Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing

PLoS ONE

Volumn 9, Issue 7, 2014, Pages

  Choi, Jung Woo ^a,d   Liao, Xiaoping ^b   Stothard, Paul ^b   Chung, Won Hyong ^c   Jeon, Heoyn Jeong ^d   Miller, Stephen P ^a   Choi, So Young ^e   Lee, Jeong Koo ^e   Yang, Bokyoung ^f   Lee, Kyung Tai ^d   Han, Kwang Jin ^g   Kim, Hyeong Cheol ^d   Jeong, Dongkee ^h   Oh, Jae Don ⁱ   Kim, Namshin ^c   Kim, Tae Hun ^d   Lee, Hak Kyo ⁱ   Lee, Sung Jin ^e  

^a UNIVERSITY OF GUELPH   (Canada)

^b UNIVERSITY OF ALBERTA   (Canada)

^c Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^d National Institute of Animal Science   (South Korea)

^e Kangwon National University   (South Korea)

^f Theragen BiO Institute   (South Korea)

^g National Agricultural Cooperative Federation   (South Korea)

^h Jeju National University   (South Korea)

ⁱ Hankyong National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ARTIFICIAL INSEMINATION; CATTLE; CONTROLLED STUDY; COPY NUMBER VARIATION; GENE DELETION; GENE INSERTION; GENE SEQUENCE; GENETIC TRAIT; GENOME ANALYSIS; GEOGRAPHIC DISTRIBUTION; HANWOO CATTLE; HOLSTEIN CATTLE; HOMOZYGOSITY; JEJU HEUGU CATTLE; KOREAN (PEOPLE); NONHUMAN; PHENOTYPIC VARIATION; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; BOVINE; BREEDING; GENETICS; GENOME; GENOMICS; HIGH THROUGHPUT SEQUENCING; HOMOZYGOTE; INDEL MUTATION; PHENOTYPE; PROCEDURES; SOUTH KOREA;

ANIMALS; BREEDING; CATTLE; DNA COPY NUMBER VARIATIONS; GENOME; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOMOZYGOTE; INDEL MUTATION; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; REPUBLIC OF KOREA;

EID: 84903778941     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0101127     Document Type: Article

References (50)

