A pedigree-based map of recombination in the domestic dog genome

G3: Genes, Genomes, Genetics

Volumn 6, Issue 11, 2016, Pages 3517-3524

  Campbell, Christopher L ^a   Bhérer, Claude ^a,b   Morrow, Bernice E ^a   Boyko, Adam R ^c   Auton, Adam ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b NEW YORK GENOME CENTER   (United States)

^c Department of Molecular Biology and Genetics   (United States)

Author keywords

Canine genetics crossover; Interference hotspots PRDM9 recombination

Indexed keywords

ARTICLE; CPG ISLAND; CROSSING OVER; DOG; GENE MAPPING; GENE MUTATION; GENETIC RECOMBINATION; GENOME; HUMAN; MEIOTIC RECOMBINATION; NONHUMAN; PEDIGREE ANALYSIS; TELOMERE; TRANSCRIPTION INITIATION SITE;

EID: 84996486919     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.116.034678     Document Type: Article

References (46)

1. Abecasis, G. R., S. S. Cherny, W. O. Cookson, and L. R. Cardon, 2002 Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat. Genet. 30: 97-101.
2. Auton, A., A. Fledel-Alon, S. Pfeifer, O. Venn, L. Ségurel et al., 2012 A finescale chimpanzee genetic map from population sequencing. Science 336: 193-198.
3. Auton, A., Y. Rui Li, J. Kidd, K. Oliveira, J. Nadel et al., 2013 Genetic recombination is targeted towards gene promoter regions in dogs. PLoS Genet. 9: e1003984.
4. Axelsson, E., M. T. Webster, A. Ratnakumar, C. P. Ponting, and K. Lindblad-Toh, 2012 Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome. Genome Res. 22: 51-63.
5. Basheva, E. A., C. J. Bidau, and P. M. Borodin, 2008 General pattern of meiotic recombination in male dogs estimated by MLH1 and RAD51 immunolocalization. Chromosome Res. 16: 709-719.
6. Baudat, F., J. Buard, C. Grey, A. Fledel-Alon, C. Ober et al., 2010 PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327: 836-840.
7. Brick, K., F. Smagulova, P. Khil, R. D. Camerini-Otero, and G. V. Petukhova, 2012 Genetic recombination is directed away from functional genomic elements in mice. Nature 485: 642-645.
8. Broman, K. W., and J. L. Weber, 2000 Characterization of human crossover interference. Am. J. Hum. Genet. 66: 1911-1926.
9. Broman, K. W., L. B. Rowe, G. A. Churchill, and K. Paigen, 2002 Crossover interference in the mouse. Genetics 160: 1123-1131.
10. Campbell, C. L., N. A. Furlotte, N. Eriksson, D. Hinds, and A. Auton, 2015 Escape from crossover interference increases with maternal age. Nat. Commun. 6: 6260.
11. Chastant-Maillard, S., C. Viaris de Lesegno, M. Chebrout, S. Thoumire, T. Meylheuc et al., 2011 The canine oocyte: uncommon features of in vivo and in vitro maturation. Reprod. Fertil. Dev. 23: 391-402.
12. Chen, W.-K., J. D. Swartz, L. J. Rush, and C. E. Alvarez, 2009 Mapping DNA structural variation in dogs. Genome Res. 19: 500-509.
13. Coop, G., X. Wen, C. Ober, J. K. Pritchard, and M. Przeworski, 2008 Highresolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans. Science 319: 1395-1398.
14. Cox, A., C. L. Ackert-Bicknell, B. L. Dumont, Y. Ding, J. T. Bell et al., 2009 A new standard genetic map for the laboratory mouse. Genetics 182: 1335-1344.
15. Delaneau, O., J.-F. Zagury, and J. Marchini, 2013 Improved wholechromosome phasing for disease and population genetic studies. Nat. Methods 10: 5-6.
16. de Massy, B., 2013 Initiation of meiotic recombination: how and where? Conservation and specificities among eukaryotes. Annu. Rev. Genet. 47: 563-599.
17. Freixa, L., M. García, and J. Egozcue, 1987 The timing of first meiotic prophase in oocytes from female domestic dogs (Canis familiaris). Genome 29: 208-210.
18. Haldane, J., 1919 The combination of linkage values, and the calculation of distance between the loci of linked factors. J. Genet. 8: 299-309.
19. Hayashi, K., K. Yoshida, and Y. Matsui, 2005 A histone H3 methyltransferase controls epigenetic events required for meiotic prophase. Nature 438: 374-378.
20. Hayward, J. J., M. G. Castelhano, K. C. Oliveira, E. Corey, C. Balkman et al., 2016 Complex disease and phenotype mapping in the domestic dog. Nat. Commun. 7: 10460.
21. Housworth, E., and F. Stahl, 2003 Crossover interference in humans. Am. J. Hum. Genet. 73: 188-197.
