Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Lee, Kyung Tai ^a   Chung, Won Hyong ^b   Lee, Sung Yeoun ^c   Choi, Jung Woo ^d   Kim, Jiwoong ^b   Lim, Dajeong ^a   Lee, Seunghwan ^a   Jang, Gul Won ^a   Kim, Bumsoo ^a   Choy, Yun Ho ^a   Liao, Xiaoping ^d   Stothard, Paul ^d   Moore, Stephen S ^d,e   Lee, Sang Heon ^b,f   Ahn, Sungmin ^c   Kim, Namshin ^b,f   Kim, Tae Hun ^a  

^a National Institute of Animal Science   (South Korea)

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

^c Gachon University   (South Korea)

^d UNIVERSITY OF ALBERTA   (Canada)

^e UNIVERSITY OF QUEENSLAND   (Australia)

^f University of Science and Technology (UST)   (South Korea)

Author keywords

Hanwoo; NS SS I; Resequencing; ROH

Indexed keywords

ALDEHYDE OXIDASE; BCL2 RELATED PROTEIN A1; CD5 ANTIGEN; CONNECTIN; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; FATTY ACID BINDING PROTEIN 4; GRANZYME A; ISOCITRATE DEHYDROGENASE 1; MELANOCORTIN 1 RECEPTOR; MONOPHENOL MONOOXYGENASE; RETINOID X RECEPTOR ALPHA; SEMAPHORIN;

ABCC4 GENE; ALS2 GENE; ARTICLE; BCL2L1 GENE; BOLA GENE; BREED DIFFERENCE; CATTLE; CD28 GENE; CD5 GENE; CONTROLLED STUDY; CREB1 GENE; CROSS BREEDING; DISEASE RESISTANCE; FABP4 GENE; FAT CONTENT; FOOD QUALITY; GENE; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC CODE; GENETIC TRAIT; GENETIC VARIABILITY; GENOME ANALYSIS; HOMOZYGOSITY; INDEL MUTATION; MEAT; NONHUMAN; QUANTITATIVE TRAIT LOCUS; RNA SPLICING; SEMA5A GENE; SINGLE NUCLEOTIDE POLYMORPHISM; TTN GENE; ZNF280B GENE;

ANIMALS; CATTLE; GENOMICS; GENOTYPE; HOMOZYGOTE; HYBRIDIZATION, GENETIC; INDEL MUTATION; MOLECULAR SEQUENCE ANNOTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS;

ANIMALIA; BOS; BOS INDICUS;

EID: 84880885023     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-519     Document Type: Article

References (58)

