SNP marker diversity in common bean (Phaseolus vulgaris L.)

Theoretical and Applied Genetics

Volumn 123, Issue 5, 2011, Pages 827-845

  Cortés, Andrés J ^a,b   Chavarro, Martha C ^a   Blair, Matthew W ^a,c  

^a INTERNATIONAL CENTER FOR TROPICAL AGRICULTURE CIAT   (Colombia)

^b UNIVERSIDAD DE LOS ANDES   (Colombia)

^c CIAT International Center for Tropical Agriculture   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LAKES; MAPPING; POLYMORPHISM; SURVEYS;

FUTURE APPLICATIONS; GENETIC DIVERSITY; GENETIC MARKERS; GENETIC TECHNOLOGY; MAPPING POPULATIONS; PHASEOLUS VULGARIS; RACE STRUCTURE; SINGLE-NUCLEOTIDE POLYMORPHISM MARKERS;

GENES;

PHASEOLUS VULGARIS;

EID: 80054787802     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-011-1630-8     Document Type: Article

References (66)

1. Afanador LK, Hadley SD (1993) Adoption of a mini-prep DNA extraction method for RAPD marker analysis in common bean. Bean Improv Coop 35:10-11
2. Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181-186
3. Bahram S, Inoko H (2007) Microsatellite markers for genome-wide association studies. Nat Rev Genet 8
4. Bauer F, Elbers CC, Adan RAH, Loos RJF, Onland-Moret NC, Grobbee DE, van Vliet-Ostaptchouk JV, Wijmenga C, van der Schouw YT (2009) Obesity genes identified in genome-wide association studies are associated with adiposity measures and potentially with nutrient-specific food preference. Am J Clin Nutr 90:951-959
5. Becerra-Velazquez L, Gepts P (1994) RFLP diversity of common bean (Phaseolus vulgaris L.) in its centres of origin. Genome 37:256-263
6. Beebe S, Skroch PW, Tohme J, Duque MC, Pedraza F, Nienhuis J (2000) Structure of genetic diversity among common bean landraces of Mesoamerican origin based on Correspondence Analysis of RAPD. Crop Sci 40:264-273
7. Beebe S, Rengifo J, Gaitan E, Duque MC, Tohme J (2001) Diversity and origin of Andean landraces of common bean. Crop Sci 41:854-862
8. Behar DM, Yunusbayev B, Metspalu M, Metspalu E, Rosset S, Parik J, Rootsi S, Chaubey G, Kutuev I, Yudkovsky G, Khusnutdinova EK, Balanovsky O, Semino O, Pereira L, Comas D, Gurwitz D, Bonne-Tamir B, Parfitt T, Hammer MF, Skorecki K, Villems R (2010) The genome-wide structure of the Jewish people. Nature 466:238-242
9. Blair MW, Pedraza F, Buendia HF, Gaitan-Solis E, Beebe SE, Gepts P, Tohme J (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet 107:1362-1374
10. Blair MW, Giraldo MC, Buendia HF, Tovar E, Duque MC, Beebe SE (2006a) Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 113:100-109
11. Blair MW, Iriarte G, Beebe S (2006b) QTL analysis of yield traits in an advanced backcross population derived from a cultivated Andean 9 wild common bean (Phaseolus vulgaris L.) cross. Theor Appl Genet 112:1149-1163
12. Blair MW, Diaz JM, Hidalgo R, Diaz LM, Duque MC (2007) Microsatellite characterization of Andean races of common bean (Phaseolus vulgaris L.). Theor Appl Genet 116:29-43
13. Blair M, Diaz LM, Buendia HF, Duque MC (2009) Genetic diversity, seed size associations and population structure of a core collection of common beans (Phaseolus vulgaris L.). Theor Appl Genet 119:955-972
14. Blair MW, Chaves A, Tofino A, Calderon JF, Palacio JD (2010a) Extensive diversity and inter-genepool introgression in a worldwide collection of indeterminate snap bean accessions. Theor Appl Genet 120:1381-1391
15. Blair MW, Prieto S, Diaz LM, Buendia HF, Cardona C (2010b) Linkage disequilibrium at the APA insecticidal seed protein locus of common bean (Phaseolus vulgaris L.). BMC Plant Biol 10:79
16. Borza T, Higgins B, Simpson G, Bowman S (2010) Integrating the markers Pan I and haemoglobin with the genetic linkage map of Atlantic cod (Gadus morhua). BMC Res Notes 3:261
17. Broughton WJ, Hernandez G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003) Beans (Phaseolus spp.)-model food legumes. Plant Soil 252:55-128
18. Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 3:1745-1756
19. Camus L, Chevin LM, Cordet CT, Charcosset A, Manicacci D, Tenaillon MI (2008) Patterns of molecular evolution associated with two selective sweeps in the Tb1-Dwarf8 region in maize. Genetics 180:1107-1121
20. Chacón MI, Pickersgill B, Debouck DG (2005) Domestication patterns in common bean (Phaseolus vulgaris L.) and the origin of the Mesoamerican and Andean cultivated races. Theor Appl Genet 110:432-444
21. Chagné D, Batley J, Edwards D, Forster JW (2007) Single nucleotide polymorphism genotyping in plants. In: Oraguzie NC, Rikkerink EHA, Gardiner SE, Silva HNd (eds) Association mapping in plants. Springer, NY, pp 77-94
22. Córdoba JM, Chavarro C, Schlueter JA, Jackson SA, Blair MW (2010) Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers. BMC Genomics 11:436
23. Cuppen E (2007) Genotyping by allele-specific amplification (KASPar). Cold Spring Harb Protocols, pp 172-173
24. David P, Sevignac M, Thareau V, Catillon Y, Kami J, Gepts P, Langin T, Geffroy V (2008) BAC end sequences corresponding to the B4 resistance gene cluster in common bean: a resource for markers and synteny analyses. Mol Genet Genomics 280:521-533
25. Díaz LM, Blair MW (2006) Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers. Theor Appl Genet 114:143-154
26. Fay JC, Wu CI (1999) A human population bottleneck can account for the discordance between patterns of mitochondrial versus nuclear DNA variation. Mol Biol Evol 16:1003-1005
27. Felsenstein J (2006) Inferring phylogenies. Sinauer Associates, New York
28. Freyre R, Skroch P, Geffroy V, Adam-Blondon AF, Shirmohamadali A, Johnson W, Llaca V, Nodari R, Pereira P, Tsai SM, Tohme J, Dron M, Nienhuis J, Vallejos CE, Gepts P (1998) Towards an integrated linkage map of common bean. 4. Development of a core map andalignment of RFLP maps. Theor Appl Genet 97:847-956
29. Gaitan E, Choi IY, Quigley C, Cregan P, Tohme J (2008) Single nucleotide polymorphisms in common bean: their discovery and genotyping using a multiplex detection system. Plant Genome 1:125-134
30. Galeano CH, Fernandez AC, Gomez M, Blair MW (2009a) Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.). BMC Genomics 10:629
31. Galeano CH, Gomez M, Rodriguez LM, Blair MW (2009b) CEL I nuclease digestion for SNP discovery and marker development in common bean (Phaseolus vulgaris L.). Crop Sci 49:381-394
32. Gepts P (1998) Origin and evolution of common bean: past events and recent trends. HortScience 33:1119-1135
33. Gepts P, Debouck DG (1991) Origin, domestication, and evolution of the common bean. In: van Schoonhaven A, Voysest O (eds) Common beans: research for crop improvement. Centro Internacional de Agricultura Tropical (CIAT), Cali
34. Gepts P, Osborn TC, Rashka K, Bliss FA (1986) Phaseolin-protein variability in wild forms and landraces of the common bean (Phaseolus vulgaris): evidence for multiple centers of domestication. Econ Bot 40:451-468
35. Hair JF, Anderson RE, Tatham RL, Black WC (1992) Multivariate data analysis with readings. Macmillan Publishing Company, New York
36. Hougaard BK, Madsen LH, Sandal N, Moretzsohn MC, Fredslund J, Schauser L, Nielsen AM, Rohde T, Sato S, Tabata S, Bertioli DJ, Stougaard JF (2008) Legume anchor markers link syntenic regions between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis. Genetics 119:2299-2312
37. Hyten DL, Cannon SB, Song QJ, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB (2010a) Highthroughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11:38
38. Hyten DL, Song Q, Fickus EW, Quigley CV, Lim J-S, Choi I-Y, Hwang E-Y, Pastor-Corrales M, Cregan PB (2010b) Highthroughput SNP discovery and assay development in common bean. BMC Genomics 11:475
39. Ioannidis J, Thomas G, Daly MJ (2009) Validating, augmenting and refining genome-wide association signals. Nat Rev Genet 10:319-329
