Inferring Genome-Wide Recombination Landscapes from Advanced Intercross Lines: Application to Yeast Crosses

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Illingworth, Christopher J R ^a   Parts, Leopold ^a,b   Bergström, Anders ^c   Liti, Gianni ^c   Mustonen, Ville ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF NICE SOPHIA ANTIPOLIS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ADVANCED INTERCROSS LINE; ARTICLE; CONTROLLED STUDY; FUNGAL GENOME; FUNGAL STRAIN; GENE SEQUENCE; GENETIC RECOMBINATION; NONHUMAN; SACCHAROMYCES CEREVISIAE; SIMULATION;

DNA BREAKS, DOUBLE-STRANDED; GENOME, FUNGAL; GENOMICS; HYBRIDIZATION, GENETIC; MODELS, GENETIC; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

EID: 84877062764     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0062266     Document Type: Article

References (38)

1. Stumpf MPH, McVean GAT, (2003) Estimating recombination rates from population-genetic data. Nat Rev Genet 4: 959-68.
2. Smukowski CS, Noor MAF, (2011) Recombination rate variation in closely related species. Heredity 107: 496-508.
3. Clark AG, Wang X, Matise T, (2010) Contrasting methods of quantifying fine structure of human recombination. Annu Rev Genom Hum G 11: 45-64.
4. Lander ES, Green P, (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci USA 84: 2363-7.
5. Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, Sigurdsson A, et al. (2010) Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467: 1099-103.
6. Hubert R, MacDonald M, Gusella J, Arnheim N, (1994) High resolution localization of recombination hot spots using sperm typing. Nat Genet 7: 420-4.
7. Wang J, Fan HC, Behr B, Quake SR, (2012) Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150: 402-12.
8. Wakeley J (2005) Coalescent Theory, an Introduction. Greenwood Village, CO: Roberts and Company. URL http://www.coalescentheory.com/.
9. McVean GAT, Myers SR, Hunt S, Deloukas P, Bentley DR, et al. (2004) The fine-scale structure of recombination rate variation in the human genome. Science 304: 581-4.
10. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P, (2005) A fine-scale map of recombination rates and hotspots across the human genome. Science 310: 321-4.
11. Auton A, Fledel-Alon A, Pfeifer S, Venn O, Ségurel L, et al. (2012) A fine-scale chimpanzee genetic map from population sequencing. Science 336: 193-8.
12. Kulathinal RJ, Bennett SM, Fitzpatrick CL, Noor MAF, (2008) Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence. Proc Natl Acad Sci USA 105: 10051-6.
13. Rockman MV, Kruglyak L, (2009) Recombinational landscape and population genomics of Caenorhabditis elegans. PLoS Genet 5: e1000419.
14. Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM, (2008) High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature 454: 479-85.
15. Philip VM, Sokoloff G, Ackert-Bicknell CL, Striz M, Branstetter L, et al. (2011) Genetic analysis in the collaborative cross breeding population. Genome research 21: 1223-38.
16. Comeron JM, Ratnappan R, Bailin S, (2012) The many landscapes of recombination in Drosophila melanogaster. PLoS Genet 8: e1002905.
17. Darvasi A, Soller M, (1995) Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141: 1199-207.
18. Hudson RR, (2001) Two-locus sampling distributions and their application. Genetics 159: 1805-17.
19. McVean G, Awadalla P, Fearnhead P, (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-41.
20. Parts L, Cubillos FA, Warringer J, Jain K, Salinas F, et al. (2011) Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res 21: 1131-8.
21. Baake E, Herms I, (2008) Single-crossover dynamics: finite versus infinite populations. Bull Math Biol 70: 603-24.
22. Illingworth CJR, Parts L, Schiffels S, Liti G, Mustonen V, (2012) Quantifying selection acting on a complex trait using allele frequency time series data. Mol Biol Evol 29: 1187-97.
23. Kaback DB, Guacci V, Barber D, Mahon JW, (1992) Chromosome size-dependent control of meiotic recombination. Science 256: 228-32.
24. Clark AG, Nielsen R, Signorovitch J, Matise TC, Glanowski S, et al. (2003) Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. Am J Hum Genet 73: 285-300.
25. Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, et al. (2000) Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci USA 97: 11383-90.
26. Tsai IJ, Burt A, Koufopanou V, (2010) Conservation of recombination hotspots in yeast. Proc Natl Acad Sci USA 107: 7847-52.
27. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639-45.
28. Wu TC, Lichten M, (1995) Factors that affect the location and frequency of meiosis-induced doublestrand breaks in Saccharomyces cerevisiae. Genetics 140: 55-66.
29. Kauppi L, Jeffreys AJ, Keeney S, (2004) Where the crossovers are: recombination distributions in mammals. Nat Rev Genet 5: 413-424.
30. Pan J, Sasaki M, Kniewel R, Murakami H, Blitzblau HG, et al. (2011) A hierarchical combination of factors shapes the genome-wide topography of yeast meiotic recombination initiation. Cell 144: 719-31.
31. Lichten M, Massy BD, (2011) The impressionistic landscape of meiotic recombination. Cell 147: 267-270.
32. Aguilera A, Klein HL, (1989) Yeast intrachromosomal recombination: long gene conversion tracts are preferentially associated with reciprocal exchange and require the rad1 and rad3 gene products. Genetics 123: 683-94.
33. Liu EY, Zhang Q, McMillan L, de Villena FPM, (2010) WangW (2010) Efficient genome ancestry inference in complex pedigrees with inbreeding. Bioinformatics 26: i199-207.
34. Liti G, Louis EJ, (2012) Advances in quantitative trait analysis in yeast. PLoS Genet 8: e1002912.
35. Cubillos FA, Billi E, Zorgo E, Parts L, Fargier P, et al. (2011) Assessing the complex architecture of polygenic traits in diverged yeast populations. Mol Ecol 20: 1401-13.
36. Broman KW, (2012) Haplotype probabilities in advanced intercross populations. G3 2: 199-202.
37. Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, et al. (2004) The collaborative cross, a community resource for the genetic analysis of complex traits. Nature Genet 36: 1133-7.
38. Auton A, McVean G, (2007) Recombination rate estimation in the presence of hotspots. Genome Res 17: 1219-27.