title: Characterization of AT-rich microsatellites in common bean (Phaseolus vulgaris L.).
abstract: Polymorphism of microsatellite markers is often associated with the simple sequence repeat motif targeted. AT-rich microsatellites tend to be highly variable and this appears to be notable, especially in legume genomes. To analyze the value of AT-rich microsatellites for common bean (Phaseolus vulgaris L.), we developed a total of 85 new microsatellite markers, 74 of which targeted ATA or other AT-rich motif loci and 11 of which were made for GA, CA or CAC motif loci. We evaluated the loci for the level of allelic diversity in comparison to previously characterized microsatellites using a panel of 18 standard genotypes and genetically mapped any loci polymorphic in the DOR364 x G19833 population. The majority of the microsatellites produced single bands and detected single loci, however, 15 of the AT-rich microsatellites produced multiple or double banding patterns; while only one of the GA or CA-rich microsatellites did. The polymorphism information content (PIC) values averaged 0.892 and 0.600 for the AT and ATA motif microsatellites, respectively, but only 0.140 for the CA-rich microsatellites. GA microsatellites, which had a large average number of repeats, had high to intermediate PIC, averaging 0.706. A total of 45 loci could be genetically mapped and distribution of the loci across the genome was skewed towards non-distal locations with a greater prevalence of loci on linkage groups b02, b09 and b11. AT-rich microsatellites were found to be a useful source of polymorphic markers for mapping and diversity assessment in common bean that appears to uncover higher diversity than other types of simple sequence repeat markers.
authors.affiliation: CIAT, International Center for Tropical Agriculture, 1380 N.W. 78th Ave., Miami, FL, 33126, USA. m.blair@cgiar.org
authors.forename: Mathew W
authors.initials: MW
authors.lastname: Blair
authors.forename: Hector F
authors.initials: HF
authors.lastname: Buendía
authors.forename: Martha C
authors.initials: MC
authors.lastname: Giraldo
authors.forename: Isabelle
authors.initials: I
authors.lastname: Métais
authors.forename: Didier
authors.initials: D
authors.lastname: Peltier
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D018744:DNA, Plant / Q000235:genetics; D005819:Genetic Markers; D018745:Genome, Plant; D018895:Microsatellite Repeats; D027805:Phaseolus / Q000235:genetics*; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers
references.citation: Genome. 2007 Mar;50(3):266-77
references.pmid: 17502900
references.citation: Plant Physiol. 2003 Mar;131(3):872-7
references.pmid: 12644639
references.citation: Theor Appl Genet. 2006 Jun;113(1):100-9
references.pmid: 16614831
references.citation: Genetics. 2000 Dec;156(4):1997-2005
references.pmid: 11102390
references.citation: Biotechniques. 1996 May;20(5):758-60
references.pmid: 8723911
references.citation: Comp Biochem Physiol B Biochem Mol Biol. 2000 Aug;126(4):455-76
references.pmid: 11026658
references.citation: Genome. 1999 Apr;42(2):210-7
references.pmid: 10231957
references.citation: Theor Appl Genet. 2003 Nov;107(8):1362-74
references.pmid: 14504741
references.citation: Theor Appl Genet. 2006 Dec;114(1):143-54
references.pmid: 17047911
references.citation: Genetics. 2006 Apr;172(4):2541-55
references.pmid: 16489220
references.citation: J Hered. 2000 Nov-Dec;91(6):429-34
references.pmid: 11218079
references.citation: Trends Genet. 1992 Aug;8(8):288-94
references.pmid: 1509520
references.citation: Theor Appl Genet. 2007 Dec;116(1):29-43
references.pmid: 17924092
references.citation: Theor Appl Genet. 2002 Jun;104(8):1346-1352
references.pmid: 12582590
references.citation: Bioinformatics. 2005 May 1;21(9):2128-9
references.pmid: 15705655
references.citation: Genome. 2002 Dec;45(6):1013-24
references.pmid: 12502245
references.citation: Genet Mol Res. 2007 Sep 30;6(3):691-706
references.pmid: 18050090
references.citation: Theor Appl Genet. 2003 Jan;106(2):205-12
references.pmid: 12582845
references.citation: Genome Res. 2001 Aug;11(8):1441-52
references.pmid: 11483586
references.citation: Theor Appl Genet. 2006 Apr;112(6):1149-63
references.pmid: 16432734
references.citation: Plant J. 1993 Jan;3(1):175-82
references.pmid: 8401603
references.citation: Mol Genet Genomics. 2001 Aug;265(6):1097-103
references.pmid: 11523782
references.citation: Mol Gen Genet. 1999 Mar;261(2):354-63
references.pmid: 10102371
references.citation: Theor Appl Genet. 2007 Apr;114(6):1081-90
references.pmid: 17287974
references.citation: Plant J. 1999 Feb;17(4):415-25
references.pmid: 10205898
references.citation: Theor Appl Genet. 2004 Feb;108(3):550-7
references.pmid: 14564394
references.citation: Plant Sci. 2001 May;160(6):1115-1123
references.pmid: 11337068
references.citation: BMC Genomics. 2005 Feb 18;6:23
references.pmid: 15720707
references.citation: Theor Appl Genet. 2004 Apr;108(6):1064-70
references.pmid: 15067392
references.citation: Theor Appl Genet. 2002 Dec;105(8):1124-1136
references.pmid: 12582890
references.citation: Curr Opin Plant Biol. 2002 Apr;5(2):94-100
references.pmid: 11856602
references.citation: Genomics. 1987 Oct;1(2):174-81
references.pmid: 3692487
references.citation: Genome. 1999 Jun;42(3):536-44
references.pmid: 10382301
references.citation: Theor Appl Genet. 2004 Jun;109(1):122-8
references.pmid: 14991109