Punctuated distribution of recombination hotspots and demarcation of pericentromeric regions in Phaseolus vulgaris L

PLoS ONE

Volumn 10, Issue 1, 2015, Pages

  Bhakta, Mehul S ^a   Jones, Valerie A ^a   Vallejos, C Eduardo ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; DNA SEQUENCE; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; GENETIC LINKAGE; GENETIC RECOMBINATION; GENOTYPING BY SEQUENCING; GENOTYPING TECHNIQUE; LINKAGE ANALYSIS; NONHUMAN; PERICENTROMERIC REGION; PHASEOLUS VULGARIS; PHENOTYPIC VARIATION; PLANT CHROMOSOME; PLANT GENOME; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; CHROMOSOMAL MAPPING; CROSS BREEDING; GENE LIBRARY; GENETICS; PHASEOLUS;

PHASEOLUS VULGARIS;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CROSSES, GENETIC; GENE LIBRARY; GENETIC LINKAGE; GENOME, PLANT; PHASEOLUS; PHYSICAL CHROMOSOME MAPPING; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84922175162     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0116822     Document Type: Article

References (63)

1. Schlötterer C (2004) The evolution of molecular markers - just a matter of fashion? Nat Rev Genet 5: 63-69. Available:http://www.ncbi.nlm.nih.gov/pubmed/14666112. Accessed 2014 July 10. doi:10.1038/nrg1249 PMID: 14666112
2. Baird N, Etter PD, Atwood TS, Currey MC, Shiver AL, et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3: e3376. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2557064&tool=pmcentrez&rendertype=abstract. Accessed 2014 July 10. doi:10.1371/journal.pone.0003376 PMID: 18852878
3. Elshire RJ, Glaubitz JC, Sun Q, Poland J, Kawamoto K, et al. (2011) A robust, simple genotyping-bysequencing (GBS) approach for high diversity species. PLoS One 6: e19379. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3087801&tool=pmcentrez&rendertype=abstract.
4. Petes TD (2001) Meiotic recombination hot spots and cold spots. Nat Rev Genet 2: 360-369. Available: http://www.ncbi.nlm.nih.gov/pubmed/24635992. doi:10.1038/35072078 PMID: 11331902
5. Henikoff S, Ahmad K, Malik HS (2001) The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293: 1098-1102. Available:http://www.ncbi.nlm.nih.gov/pubmed/11498581. doi:10.1126/science.1062939 PMID: 11498581
6. Hellsten U, Wright K, Jenkins J, Shu S, Yuan Y, et al. (2013) Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing. Proc Natl Acad Sci USA 110: 19478-19482. Available:http://www.pnas.org/content/110/48/19478.short. doi:10.1073/pnas.1319032110 PMID: 24225854
7. Drouaud J, Khademian H, Giraut L, Zanni V, Bellalou S, et al. (2013) Contrasted patterns of crossover and non-crossover at Arabidopsis thaliana meiotic recombination hotspots. PLoS Genet 9: e1003922.1. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3828143&tool=pmcentrez&rendertype=abstract. doi:10.1371/journal.pgen.1003922 PMID: 24244190
8. Cao L, Alani E, Kleckner N (1990) A pathway for generation and processing of double-strand breaks during meiotic recombination in S. cerevisiae. Cell 61: 1089-1101. Available:http://www.ncbi.nlm.nih.gov/pubmed/2190690. doi:10.1083/jcb.110.4.1089 PMID: 2190690
9. Matos J, West SC (2014) Holliday junction resolution: Regulation in space and time. DNA Repair (Amst) 19: 176-181. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4065333&tool=pmcentrez&rendertype=abstract. doi:10.1016/j.dnarep.2014.03.013
10. Cole F, Keeney S, Jasin M (2012) Preaching about the converted: how meiotic gene conversion influences genomic diversity. Ann New York Acad Sci 1267: 95-102. Available:http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.2012.06595.x/full. doi:10.1111/j.1749-6632.2012.06595.x
11. Da Ines O, Degroote F, Amiard S, Goubely C, Gallego ME, et al. (2013) Effects of XRCC2 and RAD51B mutations on somatic and meiotic recombination in Arabidopsis thaliana. Plant J 74: 959-970. Available:http://www.ncbi.nlm.nih.gov/pubmed/23521529. doi:10.1111/tpj.12182 PMID: 23521529
12. Pradillo M, Varas J, Oliver C, Santos JL (2014) On the role of AtDMC1, AtRAD51 and its paralogs during Arabidopsis meiosis. Front Plant Sci 5(23): 1-13. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3925842&tool=pmcentrez&rendertype=abstract.
