title: Punctuated distribution of recombination hotspots and demarcation of pericentromeric regions in Phaseolus vulgaris L.
abstract: High density genetic maps are a reliable tool for genetic dissection of complex plant traits. Mapping resolution is often hampered by the variable crossover and non-crossover events occurring across the genome, with pericentromeric regions (pCENR) showing highly suppressed recombination rates. The efficiency of linkage mapping can further be improved by characterizing and understanding the distribution of recombinational activity along individual chromosomes. In order to evaluate the genome wide recombination rate in common beans (Phaseolus vulgaris L.) we developed a SNP-based linkage map using the genotype-by-sequencing approach with a 188 recombinant inbred line family generated from an inter gene pool cross (Andean x Mesoamerican). We identified 1,112 SNPs that were subsequently used to construct a robust linkage map with 11 groups, comprising 513 recombinationally unique marker loci spanning 943 cM (LOD 3.0). Comparative analysis showed that the linkage map spanned >95% of the physical map, indicating that the map is almost saturated. Evaluation of genome-wide recombination rate indicated that at least 45% of the genome is highly recombinationally suppressed, and allowed us to estimate locations of pCENRs. We observed an average recombination rate of 0.25 cM/Mb in pCENRs as compared to the rest of genome that showed 3.72 cM/Mb. However, several hot spots of recombination were also detected with recombination rates reaching as high as 34 cM/Mb. Hotspots were mostly found towards the end of chromosomes, which also happened to be gene-rich regions. Analyzing relationships between linkage and physical map indicated a punctuated distribution of recombinational hot spots across the genome.
authors: Horticultural Sciences Department, University of Florida, Gainesville, Florida, United States of America.
authors: Mehul S
authors: MS
authors: Bhakta
authors: Horticultural Sciences Department, University of Florida, Gainesville, Florida, United States of America.
authors: Valerie A
authors: VA
authors: Jones
authors: Horticultural Sciences Department, University of Florida, Gainesville, Florida, United States of America; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida, United States of America.
authors: C Eduardo
authors: CE
authors: Vallejos
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D003433:Crosses, Genetic; D015723:Gene Library; D008040:Genetic Linkage; D018745:Genome, Plant; D027805:Phaseolus / Q000235:genetics*; D020161:Physical Chromosome Mapping; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
references: Nat Rev Genet. 2001 May;2(5):360-9
references: 11331902
references: Science. 2001 Aug 10;293(5532):1098-102
references: 11498581
references: Genome. 2002 Dec;45(6):1013-24
references: 12502245
references: Theor Appl Genet. 2003 Jan;106(2):205-12
references: 12582845
references: Genetics. 1992 Jul;131(3):733-40
references: 1352759
references: Theor Appl Genet. 2003 Nov;107(8):1362-74
references: 14504741
references: Nat Rev Genet. 2004 Jan;5(1):63-9
references: 14666112
references: Genes Dev. 2004 Jan 15;18(2):117-25
references: 14752007
references: Genetics. 2005 Jul;170(3):1221-30
references: 15879505
references: Theor Appl Genet. 2005 Dec;112(1):30-40
references: 16228189
references: Mol Cell. 2005 Nov 23;20(4):563-73
references: 16307920
references: Curr Opin Plant Biol. 2006 Dec;9(6):647-53
references: 17015032
references: Trends Genet. 2007 Mar;23(3):134-9
references: 17275131
references: Plant Cell. 2007 Mar;19(3):862-76
references: 17337626
references: Chromosome Res. 2007;15(5):591-605
references: 17674148
references: Nucleic Acids Res. 2007;35(19):e127
references: 17897966
references: Nature. 2008 Mar 13;452(7184):215-9
references: 18278030
references: PLoS One. 2008;3(10):e3376
references: 18852878
references: Bioinformatics. 2009 Apr 1;25(7):967-8
references: 19218350
references: Bioinformatics. 2009 Aug 15;25(16):2078-9
references: 19505943
references: BMC Bioinformatics. 2009 Dec 15;10:421
references: 20003500
references: Science. 2010 Feb 12;327(5967):836-40
references: 20044539
references: Nature. 2010 Jan 14;463(7278):178-83
references: 20075913
references: Nat Rev Genet. 2010 Mar;11(3):204-20
references: 20142834
references: CSH Protoc. 2007 Jun 01;2007:pdb.prot4765
references: 21357104
references: PLoS One. 2011 May 04;6(5):e19379
references: 21573248
references: Nat Rev Genet. 2011 Jun 17;12(7):499-510
references: 21681211
references: Cell. 1990 Jun 15;61(6):1089-101
references: 2190690
references: Mol Genet Genomics. 2011 Dec;286(5-6):307-19
references: 21918817
references: Genome Res. 2012 Mar;22(3):568-76
references: 22300766
references: Theor Appl Genet. 2012 May;124(8):1539-47
references: 22331140
references: BMC Genet. 2012 Jun 28;13:51
references: 22742069
references: BMC Plant Biol. 2012 Aug 09;12:136
references: 22873566
references: Ann N Y Acad Sci. 2012 Sep;1267:95-102
references: 22954222
references: PLoS One. 2012;7(11):e49488
references: 23145179
references: Heredity (Edinb). 2013 Mar;110(3):267-76
references: 23169559
references: Plant J. 2013 Jun;74(6):959-70
references: 23521529
references: Theor Appl Genet. 2013 Oct;126(10):2563-74
references: 23860723
references: Genetics. 2013 Nov;195(3):769-79
references: 24026099
references: Nat Genet. 2013 Nov;45(11):1327-36
references: 24056716
references: Theor Appl Genet. 1991 Jun;81(6):806-11
references: 24221445
references: Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19478-82
references: 24225854
references: PLoS Genet. 2013 Nov;9(11):e1003922
references: 24244190
references: Genetics. 2014 May;197(1):401-4
references: 24583583
references: PLoS One. 2014 Feb 28;9(2):e90346
references: 24587335
references: Front Plant Sci. 2014 Feb 17;5:23
references: 24596572
references: DNA Repair (Amst). 2014 Jul;19:176-81
references: 24767945
references: Nat Genet. 2014 Jul;46(7):707-13
references: 24908249
references: Genomics. 1987 Oct;1(2):174-81
references: 3692487
references: Nucleic Acids Res. 1984 Jul 11;12(13):5165-73
references: 6087274
references: Gene. 1980 Jul;10(2):105-12
references: 6248417
references: Nucleic Acids Res. 1981 Jun 11;9(11):2509-15
references: 6269052
references: Nucleic Acids Res. 1995 Jul 11;23(13):2367-70
references: 7630713
references: Nucleic Acids Res. 1993 Feb 11;21(3):681-6
references: 8441677
references: Genetics. 1998 Jan;148(1):479-94
references: 9475757