Runs of homozygosity and distribution of functional variants in the cattle genome

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Zhang, Qianqian ^a,b   Guldbrandtsen, Bernt ^a   Bosse, Mirte ^b   Lund, Mogens S ^a   Sahana, Goutam ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Cattle; Genome sequencing; Inbreeding; Polymorphisms; Runs of homozygosity

Indexed keywords

ARTICLE; AUTOSOME; BOVINE; CATTLE BREED; CONTROLLED STUDY; GENE FREQUENCY; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOMICS; HETEROZYGOSITY; HIGH THROUGHPUT SEQUENCING; HOLSTEIN CATTLE; HOMOZYGOSITY; INBREEDING; JERSEY CATTLE; NEW RED DANISH DAIRY CATTLE; NONHUMAN; OLD RED DANISH DAIRY CATTLE; POPULATION GENETICS; RUNS OF HOMOZYGOSITY; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION REGULATION; ALLELE; ANIMAL; BREEDING; GENETICS; GENOTYPE; HOMOZYGOTE; HUMAN; HUMAN GENOME;

BOS;

ALLELES; ANIMALS; BREEDING; CATTLE; GENETICS, POPULATION; GENOME, HUMAN; GENOTYPE; HOMOZYGOTE; HUMANS; INBREEDING; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84937717009     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1715-x     Document Type: Article

References (57)

1. Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME. Invited review: Genomic selection in dairy cattle: progress and challenges (vol 92, pg 433, 2009). J Dairy Sci. 2009;92(3):1313-3.
2. Brade W, Brade E. Breeding History of German Holstein Cattle. Ber Landwirtsch 2013, 91(2). http://dx.doi.org/10.12767/buel.v91i2.25.g70 .
3. Christensen LG. Cattle-Breeding after 1992. Zuchtungskunde. 1989;61(6):428-39.
4. Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci U S A. 2005;102(44):15942-7.
5. Wright S. Systems of mating. II. The effects of inbreeding on the genetic composition of a population. Genetics. 1921;6(2):124-43.
6. Sorensen AC, Sorensen MK, Berg P. Inbreeding in Danish dairy cattle breeds. J Dairy Sci. 2005;88(5):1865-72.
7. Bjelland DW, Weigel KA, Vukasinovic N, Nkrumah JD. Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. J Dairy Sci. 2013;96(7):4697-706.
8. Nomura T, Honda T, Mukai F. Inbreeding and effective population size of Japanese Black cattle. J Anim Sci. 2001;79(2):366-70.
9. Miglior F, Muir BL, Van Doormaal BJ. Selection indices in Holstein cattle of various countries. J Dairy Sci. 2005;88(3):1255-63.
10. Gonzalez-Recio O, de Maturana EL, Gutierrez JP. Inbreeding depression on female fertility and calving ease in Spanish dairy cattle. J Dairy Sci. 2007;90(12):5744-52.
11. Freyer G, Hernandez-Sanchez J, Cassell BG. A note on inbreeding in dairy cattle breeding. Arch Tierzucht. 2005;48(2):130-7.
12. 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.
13. Miglior F, Szkotnicki B, Burnside EB. Analysis of Levels of Inbreeding and Inbreeding Depression in Jersey Cattle. J Dairy Sci. 1992;75(4):1112-8.
14. Weigel K. Controlling inbreeding in modern dairy breeding programs. Adv Dairy Technol. 2006;18:263-74.
15. Bosse M, Megens HJ, Madsen O, Paudel Y, Frantz LA, Schook LB, et al. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLoS Genet. 2012;8(11):e1003100.
16. Pusey A, Wolf M. Inbreeding avoidance in animals. Trends Ecol Evol. 1996;11(5):201-6.
17. Koenig S, Simianer H. Approaches to the management of inbreeding and relationship in the German Holstein dairy cattle population. Livest Sci. 2006;103(1-2):40-53.
18. Margolin S, Bartlett JW. The Influence of Inbreeding Upon the Weight and Size of Dairy Cattle. J Anim Sci. 1945;4(1):3-12.
19. Purfield DC, Berry DP, McParland S, Bradley DG. Runs of homozygosity and population history in cattle. BMC Genet. 2012;13.
20. Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV, Kane JM, et al. Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci U S A. 2007;104(50):19942-7.
21. Nalls MA, Guerreiro RJ, Simon-Sanchez J, Bras JT, Traynor BJ, Gibbs JR, et al. Extended tracts of homozygosity identify novel candidate genes associated with late-onset Alzheimer's disease. Neurogenetics. 2009;10(3):183-90.
22. Charlesworth B, Morgan MT, Charlesworth D. The Effect of Deleterious Mutations on Neutral Molecular Variation. Genetics. 1993;134(4):1289-303.
23. Lohmueller KE, Albrechtsen A, Li YR, Kim SY, Korneliussen T, Vinckenbosch N, et al. Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome. PLoS Genetics 2011, 7(10). doi: 10.1371/journal.pgen.1002326 .
24. Szpiech ZA, Xu JS, Pemberton TJ, Peng WP, Zollner S, Rosenberg NA, et al. Long Runs of Homozygosity Are Enriched for Deleterious Variation. Am J Hum Genet. 2013;93(1):90-102.
25. Loftus RT, MacHugh DE, Bradley DG, Sharp PM, Cunningham P. Evidence for two independent domestications of cattle. Proc Natl Acad Sci U S A. 1994;91(7):2757-61.
26. Kim ES, Cole JB, Huson H, Wiggans GR, Van Tassell CP, Crooker BA et al. Effect of Artificial Selection on Runs of Homozygosity in US Holstein Cattle. Plos One 2013, 8(11). doi: 10.1371/journal.pone.0080813
27. Leocard S. Selective Sweep and the Size of the Hitchhiking Set. Adv Appl Probab. 2009;41(3):731-64.
28. Pemberton TJ, Absher D, Feldman MW, Myers RM, Rosenberg NA, Li JZ. Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet. 2012;91(2):275-92.
29. Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, et al. Proportionally more deleterious genetic variation in European than in African populations. Nature. 2008;451(7181):994-U995.
30. Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, Wilson JF. Genomic Runs of Homozygosity Record Population History and Consanguinity. Plos One 2010, 5(11). doi: 10.1371/journal.pone.0013996
31. Carbone I, Jakobek JL, Ramirez-Prado JH, Horn BW. Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus. Mol Ecol. 2007;16(20):4401-17.
32. Jansen S, Aigner B, Pausch H, Wysocki M, Eck S, Benet-Pages A, et al. Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage. BMC Genomics. 2013;14.
33. Zhan BJ, Fadista J, Thomsen B, Hedegaard J, Panitz F, Bendixen C. Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping. BMC Genomics. 2011;12.
34. Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao XP, et al. Whole genome resequencing of Black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics. 2011;12.
35. McLaren W, Pritchard B, Rios D, Chen YA, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics. 2010;26(16):2069-70.
36. Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, et al. SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Res. 2013;41(D1):D483-9.
37. Andersen B, Jensen B, Nielsen A, Christensen LG, Liboriussen T. Rød Dansk Malkerace-avlsmæssigt of kulturhistorisk belyst. Danmarks HordbrugsForskning. Denmark. 2003.
38. Andersson L, Lunden A, Sigurdardottir S, Davies CJ, Rask L. Linkage Relationships in the Bovine Mhc Region - High Recombination Frequency between Class-Ii Subregions. Immunogenetics. 1988;27(4):273-80.
39. Ellis SA, Ballingall KT. Cattle MHC: evolution in action? Immunol Rev. 1999;167:159-68.
40. Kauppi L, Sajantila A, Jeffreys AJ. Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region. Hum Mol Genet. 2003;12(1):33-40.
41. Kambadur R, Sharma M, Smith TPL, Bass JJ. Mutations in myostatin (GDF8) in double-muscled Belgian blue and Piedmontese cattle. Genome Res. 1997;7(9):910-6.
42. Hoglund JK, Sahana G, Guldbrandtsen B, Lund MS. Validation of associations for female fertility traits in Nordic Holstein, Nordic Red and Jersey dairy cattle. BMC Genetics 2014, 15. doi: 10.1186/1471-2156-15-8
43. Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D et al. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 2009, 10(4). doi: 10.1186/gb-2009-10-4-r42
44. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754-60.
45. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9.
46. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297-303.
47. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29(1):308-11.
48. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2000;29(1):38-311.
49. Nei M, Li WH. Mathematical-Model for Studying Genetic-Variation in Terms of Restriction Endonucleases. Proc Natl Acad Sci U S A. 1979;76(10):5269-73.
50. Yang JA, Lee SH, Goddard ME, Visscher PM. GCTA: A Tool for Genome-wide Complex Trait Analysis. Am J Hum Genet. 2011;88(1):76-82.
51. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006;38(8):904-9.
52. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559-75.
53. Weir BS, Cockerham CC. Estimating F-Statistics for the Analysis of Population-Structure. Evolution. 1984;38(6):1358-70.
54. Gautier M, Vitalis R. rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics. 2012;28(8):1176-7.
55. Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, Schaffner SF, et al. Detecting recent positive selection in the human genome from haplotype structure. Nature. 2002;419(6909):832-7.
56. Tang K, Thornton KR, Stoneking M. A new approach for using genome scans to detect recent positive selection in the human genome. PLos Biol. 2007;5(7):1587-602.
57. Zhang Q, Calus M, Guldbrandtsen B, Lund MS, Sahana G. Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds. BMC Genetics, in press. 2015.