40. Jorgenson E, Witte JS (2007) Microsatellite markers for genome-wide association studies. Nat Rev Genet 8
41. Koopman WJM, Li Y, Coart E, Weg WEVD, Vosman B, Roldán-Ruiz I, Smulders MJM (2007) Linked vs. unlinked markers: multilocus microsatellite haplotype-sharing as a tool to estimate gene flow and introgression. Mol Ecol 16:243-256
42. Kwak M, Gepts P (2009) Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae). Theor Appl Genet 118:979-992
43. Kwak M, Kami JA, Gepts P (2009) The putative mesoamerican domestication center of Phaseolus vulgaris is located in the Lerma-Santiago Basin of Mexico. Crop Sci 49:554-563
44. Liu S, Zhou Z, Lu J, Sun F, Wang S, Liu H, Jiang Y, Kucuktas H, Kaltenboeck L, Peatman E, Liu Z (2011) Generation of genomescale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics 12:53
45. Makunde GS, Beebe S, Blair MW, Chirwa R, Lungu D (2007) Inheritance of drought tolerance traits in Andean 9 Andean and Andean 9 Mesoamerican F2 Populations. Bean Improv Coop 50:159-160
46. McConnell M, Mamidi S, Lee R, Chikara S, Rossi M, Papa R, McClean P (2010) Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.). Theor Appl Genet 121:1103-1116
47. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
48. Nijman IJ, Kuipers S, Verheul M, Guryev V, Cuppen E (2008) A genome-wide SNP panel for mapping and association studies in the rat. BMC Genomics 9:95
49. Papa R, Gepts P (2003) Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica. Theor Appl Genet 106:239-250
50. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945-959
51. Ramirez M, Graham MA, Blanco-Lopez L, Silvente S, Medrano-Soto A, Blair MW, Hernandez G, Vance CP, Lara M (2005) Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol 137:1211-1227
52. Reagon M, Thurber CS, Gross BL, Olsen KM, Jia YL, Caicedo AL (2010) Genomic patterns of nucleotide diversity in divergent populations of US weedy rice. BMC Evol Biol 10:180
53. Rogers AR (1995) Genetic evidence for a Pleistocene population explosion. Evolution 49:608-615
54. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497
55. Schmutz J, Cannon SB, Schlueter J, Ma JX, Mitros T, Nelson W, Hyten DL, Song QJ, Thelen JJ, Cheng JL, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu SQ, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du JC, Tian ZX, Zhu LC, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178-183
56. Schoonhoven Av, Voysest O (1991) Common beans: research for crop improvement. Centro Internacional de Agricultura Tropical, Cali
57. Singh SP (1982) A key for identification of different growth habits of Phaseolus vulgaris L. Bean Improv Coop 25:92-95
58. Singh SP, Gepts P, Debouck DG (1991) Races of common bean (Phaseolus vulgaris, Fabaceae). Econ Bot 45:379-396
59. Sonnante G, Stockton T, Nodari R, Becerra Velasquez V, Gepts P (1994) Evolution of genetic diversity during the domestication of common bean (Phaseolus vulgaris L.). Theor Appl Genet 89:629-635
60. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599
61. Tohme J, González O, Beebe S, Duque MC (1996) AFLP analysis of gene pools of a wild bean core collection. Crop Sci 36:1375-1384
62. Wakeley J (2008) Coalescent theory: an introduction. Harvard University, Cambridge
63. Wright S (1969) Evolution and the genetics of populations, volume 2: the theory of gene frequencies. University of Chicago Press, Chicago
64. Xia H, Camus-Kulandaivelu LT, Stephan W, Tellier AL, Zhang Z (2010) Nucleotide diversity patterns of local adaptation at drought-related candidate genes in wild tomatoes. Mol Ecol (online version)
65. Yan JB, Yang XH, Shah T, Sanchez-Villeda H, Li JS, Warburton M, Zhou Y, Crouch JH, Xu YB (2010) High-throughput SNP genotyping with the GoldenGate assay in maize. Mol Breed 25:441-451
66. Zhao KY, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR (2010) Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. Plos One 5:e10780