13. Choi K, Zhao X, Kelly K, Venn O (2013) Arabidopsis meiotic crossover hot spots overlap with H2A. Z nucleosomes at gene promoters. Nat Genet 45: 1-24. Available:http://www.nature.com/ng/journal/v45/n11/abs/ng.2766.html.
14. Vallejos C, Sakiyama N, Chase C (1992) A molecular marker-based linkage map of Phaseolus vulgaris L. Genetics 131: 733-740. Available:http://www.genetics.org/content/131/3/733.short. PMID: 1352759
15. Blair MW, Soler A, Cortés AJ (2012) Diversification and population structure in common beans (Phaseolus vulgaris L.). PLoS One 7: e49488. doi:10.1371/journal.pone.0049488 PMID: 23145179
16. Jung G, Skroch P, Coyne D, Neinhuis J, Arnaud-Santana E (2002) Molecular-marker-based genetic analysis of tepary bean-derived common bacterial blight resistance in different developmental stages of common bean. J Am Soc Hortic Sci 122: 329-337.
17. Blair MW, Pedraza F, Buendia HF, Gaitán-Solís E, Beebe SE, et al. (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor. Appl. Genet. 107: 1362-1374. Available:http://www.ncbi.nlm.nih.gov/pubmed/14504741. doi:10.1007/s00122-003-1398-6 PMID: 14504741
18. Freyre R, Skroch P, Geffroy V, Adam-Blondon A, Shirmohamadali A (1998) Towards an integrated linkage map of common bean. 4. Development of a core linkage map and alignment of RFLP maps. Theor. Appl. Genet. 97: 847-856.
19. Vallejos C, Skroch P, Neinhuis J (2001) DNA-Based Markers in Plants. 2nd. Phillips R, Vasil I, editors Dordrecht, The Netherlands: Kluwer Academic.
20. Murray J, Larsen J, Michaels T (2002) Identification of putative genes in bean (Phaseolus vulgaris) genomic (Bng) RFLP clones and their conversion to STSs. Genome 45: 1013-1024. doi:10.1139/g02-069 PMID: 12502245
21. Prakken R (1974) Inheritance of Colours in Phaseolus Vulgaris L.: IV Recombination within the'Complex Locus C'. Meded Landbouwhogesch Wageningen 24: 1-36.
22. Repinski SL, Kwak M, Gepts P (2012) The common bean growth habit gene PvTFL1y is a functional homolog of Arabidopsis TFL1. Theor Appl Genet 124: 1539-1547. Available:http://www.ncbi.nlm.nih.gov/pubmed/22331140. doi:10.1007/s00122-012-1808-8 PMID: 22331140
23. Lamprecht H (1936) Zur Genetik von Phaseolus Vulgaris XII. Über die Vererbung der Blüten?und Stammfarbe. Hereditas 21: 129-166. Available:http://onlinelibrary.wiley.com/doi/10.1111/j.1601-5223.1936.tb03196.x/abstract.
24. Vallejos CE (2007) An expedient and versatile protocol for extracting high-quality DNA from plant leaves. CSH Protocols, doi:10.1101/pdb.prot4765 Accessed 2014 July 10. PMID: 21357104
25. Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, et al. (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One 9: e90346. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3938676&tool=pmcentrez&rendertype=abstract. doi:10.1371/journal.pone.0090346 PMID: 24587335
26. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 42. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2803857&tool=pmcentrez&rendertype=abstract. doi:10.1186/1471-2105-10-421
27. Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, et al. (2009) PASS: a program to align short sequences. Bioinformatics 25: 967-968. Available:http://www.ncbi.nlm.nih.gov/pubmed/19218350. doi:10.1093/bioinformatics/btp087 PMID: 19218350
28. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2723002&tool=pmcentrez&rendertype=abstract. Accessed 2012 November 1. doi:10.1093/bioinformatics/btp352 PMID: 19505943
29. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, et al. (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22: 568-576. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3290792&tool=pmcentrez&rendertype=abstract. Accessed 2012 October 26. doi:10.1101/gr.129684.111 PMID: 22300766
30. Kozik A, Michelmore R (2006) MadMapper and CheckMatrix - python scripts to infer orders of genetic markers and for visualization and validation of genetic maps and haplotypes. Proceedings of the Plant and Animal Genome XIV Conference. San Diego. p. P957/CP013. Available:http://www.intl-pag.org/14/abstracts/PAG14-C013.html.