1. Tellam RL, Lemay DG, Van Tassell CP, Lewin HA, Worley KC, Elsik CG. Unlocking the bovine genome. BMC Genomics 2009, 10:193. 10.1186/1471-2164-10-193, 2680899, 19393070.
2. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigo R, et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009, 324(5926):522-528. 2943200, 19390049.
3. Liu Y, Qin X, Song XZ, Jiang H, Shen Y, Durbin KJ, Lien S, Kent MP, Sodeland M, Ren Y, et al. Bos taurus genome assembly. BMC Genomics 2009, 10:180. 10.1186/1471-2164-10-180, 2686734, 19393050.
4. Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, et al. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 2009, 10(4):R42. 10.1186/gb-2009-10-4-r42, 2688933, 19393038.
5. Van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 2008, 5(3):247-252. 10.1038/nmeth.1185, 18297082.
6. Eck SH, Benet-Pages A, Flisikowski K, Meitinger T, Fries R, Strom TM. Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery. Genome Biol 2009, 10(8):R82. 10.1186/gb-2009-10-8-r82, 2745763, 19660108.
7. Kawahara-Miki R, Tsuda K, Shiwa Y, Arai-Kichise Y, Matsumoto T, Kanesaki Y, Oda S, Ebihara S, Yajima S, Yoshikawa H, et al. Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi. BMC Genomics 2011, 12:103. 10.1186/1471-2164-12-103, 3048544, 21310019.
8. Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS. Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 2011, 12:559. 10.1186/1471-2164-12-559, 3229636, 22085807.
9. Gibson J, Morton NE, Collins A. Extended tracts of homozygosity in outbred human populations. Hum Mol Genet 2006, 15(5):789-795. 10.1093/hmg/ddi493, 16436455.
10. Voight BF, Kudaravalli S, Wen X, Pritchard JK. A map of recent positive selection in the human genome. PLoS Biol 2006, 4(3):e72. 10.1371/journal.pbio.0040072, 1382018, 16494531.
11. Weir BS, Cardon LR, Anderson AD, Nielsen DM, Hill WG. Measures of human population structure show heterogeneity among genomic regions. Genome Res 2005, 15(11):1468-1476. 10.1101/gr.4398405, 1310634, 16251456.
12. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 2002, 419(6909):832-837. 10.1038/nature01140, 12397357.
13. Lee C, Pollak EJ. Genetic antagonism between body weight and milk production in beef cattle. J Anim Sci 2002, 80(2):316-321.
14. Han SW. The breed of cattle. Breeds of Livestock 1996, 148-160. Seoul: Sun-Jin publishing, 1.
15. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20(9):1297-1303. 10.1101/gr.107524.110, 2928508, 20644199.
16. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011, 43(5):491-498. 10.1038/ng.806, 3083463, 21478889.
17. Decker JE, Pires JC, Conant GC, McKay SD, Heaton MP, Chen K, Cooper A, Vilkki J, Seabury CM, Caetano AR, et al. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc Natl Acad Sci USA 2009, 106(44):18644-18649. 10.1073/pnas.0904691106, 2765454, 19846765.
18. Marquez B, Ameye G, Vallet CM, Tulkens PM, Poirel HA, Van Bambeke F. Characterization of Abcc4 gene amplification in stepwise-selected mouse J774 macrophages resistant to the topoisomerase II inhibitor ciprofloxacin. PLoS One 2011, 6(12):e28368. 10.1371/journal.pone.0028368, 3230599, 22162766.
19. Schaeren-Wiemers N, Bonnet A, Erb M, Erne B, Bartsch U, Kern F, Mantei N, Sherman D, Suter U. The raft-associated protein MAL is required for maintenance of proper axon-glia interactions in the central nervous system. J Cell Biol 2004, 166(5):731-742. 10.1083/jcb.200406092, 2172435, 15337780.
20. Hu ZL, Fritz ER, Reecy JM. AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Res 2007, 35(Database issue):D604-D609. 1781224, 17135205.
21. Hu ZL, Reecy JM. Animal QTLdb: beyond a repository. A public platform for QTL comparisons and integration with diverse types of structural genomic information. Mamm Genome 2007, 18(1):1-4. 10.1007/s00335-006-0105-8, 17245610.
22. Sasaki Y, Nagai K, Nagata Y, Doronbekov K, Nishimura S, Yoshioka S, Fujita T, Shiga K, Miyake T, Taniguchi Y, et al. Exploration of genes showing intramuscular fat deposition-associated expression changes in musculus longissimus muscle. Anim Genet 2006, 37(1):40-46. 10.1111/j.1365-2052.2005.01380.x, 16441294.
23. Yamada T, Sasaki S, Sukegawa S, Yoshioka S, Takahagi Y, Morita M, Murakami H, Morimatsu F, Fujita T, Miyake T, et al. Association of a single nucleotide polymorphism in titin gene with marbling in Japanese Black beef cattle. BMC Res Notes 2009, 2:78. 10.1186/1756-0500-2-78, 2683863, 19419586.