22. Kong, A., G. Thorleifsson, D. F. Gudbjartsson, G. Masson, A. Sigurdsson et al., 2010 Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467: 1099-1103.
23. Lam, I., and S. Keeney, 2015 Nonparadoxical evolutionary stability of the recombination initiation landscape in yeast. Science 350: 932-937.
24. Lander, E. S., and P. Green, 1987 Construction of multilocus genetic linkage maps in humans. Proc. Natl. Acad. Sci. USA 84: 2363-2367.
25. Lindblad-Toh, K., C. M. Wade, T. S. Mikkelsen, E. K. Karlsson, D. B. Jaffe et al., 2005 Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438: 803-819.
26. Ma, L., J. R. O'Connell, P. M. VanRaden, B. Shen, A. Padhi et al., 2015 Cattle sex-specific recombination and genetic control from a large pedigree analysis. PLoS Genet. 11: e1005387.
27. Mank, J. E., 2009 The evolution of heterochiasmy: the role of sexual selection and sperm competition in determining sex-specific recombination rates in eutherian mammals. Genet. Res. 91: 355-363.
28. Mateescu, R. G., N. I. Burton-Wurster, K. Tsai, J. Phavaphutanon, Z. Zhang et al., 2008 Identification of quantitative trait loci for osteoarthritis of hip joints in dogs. Am. J. Vet. Res. 69: 1294-1300.
29. Mellersh, C. S., A. A. Langston, G. M. Acland, M. A. Fleming, K. Ray et al., 1997 A linkage map of the canine genome. Genomics 46: 326-336.
30. Muñoz-Fuentes, V., A. Di Rienzo, and C. Vilà, 2011 Prdm9, a major determinant of meiotic recombination hotspots, is not functional in dogs and their wild relatives, wolves and coyotes. PLoS One 6: e25498.
31. Myers, S., R. Bowden, A. Tumian, R. E. Bontrop, C. Freeman et al., 2010 Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science 327: 876-879.
32. Narasimhan, V. M., K. A. Hunt, D. Mason, C. L. Baker, K. J. Karczewski et al., 2016 Health and population effects of rare gene knockouts in adult humans with related parents. Science 352: 474-477.
33. Neff, M. W., K. W. Broman, C. S. Mellersh, K. Ray, G. M. Acland et al., 1999 A second-generation genetic linkage map of the domestic dog, Canis familiaris. Genetics 151: 803-820.
34. Nicholas, T. J., Z. Cheng, M. Ventura, K. Mealey, E. E. Eichler et al., 2009 The genomic architecture of segmental duplications and associated copy number variants in dogs. Genome Res. 19: 491-499.
35. O'Connell, J., D. Gurdasani, O. Delaneau, N. Pirastu, S. Ulivi et al., 2014 A general approach for haplotype phasing across the full spectrum of relatedness. PLoS Genet. 10: e1004234.
36. Oliver, P. L., L. Goodstadt, J. J. Bayes, Z. Birtle, K. C. Roach et al., 2009 Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genet. 5: e1000753.
37. Parvanov, E. D., P. M. Petkov, and K. Paigen, 2010 Prdm9 controls activation of mammalian recombination hotspots. Science 327: 835.
38. Phavaphutanon, J., R. G. Mateescu, K. L. Tsai, P. A. Schweitzer, E. E. Corey et al., 2009 Evaluation of quantitative trait loci for hip dysplasia in Labrador Retrievers. Am. J. Vet. Res. 70: 1094-1101.
39. Ptak, S. E., D. A. Hinds, K. Koehler, B. Nickel, N. Patil et al., 2005 Fine-scale recombination patterns differ between chimpanzees and humans. Nat. Genet. 37: 429-434.
40. Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira et al., 2007 PLINK: a tool set for whole-genome association and populationbased linkage analyses. Am. J. Hum. Genet. 81: 559-575.
41. Sandor, C., W. Li, W. Coppieters, T. Druet, C. Charlier et al., 2012 Genetic variants in REC8, RNF212, and PRDM9 influence male recombination in cattle. PLoS Genet. 8: e1002854.
42. Singhal, S., E. M. Leffler, K. Sannareddy, I. Turner, O. Venn et al., 2015 Stable recombination hotspots in birds. Science 350: 928-932.
43. The International HapMap Consortium, 2007 A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
44. Todhunter, R. J., G. Casella, S. P. Bliss, G. Lust, A. J. Williams et al., 2003 Power of a Labrador Retriever-Greyhound pedigree for linkage analysis of hip dysplasia and osteoarthritis. Am. J. Vet. Res. 64: 418-424.
45. Winckler, W., S. R. Myers, D. J. Richter, R. C. Onofrio, G. J. McDonald et al., 2005 Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308: 107-111.
46. Wong, A. K., A. L. Ruhe, B. L. Dumont, K. R. Robertson, G. Guerrero et al., 2010 A comprehensive linkage map of the dog genome. Genetics 184: 595-605.