31. Van Os H, Stam P, Visser RGF, Van Eck HJ (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theor Appl Genet 112: 30-40. Available:http://www.ncbi.nlm.nih.gov/pubmed/16228189. doi:10.1007/s00122-005-0097-x PMID: 16228189
32. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, et al. (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181. Available:http://www.ncbi.nlm.nih.gov/pubmed/3692487. doi:10.1016/0888-7543(87)90010-3 PMID: 3692487
33. Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, et al. (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46: 707-713. Available:http://www.ncbi.nlm.nih.gov/pubmed/24908249. Accessed 2014 July 10. doi:10.1038/ng.3008 PMID: 24908249
34. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, et al. (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148: 479-494. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1459786&tool=pmcentrez&rendertype=abstract. PMID: 9475757
35. Palhares AC, Rodrigues-Morais TB, Van Sluys M-A, Domingues DS, Maccheroni W, et al. (2012) A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers. BMC Genet 13: 51. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3443450&tool=pmcentrez&rendertype=abstract. doi:10.1186/1471-2156-13-51 PMID: 22742069
36. Basten C, Weir B, Zeng Z (2003) QTL Cartographer: Version 1.17. http://statgen.ncsu.edu/qtlcart/.
37. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183. Available:http://www.ncbi.nlm.nih.gov/pubmed/20075913. doi:10.1038/nature08670 PMID: 20075913
38. Chase C, Ortega V, Vallejos C (1991) DNA restriction fragment length polymorphisms correlate with isozyme diversity in Phaseolus vulgaris L. Theor Appl Genet 81: 806-811. Available:http://www.ncbi.nlm.nih.gov/pubmed/24221445. Accessed 2014 April 8. doi:10.1007/BF00224994 PMID: 24221445
39. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Report 9: 208-218. Available:http://link.springer.com/10.1007/BF02672016. doi:10.1007/BF02672069
40. Pedrosa A, Vallejos C, Bachmair A, Schweizer D (2003) Integration of common bean (Phaseolus vulgaris L.) linkage and chromosomal maps. Theor Appl Genet 106: 205-212. Available:http://link.springer.com/article/10.1007/s00122-002-1138-3. Accessed 2014 April 7. PMID: 12582845
41. Yuste-Lisbona FJ, Santalla M, Capel C, García-Alcázar M, De La Fuente M, et al. (2012) Marker-based linkage map of Andean common bean (Phaseolus vulgaris L.) and mapping of QTLs underlying popping ability traits. BMC Plant Biol 12: 1-16. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3490973&tool=pmcentrez&rendertype=abstract. doi:10.1186/1471-2229-12-136
42. Davey JW, Hohenlohe P, Etter PD, Boone JQ, Catchen JM, et al. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12: 499-510. Available: http://www.ncbi.nlm.nih.gov/pubmed/21681211. doi:10.1038/nrg3012 PMID: 21681211
43. Gruenbaum Y, Cedar H, Razin A (1981) Restriction enzyme digestion of hemimethylated DNA. Nucleic Acids Res 9: 2509-2515. Available:http://nar.oxfordjournals.org/content/9/11/2509.short. doi:10.1093/nar/9.11.2509 PMID: 6269052
44. Huang BE, Raghavan C, Mauleon R, Broman KW, Leung H (2014) Efficient imputation of missing markers in low-coverage genotyping-by-sequencing data from multiparental crosses. Genetics 197: 401-404. Available:http://www.ncbi.nlm.nih.gov/pubmed/24583583. doi:10.1534/genetics.113.158014 PMID: 24583583
45. Stange M, Utz H, Schrag T, Melchinger A, Wurschum T (2013) High-density genotyping: an overkill for QTL mapping? Lessons learned from a case study in maize and simulations. Theor Appl. 126: 2563-2574. Available:http://link.springer.com/article/10.1007/s00122-013-2155-0. doi:10.1007/s00122-013-2155-0
46. Mamidi S, Rossi M, Moghaddam SM, Annam D, Lee R, et al. (2013) Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L. Heredity (Edinb) 110: 267-276. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3668653&tool=pmcentrez&rendertype=abstract. doi:10.1038/hdy.2012.82
47. Matsubara K, Ebana K, Mizubayashi T, Itoh S, Ando T, et al. (2011) Relationship between transmission ratio distortion and genetic divergence in intraspecific rice crosses. Mol Genet Genomics 286: 307-319. Available:http://www.ncbi.nlm.nih.gov/pubmed/21918817. doi:10.1007/s00438-011-0648-6 PMID: 21918817
48. Dobritsa A, Dobritsa S (1980) DNA protection with the DNA methylase M. Bbv I from Bacillus brevis var. GB against cleavage by the restriction endonucleases Pst I and PvuII. Gene 10: 105-112. Available: http://www.sciencedirect.com/science/article/pii/0378111980901286.