1. Jo C, Cho SH, Chang J, Nam KC (2012) Keys to production and processing of Hanwoo beef: A perspective of tradition and science. Anim Frontiers 2:32-38.
2. Food and Agriculture Organization (2012) Domestic Animal Diversity Information Service (DAD-IS). Available: http://dad.fao.org/. Accessed 2013 April 21.
3. National Institute of Animal Science (2012) The status of local livestock breeds in Korea, registered in DAD-IS. Available: http://www.nias.go.kr/. Accessed 2013 April 21.
4. Choi TJ (2009) Establishment of phylogenomic characteristics for Korean traditional cattle breeds (Hanwoo, Korean brindle and black). Doctoral Thesis. Jeon-buk National University. Available: http://www.riss.kr/. Accessed 2013 April 21.
5. National Institute of Animal Science (NIAS) (2011) Annual report for Hanwoo genetic evaluation. In: Annual report for livestock improvement in 2010. Available: http://www.nias.go.kr/. Accessed 2013 April 21.
6. Ministry for Food, Agriculture Forestry and Fisheries (2013) 2012 Dairy Herd Improvement annual report in Korea, Republic of Korea. Available: http://rd.dcic.co.kr/. Accessed 2013 April 21.
7. Bovine Genome S, Analysis C, Elsik CG, Tellam RL, Worley KC, et al. (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324: 522-528.
8. Bovine HapMap C, Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, et al. (2009) Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324: 528-532.
9. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, et al. (2009) Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4: e5350.
10. Barendse W, Harrison BE, Bunch RJ, Thomas MB, Turner LB (2009) Genome wide signatures of positive selection: the comparison of independent samples and the identification of regions associated to traits. BMC Genomics 10: 178.
11. Qanbari S, Gianola D, Hayes B, Schenkel F, Miller S, et al. (2011) Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics 12: 318.
12. Kolbehdari D, Wang Z, Grant JR, Murdoch B, Prasad A, et al. (2009) A whole genome scan to map QTL for milk production traits and somatic cell score in Canadian Holstein bulls. J Anim Breed Genet 126: 216-227.
13. Sherman EL, Nkrumah JD, Moore SS (2010) Whole genome single nucleotide polymorphism associations with feed intake and feed efficiency in beef cattle. J Anim Sci 88: 16-22.
14. Bolormaa S, Hayes BJ, Savin K, Hawken R, Barendse W, et al. (2011) Genomewide association studies for feedlot and growth traits in cattle. J Anim Sci 89: 1684-1697.
15. Jiang L, Liu J, Sun D, Ma P, Ding X, et al. (2010) Genome wide association studies for milk production traits in Chinese Holstein population. PLoS One 5: e13661.
16. Eck SH, Benet-Pages A, Flisikowski K, Meitinger T, Fries R, et al. (2009) Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery. Genome Biol 10: R82.
17. Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, et al. (2011) Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12: 559.
18. Kawahara-Miki R, Tsuda K, Shiwa Y, Arai-Kichise Y, Matsumoto T, et al. (2011) Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi. BMC Genomics 12: 103.
19. Lee KT, Chung WH, Lee SY, Choi JW, Kim J, et al. (2013) Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity. BMC Genomics 14: 519.
20. Choi JW, Liao X, Park S, Jeon HJ, Chung WH, et al. (2013) Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels. Mol Cells 36: 203-211.
21. Bae JS, Cheong HS, Kim LH, NamGung S, Park TJ, et al. (2010) Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genomics 11: 232.
22. Hou Y, Liu GE, Bickhart DM, Cardone MF, Wang K, et al. (2011) Genomic characteristics of cattle copy number variations. BMC Genomics 12: 127.
23. Jiang L, Jiang J, Wang J, Ding X, Liu J, et al. (2012) Genome-wide identification of copy number variations in Chinese Holstein. PLoS One 7: e48732.
24. Hou Y, Bickhart DM, Hvinden ML, Li C, Song J, et al. (2012) Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. BMC Genomics 13: 376.
25. Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, et al. (2012) Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res 22: 778-790.
26. Choi JW, Lee KT, Liao X, Stothard P, An HS, et al. (2013) Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle. Mamm Genome 24: 151-163.
27. Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, et al. (2009) A wholegenome assembly of the domestic cow, Bos taurus. Genome Biol 10: R42.
28. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
29. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303.
30. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
31. Grant JR, Arantes AS, Liao X, Stothard P (2011) In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. Bioinformatics 27: 2300-2301.
32. Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2012) Ensembl 2012. Nucleic Acids Res 40: D84-90.
33. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 40: D13-25.
34. UniProt C (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res 41: D43-47.
35. Xie C, Tammi MT (2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10: 80.
36. Haider S, Ballester B, Smedley D, Zhang J, Rice P, et al. (2009) BioMart Central Portal-unified access to biological data. Nucleic Acids Res 37: W23-27.
37. Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38: W64-70.
38. Dadi H, Lee SH, Jung KS, Choi JW, Ko MS, et al. (2012) Effect of population reduction on mtDNA diversity and demographic history of Korean Cattle populations. Asian Austral J Anim 25: 1223-1228.
39. Genomes Project C, Abecasis GR, Auton A, Brooks LD, DePristo MA, et al. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
40. Fujimoto A, Nakagawa H, Hosono N, Nakano K, Abe T, et al. (2010) Wholegenome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet 42: 931-936.
41. Merchen NR, Titgemeyer EC (1992) Manipulation of amino acid supply to the growing ruminant. J Anim Sci 70: 3238-3247.
42. Liao SF, Vanzant ES, Harmon DL, McLeod KR, Boling JA, et al. (2009) Ruminal and abomasal starch hydrolysate infusions selectively decrease the expression of cationic amino acid transporter mRNA by small intestinal epithelia of forage-fed beef steers. J Dairy Sci 92: 1124-1135.
43. Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, et al. (2010) Analysis of copy number variations among diverse cattle breeds. Genome Res 20: 693-703.
44. Seo K, Mohanty TR, Choi T, Hwang I (2007) Biology of epidermal and hair pigmentation in cattle: a mini-review. Vet Dermatol 18: 392-400. (Pubitemid 350076182)
45. Klungland H, Vage DI, Gomez-Raya L, Adalsteinsson S, Lien S (1995) The role of melanocyte-stimulating hormone (MSH) receptor in bovine coat color determination. Mamm Genome 6: 636-639.
46. Iizuka T, Sasaki M, Oishi K, Uemura S, Koike M (1998) The presence of nitric oxide synthase in the mammary glands of lactating rats. Pediatr Res 44: 197-200. (Pubitemid 28347896)
47. Zaragoza R, Miralles VJ, Rus AD, Garcia C, Carmena R, et al. (2005) Weaning induces NOS-2 expression through NF-kappaB modulation in the lactating mammary gland: importance of GSH. Biochem J 391: 581-588. (Pubitemid 41634784)
48. Oakes SR, Rogers RL, Naylor MJ, Ormandy CJ (2008) Prolactin regulation of mammary gland development. J Mammary Gland Biol Neoplasia 13: 13-28.
49. Zaragoza R, Bosch A, Garcia C, Sandoval J, Serna E, et al. (2010) Nitric oxide triggers mammary gland involution after weaning: remodelling is delayed but not impaired in mice lacking inducible nitric oxide synthase. Biochem J 428: 451-462.
50. Mc Parland S, Kearney JF, Rath M, Berry DP (2007) Inbreeding effects on milk production, calving performance, fertility, and conformation in Irish Holstein-Friesians. J Dairy Sci 90: 4411-4419. (Pubitemid 350045219)