A Pedigree-Based Map of Recombination in the Domestic Dog Genome

被引:49
作者
Campbell, Christopher L. [1 ]
Bherer, Claude [1 ,2 ]
Morrow, Bernice E. [1 ]
Boyko, Adam R. [3 ]
Auton, Adam [1 ]
机构
[1] Albert Einstein Coll Med, Dept Genet, Bronx, NY 10461 USA
[2] New York Genome Ctr, New York, NY 10013 USA
[3] Cornell Univ, Dept Biomed Sci, Coll Vet Med, Ithaca, NY 14853 USA
关键词
canine genetics; crossover interference; hotspots; PRDM9; recombination; QUANTITATIVE TRAIT LOCI; CROSSOVER INTERFERENCE; MEIOTIC RECOMBINATION; LINKAGE MAP; CANIS-FAMILIARIS; HIP-DYSPLASIA; GENETIC-MAP; HUMANS; PRDM9; HOTSPOTS;
D O I
10.1534/g3.116.034678
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Meiotic recombination in mammals has been shown to largely cluster into hotspots, which are targeted by the chromatin modifier PRDM9. The canid family, including wolves and dogs, has undergone a series of disrupting mutations in this gene, rendering PRDM9 inactive. Given the importance of PRDM9, it is of great interest to learn how its absence in the dog genome affects patterns of recombination placement. We have used genotypes from domestic dog pedigrees to generate sex-specific genetic maps of recombination in this species. On a broad scale, we find that placement of recombination events in dogs is consistent with that in mice and apes, in that the majority of recombination occurs toward the telomeres in males, while female crossing over is more frequent and evenly spread along chromosomes. It has been previously suggested that dog recombination is more uniform in distribution than that of humans; however, we found that recombination in dogs is less uniform than in humans. We examined the distribution of recombination within the genome, and found that recombination is elevated immediately upstream of the transcription start site and around CpG islands, in agreement with previous studies, but that this effect is stronger in male dogs. We also found evidence for positive crossover interference influencing the spacing between recombination events in dogs, as has been observed in other species including humans and mice. Overall our data suggests that dogs have similar broad scale properties of recombination to humans, while fine scale recombination is similar to other species lacking PRDM9.
引用
收藏
页码:3517 / 3524
页数:8
相关论文
共 46 条
[1]   Merlin-rapid analysis of dense genetic maps using sparse gene flow trees [J].
Abecasis, GR ;
Cherny, SS ;
Cookson, WO ;
Cardon, LR .
NATURE GENETICS, 2002, 30 (01) :97-101
[2]   Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs [J].
Auton, Adam ;
Li, Ying Rui ;
Kidd, Jeffrey ;
Oliveira, Kyle ;
Nadel, Julie ;
Holloway, J. Kim ;
Hayward, Jessica J. ;
Cohen, Paula E. ;
Greally, John M. ;
Wang, Jun ;
Bustamante, Carlos D. ;
Boyko, Adam R. .
PLOS GENETICS, 2013, 9 (12)
[3]   A Fine-Scale Chimpanzee Genetic Map from Population Sequencing [J].
Auton, Adam ;
Fledel-Alon, Adi ;
Pfeifer, Susanne ;
Venn, Oliver ;
Segurel, Laure ;
Street, Teresa ;
Leffler, Ellen M. ;
Bowden, Rory ;
Aneas, Ivy ;
Broxholme, John ;
Humburg, Peter ;
Iqbal, Zamin ;
Lunter, Gerton ;
Maller, Julian ;
Hernandez, Ryan D. ;
Melton, Cord ;
Venkat, Aarti ;
Nobrega, Marcelo A. ;
Bontrop, Ronald ;
Myers, Simon ;
Donnelly, Peter ;
Przeworski, Molly ;
McVean, Gil .
SCIENCE, 2012, 336 (6078) :193-198
[4]   Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome [J].
Axelsson, Erik ;
Webster, Matthew T. ;
Ratnakumar, Abhirami ;
Ponting, Chris P. ;
Lindblad-Toh, Kerstin .
GENOME RESEARCH, 2012, 22 (01) :51-63
[5]   General pattern of meiotic recombination in male dogs estimated by MLH1 and RAD51 immunolocalization [J].
Basheva, E. A. ;
Bidau, C. J. ;
Borodin, P. M. .
CHROMOSOME RESEARCH, 2008, 16 (05) :709-719
[6]   PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice [J].
Baudat, F. ;
Buard, J. ;
Grey, C. ;
Fledel-Alon, A. ;
Ober, C. ;
Przeworski, M. ;
Coop, G. ;
de Massy, B. .
SCIENCE, 2010, 327 (5967) :836-840
[7]   Genetic recombination is directed away from functional genomic elements in mice [J].
Brick, Kevin ;
Smagulova, Fatima ;
Khil, Pavel ;
Camerini-Otero, R. Daniel ;
Petukhova, Galina V. .
NATURE, 2012, 485 (7400) :642-645
[8]   Characterization of human crossover interference [J].
Broman, KW ;
Weber, JL .
AMERICAN JOURNAL OF HUMAN GENETICS, 2000, 66 (06) :1911-1926
[9]  
Broman KW, 2002, GENETICS, V160, P1123
[10]   Escape from crossover interference increases with maternal age [J].
Campbell, Christopher L. ;
Furlotte, Nicholas A. ;
Eriksson, Nick ;
Hinds, David ;
Auton, Adam .
NATURE COMMUNICATIONS, 2015, 6