49. Gudnason H, Dufva M, Bang DD, Wolff A (2007) Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature. Nucleic Acids Res 35: e127. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2095797&tool=pmcentrez&rendertype=abstract. doi:10.1093/nar/gkm671 PMID: 17897966
50. Nelson M, Christ C, Schildkraut I (1984) Alteration of apparent restriction endonuclease recognition specificities by DNA methylases. Nucleic Acids Res 12: 5165-5173. Available:http://nar.oxfordjournals.org/content/12/13/5165.short. doi:10.1093/nar/12.13.5165 PMID: 6087274
51. Nelson PS, Papas TS, Schweinfest CW(1993) Restriction endonuclease cleavage of 5-methyldeoxycytosine hemimethylated DNA at high enzyme-to-substrate ratios. Nucleic Acids Res 21: 681-686. Available:www.pubmedcentral.nih.gov/articlerender.fcgi?artid=309169&tool=pmcentrez&rendertype=abstract. doi:10.1093/nar/21.3.681 PMID: 8441677
52. Sagawa H, Ohshima A, Kato I (1995) Sse83871, a useful eight cutter for mammalian genome analysis (influence of methylation on the activity of Sse83871). Nucleic Acids Res 23: 2-5. Available:http://nar.oxfordjournals.org/content/23/13/2367.short. doi:10.1093/nar/23.13.2367
53. Law J, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11: 204-220. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3034103&tool=pmcentrez&rendertype=abstract. doi:10.1038/nrg2719 PMID: 20142834
54. Cokus S, Feng S, Zhang X, Chen Z, Merriman B, et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452: 215-219. Available:http://www.nature.com/nature/journal/v452/n7184/abs/nature06745.html. Accessed 2014 July 18. doi:10.1038/nature06745 PMID: 18278030
55. Hollingsworth NM, Brill SJ (2004) The Mus81 solution to resolution: generating meiotic crossovers without Holliday junctions. Genes Dev 18: 117-125. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1851908&tool=pmcentrez&rendertype=abstract. doi:10.1101/gad.1165904 PMID: 14752007
56. Guillon H, Baudat F, Grey C, Liskay RM, de Massy B (2005) Crossover and noncrossover pathways in mouse meiosis. Mol Cell 20: 563-573. Available:http://www.ncbi.nlm.nih.gov/pubmed/16307920. doi:10.1016/j.molcel.2005.09.021 PMID: 16307920
57. Lhuissier FGP, Offenberg HH, Wittich PE, Vischer NOE, Heyting C (2007) The mismatch repair protein MLH1 marks a subset of strongly interfering crossovers in tomato. Plant Cell 19: 862-876. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1867368&tool=pmcentrez&rendertype=abstract. doi:10.1105/tpc.106.049106 PMID: 17337626
58. Basu-Roy S, Gauthier F, Giraut L, Mézard C, Falque M, et al. (2013) Hot regions of noninterfering crossovers coexist with a nonuniformly interfering pathway in Arabidopsis thaliana. Genetics 195: 769-779. Available:http://www.ncbi.nlm.nih.gov/pubmed/24026099. doi:10.1534/genetics.113.155549 PMID: 24026099
59. Lin J-Y, Jacobus BH, SanMiguel P, Walling JG, Yuan Y, et al. (2005) Pericentromeric regions of soybean (Glycine max L. Merr.) chromosomes consist of retroelements and tandemly repeated DNA and are structurally and evolutionarily labile. Genetics 170: 1221-1230. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1451161&tool=pmcentrez&rendertype=abstract.
60. Topp C, Dawe R (2006) Reinterpreting pericentromeric heterochromatin. Curr Opin Plant Biol 9: 647-653. Available:http://www.sciencedirect.com/science/article/pii/S136952660600149X. Accessed 2014 August 8. doi:10.1016/j.pbi.2006.09.008 PMID: 17015032
61. Ma J, Wing R, Bennetzen JL, Jackson S (2007) Plant centromere organization: a dynamic structure with conserved functions. Trends Genet 23: 134-139. Available:http://www.sciencedirect.com/science/article/pii/S136952660600149X. doi:10.1016/j.tig.2007.01.004 PMID: 17275131
62. Lynn A, Soucek R, Börner GV (2007) ZMM proteins during meiosis: crossover artists at work. Chromosome Res 15: 591-605. Available:http://www.ncbi.nlm.nih.gov/pubmed/17674148. doi:10.1007/s10577-007-1150-1 PMID: 17674148
63. Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C, et al. (2010) PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327: 836-840. Available:http://www.ncbi.nlm.nih.gov/pubmed/20044539. doi:10.1126/science.1183439 PMID: 20044539