24. Labeit S, Kolmerer B. Titins: giant proteins in charge of muscle ultrastructure and elasticity. Science 1995, 270(5234):293-296. 10.1126/science.270.5234.293, 7569978.
25. Ku CS, Naidoo N, Teo SM, Pawitan Y. Regions of homozygosity and their impact on complex diseases and traits. Hum Genet 2011, 129(1):1-15. 10.1007/s00439-010-0920-6, 21104274.
26. Weidemann JF, Kaess G, Carrljthers LD. The histology of pre-rigor and post-rigor ox muscle before and after cooking and its relation to tenderness. J Food Sci 1967, 32(1):7-13.
27. Solomon C, White JH, Kremer R. Mitogen-activated protein kinase inhibits 1,25-dihydroxyvitamin D3-dependent signal transduction by phosphorylating human retinoid X receptor alpha. J Clin Invest 1999, 103(12):1729-1735. 10.1172/JCI6871, 408392, 10377179.
28. Lim D, Kim NK, Park HS, Lee SH, Cho YM, Oh SJ, Kim TH, Kim H. Identification of candidate genes related to bovine marbling using protein-protein interaction networks. Int J Biol Sci 2011, 7(7):992-1002. 3164149, 21912507.
29. Huq MD, Tsai NP, Lin YP, Higgins L, Wei LN. Vitamin B6 conjugation to nuclear corepressor RIP140 and its role in gene regulation. Nat Chem Biol 2007, 3(3):161-165. 10.1038/nchembio861, 17277785.
30. Brandes R, Arad R, Bar-Tana J. Inducers of adipose conversion activate transcription promoted by a peroxisome proliferators response element in 3T3-L1 cells. Biochem Pharmacol 1995, 50(11):1949-1951. 10.1016/0006-2952(95)02082-9, 8615877.
31. Kuhn C, Weikard R. An investigation into the genetic background of coat colour dilution in a Charolais x German Holstein F2 resource population. Anim Genet 2007, 38(2):109-113. 10.1111/j.1365-2052.2007.01569.x, 17302792.
32. Abu Safieh L, Aldahmesh MA, Shamseldin H, Hashem M, Shaheen R, Alkuraya H, Al Hazzaa SA, Al-Rajhi A, Alkuraya FS. Clinical and molecular characterisation of Bardet-Biedl syndrome in consanguineous populations: the power of homozygosity mapping. J Med Genet 2010, 47(4):236-241. 10.1136/jmg.2009.070755, 19858128.
33. Collin RW, Safieh C, Littink KW, Shalev SA, Garzozi HJ, Rizel L, Abbasi AH, Cremers FP, den Hollander AI, Klevering BJ, et al. Mutations in C2ORF71 cause autosomal-recessive retinitis pigmentosa. Am J Hum Genet 2010, 86(5):783-788. 10.1016/j.ajhg.2010.03.016, 2869006, 20398884.
34. Harville HM, Held S, Diaz-Font A, Davis EE, Diplas BH, Lewis RA, Borochowitz ZU, Zhou W, Chaki M, MacDonald J, et al. Identification of 11 novel mutations in eight BBS genes by high-resolution homozygosity mapping. J Med Genet 2010, 47(4):262-267. 10.1136/jmg.2009.071365, 3017466, 19797195.
35. Iseri SU, Wyatt AW, Nurnberg G, Kluck C, Nurnberg P, Holder GE, Blair E, Salt A, Ragge NK. Use of genome-wide SNP homozygosity mapping in small pedigrees to identify new mutations in VSX2 causing recessive microphthalmia and a semidominant inner retinal dystrophy. Hum Genet 2010, 128(1):51-60. 10.1007/s00439-010-0823-6, 20414678.
36. Lapunzina P, Aglan M, Temtamy S, Caparros-Martin JA, Valencia M, Leton R, Martinez-Glez V, Elhossini R, Amr K, Vilaboa N, et al. Identification of a frameshift mutation in Osterix in a patient with recessive osteogenesis imperfecta. Am J Hum Genet 2010, 87(1):110-114. 10.1016/j.ajhg.2010.05.016, 2896769, 20579626.
37. Nicolas E, Poitelon Y, Chouery E, Salem N, Levy N, Megarbane A, Delague V. CAMOS, a nonprogressive, autosomal recessive, congenital cerebellar ataxia, is caused by a mutant zinc-finger protein, ZNF592. Eur J Hum Genet 2010, 18(10):1107-1113. 10.1038/ejhg.2010.82, 2987462, 20531441.
38. Pang J, Zhang S, Yang P, Hawkins-Lee B, Zhong J, Zhang Y, Ochoa B, Agundez JA, Voelckel MA, Fisher RB, et al. Loss-of-function mutations in HPSE2 cause the autosomal recessive urofacial syndrome. Am J Hum Genet 2010, 86(6):957-962. 10.1016/j.ajhg.2010.04.016, 3032074, 20560209.
39. Uz E, Alanay Y, Aktas D, Vargel I, Gucer S, Tuncbilek G, von Eggeling F, Yilmaz E, Deren O, Posorski N, et al. Disruption of ALX1 causes extreme microphthalmia and severe facial clefting: expanding the spectrum of autosomal-recessive ALX-related frontonasal dysplasia. Am J Hum Genet 2010, 86(5):789-796. 10.1016/j.ajhg.2010.04.002, 2869009, 20451171.
