, E.V. (2013). OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res. 41, D358-365.   DOI
46 Yang, J., Lee, S.H., Goddard, M.E., and Visscher, P.M. (2011). GCTA: a tool for genome-wide complex trait analysis. Am J. Hum. Genet. 88, 76-82.   DOI