40. Walsh T, Shahin H, Elkan-Miller T, Lee MK, Thornton AM, Roeb W, Abu Rayyan A, Loulus S, Avraham KB, King MC, et al. Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82. Am J Hum Genet 2010, 87(1):90-94. 10.1016/j.ajhg.2010.05.010, 2896776, 20602914.
41. Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV, Kane JM, Kucherlapati R, Malhotra AK. Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci USA 2007, 104(50):19942-19947. 10.1073/pnas.0710021104, 2148402, 18077426.
42. Nalls MA, Guerreiro RJ, Simon-Sanchez J, Bras JT, Traynor BJ, Gibbs JR, Launer L, Hardy J, Singleton AB. Extended tracts of homozygosity identify novel candidate genes associated with late-onset Alzheimer's disease. Neurogenetics 2009, 10(3):183-190. 10.1007/s10048-009-0182-4, 2908484, 19271249.
43. Yang TL, Guo Y, Zhang LS, Tian Q, Yan H, Papasian CJ, Recker RR, Deng HW. Runs of homozygosity identify a recessive locus 12q21.31 for human adult height. J Clin Endocrinol Metab 2010, 95(8):3777-3782. 10.1210/jc.2009-1715, 2913044, 20466785.
44. Barendse W, Bunch RJ, Thomas MB, Harrison BE. A splice site single nucleotide polymorphism of the fatty acid binding protein 4 gene appears to be associated with intramuscular fat deposition in longissimus muscle in Australian cattle. Anim Genet 2009, 40(5):770-773. 10.1111/j.1365-2052.2009.01913.x, 19466936.
45. Hoashi S, Hinenoya T, Tanaka A, Ohsaki H, Sasazaki S, Taniguchi M, Oyama K, Mukai F, Mannen H. Association between fatty acid compositions and genotypes of FABP4 and LXR-alpha in Japanese black cattle. BMC Genet 2008, 9:84. 2628680, 19077218.
46. Cho S, Park TS, Yoon DH, Cheong HS, Namgoong S, Park BL, Lee HW, Han CS, Kim EM, Cheong IC, et al. Identification of genetic polymorphisms in FABP3 and FABP4 and putative association with back fat thickness in Korean native cattle. BMB Rep 2008, 41(1):29-34. 10.5483/BMBRep.2008.41.1.029, 18304447.
47. Lee SH, van der Werf JH, Park EW, Oh SJ, Gibson JP, Thompson JM. 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 2010, 41(4):442-444.
48. Laliotis GP, Bizelis I, Rogdakis E. Comparative approach of the de novo fatty acid synthesis (Lipogenesis) between ruminant and non ruminant mammalian species: from biochemical level to the main regulatory lipogenic genes. Curr Genomics 2010, 11(3):168-183. 10.2174/138920210791110960, 2878982, 21037855.
49. Lee SH, Kim SC, Choi BH, Lim D, Kim NK, Lee JH, Kim OH, Lee CS, Kim HC, Yang BS. mt-COX1, mt-ND1 and CREBP are indicators of intramuscular fat content in Hanwoo (Korean cattle). Livest Sci 2012, 146:160-167.
50. Yamamoto KK, Gonzalez GA, Biggs WH, Montminy MR. Phosphorylation-induced binding and transcriptional efficacy of nuclear factor CREB. Nature 1988, 334(6182):494-498. 10.1038/334494a0, 2900470.
51. Casimir DA, Ntambi JM. cAMP activates the expression of stearoyl-CoA desaturase gene 1 during early preadipocyte differentiation. J Biol Chem 1996, 271(47):29847-29853. 10.1074/jbc.271.47.29847, 8939924.
52. Wang YH, Bower NI, Reverter A, Tan SH, De Jager N, Wang R, McWilliam SM, Cafe LM, Greenwood PL, Lehnert SA. Gene expression patterns during intramuscular fat development in cattle. J Anim Sci 2009, 87(1):119-130.
53. Dooley KA, Bennett MK, Osborne TF. A critical role for CREB as a co-activator in sterol regulated transcription of HMG CoA synthase promoter. J Biol Chem 1999, 274:5285-5291. 10.1074/jbc.274.9.5285, 10026135.
54. Homer N, Merriman B, Nelson SF. BFAST: an alignment tool for large scale genome resequencing. PLoS One 2009, 4(11):e7767. 10.1371/journal.pone.0007767, 2770639, 19907642.
55. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009, 4(7):1073-1081.
56. Seelow D, Schuelke M, Hildebrandt F, Nurnberg P. HomozygosityMapper--an interactive approach to homozygosity mapping. Nucleic Acids Res 2009, 37(Web Server issue):W593-W599. 2703915, 19465395.
57. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, O'Connell J, Moore SS, Smith TP, Sonstegard TS, et al. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 2009, 4(4):e5350. 10.1371/journal.pone.0005350, 2669730, 19390634.
58. Nikitin A, Egorov S, Daraselia N, Mazo I. Pathway studio-the analysis and navigation of molecular networks. Bioinformatics 2003, 19(16):2155. 10.1093/bioinformatics/btg290, 14594725.